Contacts of the helix formed by residues 72 - 107 (chain P) in PDB entry 2DYS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 72 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P ALA* 2.7 38.6 + - + +
70P HIS 3.1 6.1 + - - +
71P HIS* 1.3 74.8 - - - +
73P PRO* 1.3 75.8 - - - +
74P ALA 3.7 0.5 + - - -
75P VAL* 3.0 13.1 + - - +
76P GLN* 3.0 20.3 + - - +
16S LEU* 3.6 33.9 - - + -
17S GLU* 3.9 17.0 - - - +
20S VAL* 4.0 9.4 - - + -
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Residues in contact with PRO 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P HIS 4.7 0.4 - - - +
72P THR* 1.3 87.4 - - - +
74P ALA* 1.3 55.5 + - - +
76P GLN* 3.4 11.5 + - + +
77P LYS* 3.0 29.7 + - - +
17S GLU* 5.2 7.4 - - + +
20S VAL* 4.2 21.3 - - + -
33S ILE* 5.6 4.5 - - + -
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Residues in contact with ALA 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170N ASN* 3.0 26.8 + - - +
7P ALA* 4.2 13.9 - - + -
8P TYR* 3.9 29.2 - - + +
72P THR* 3.1 7.9 + - - +
73P PRO* 1.3 75.7 - - - +
75P VAL* 1.3 66.9 + - - +
77P LYS* 3.3 6.7 + - - +
78P GLY 3.2 6.6 + - - -
33S ILE* 5.6 6.4 - - + +
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Residues in contact with VAL 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N PHE* 5.6 0.7 - - - -
170N ASN* 5.2 0.2 - - - +
609N PGV 4.1 14.4 - - - +
7P ALA 3.5 12.1 - - - +
8P TYR* 4.2 7.2 - - + -
9P HIS* 3.8 20.0 - - + +
70P HIS 3.5 12.1 - - - +
71P HIS* 3.8 29.2 - - + -
72P THR* 3.0 24.8 + - - +
74P ALA* 1.3 75.9 - - - +
76P GLN* 1.3 63.1 + - - +
78P GLY* 3.3 3.4 + - - -
79P LEU* 3.2 27.3 + - + +
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Residues in contact with GLN 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P HIS* 4.7 4.4 - - + +
72P THR 3.0 10.0 + - - +
73P PRO* 3.6 14.2 - - - +
75P VAL* 1.3 79.9 - - - +
77P LYS* 1.3 60.7 + - - +
79P LEU* 3.2 15.2 + - + +
80P ARG* 3.1 49.9 + - - +
230P ASN 5.0 3.1 + - - +
231P HIS* 3.3 48.8 + - + +
232P HIS 4.5 2.4 - - - +
233P PHE* 3.8 29.0 - - + +
236P GLU* 5.2 0.6 + - - -
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Residues in contact with LYS 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLY 6.2 0.2 - - - -
102G PEK 3.1 41.8 + - - +
170N ASN* 3.6 12.1 - - - +
73P PRO 3.0 14.8 + - - +
74P ALA* 3.3 13.7 + - - +
76P GLN* 1.3 74.1 - - - +
78P GLY* 1.3 61.9 + - - +
80P ARG* 3.3 22.5 + - - +
81P TYR* 3.2 56.4 + - + -
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Residues in contact with GLY 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N ALA* 5.5 1.6 - - - -
94N PHE* 3.4 6.5 - - - -
166N THR* 3.3 25.2 - - - +
170N ASN* 3.5 18.6 - - - +
74P ALA 3.2 6.5 + - - -
75P VAL* 3.3 4.0 + - - -
76P GLN 3.2 0.2 - - - -
77P LYS* 1.3 78.3 - - - +
79P LEU* 1.3 59.4 + - - +
81P TYR* 3.2 2.8 + - - -
82P GLY 2.9 23.6 + - - -
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N PHE* 3.5 27.3 - - + -
609N PGV 3.6 30.5 - - - +
71P HIS* 3.5 35.7 - - + +
75P VAL* 3.2 21.4 + - + +
76P GLN* 3.2 15.8 + - + +
78P GLY* 1.3 75.2 - - - +
80P ARG* 1.3 62.9 + - - +
82P GLY* 3.3 1.0 + - - -
83P MET* 3.0 18.9 + - - +
233P PHE* 3.5 25.7 - - + -
307P PGV 4.3 20.2 - - - +
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Residues in contact with ARG 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G PEK 3.0 41.9 + - - +
76P GLN* 3.1 39.5 + - - +
77P LYS* 3.4 12.3 - - - +
78P GLY 3.2 0.4 - - - -
79P LEU* 1.3 76.9 - - - +
81P TYR* 1.3 62.1 + - - +
83P MET 3.3 0.3 + - - -
84P ILE* 3.0 30.1 + - - +
233P PHE* 3.7 23.5 - - + -
236P GLU* 3.2 39.5 + - - -
240P TRP* 3.7 24.1 - - + -
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Residues in contact with TYR 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G HIS 4.0 10.5 + - - -
9G GLY* 4.8 4.0 + - - -
102G PEK 3.6 57.1 + - + +
166N THR* 4.0 14.1 - - + +
169N ILE* 3.8 33.8 - - + +
170N ASN* 4.0 23.6 - - + -
77P LYS* 3.2 52.4 + - + -
78P GLY* 3.2 7.5 + - - +
80P ARG* 1.3 78.8 - - - +
82P GLY* 1.3 57.5 + - - +
84P ILE* 3.2 5.7 + - - +
85P LEU* 2.9 40.0 + - + +
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Residues in contact with GLY 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94N PHE* 4.0 9.2 - - - -
162N ILE* 3.8 23.0 - - - +
166N THR* 3.7 5.8 + - - -
609N PGV 3.6 10.7 - - - +
78P GLY 2.9 14.2 + - - -
79P LEU 3.3 3.5 + - - -
81P TYR* 1.3 76.7 - - - +
83P MET* 1.3 56.2 + - - +
85P LEU* 3.4 2.3 + - - +
86P PHE* 2.9 28.4 + - - +
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Residues in contact with MET 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609N PGV 3.8 8.2 - - + +
79P LEU 3.0 16.6 + - - +
80P ARG 3.7 3.8 - - - +
82P GLY* 1.3 71.5 - - - +
84P ILE* 1.3 66.0 + - - +
86P PHE* 3.2 16.4 + - + +
87P ILE* 3.0 37.1 + - + +
214P PHE* 4.5 1.1 - - + -
233P PHE* 3.9 9.4 - - + -
237P ALA* 3.7 42.6 - - + +
240P TRP* 4.0 15.0 - - + -
241P TYR* 3.9 29.4 - - + -
307P PGV 4.1 32.1 - - + -
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Residues in contact with ILE 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 3.5 84.1 - - + +
80P ARG 3.0 19.5 + - - +
81P TYR* 3.6 7.2 - - - +
83P MET* 1.3 77.6 - - - +
85P LEU* 1.3 62.7 + - - +
87P ILE* 3.4 7.8 + - - +
88P ILE* 3.1 42.5 + - + +
240P TRP* 3.8 17.5 - - + -
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Residues in contact with LEU 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G PEK 3.6 40.8 - - + -
162N ILE* 4.0 20.4 - - + +
165N ILE* 3.8 29.2 - - + -
166N THR* 3.7 20.9 - - - +
196N LEU* 3.8 30.3 - - + +
81P TYR* 2.9 24.9 + - + +
82P GLY 3.8 4.3 - - - +
84P ILE* 1.3 76.6 - - - +
86P PHE* 1.3 61.4 + - - +
88P ILE* 3.3 11.8 + - + +
89P SER 3.2 17.2 + - - -
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Residues in contact with PHE 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158N ILE* 5.9 1.8 - - + -
159N LEU* 6.1 0.4 - - + -
162N ILE* 4.1 13.4 - - + +
609N PGV 3.7 48.0 - - + -
82P GLY 2.9 18.0 + - - +
83P MET* 3.2 19.2 + - + +
85P LEU* 1.3 75.7 - - - +
87P ILE* 1.3 62.1 + - - +
89P SER* 2.7 27.3 + - - -
90P GLU* 3.0 27.3 + - + +
241P TYR* 3.9 7.9 - + - -
301P DCW 2.9 42.2 - - + -
307P PGV 3.7 30.3 - - + -
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Residues in contact with ILE 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G PEK 4.6 20.2 - - + -
83P MET* 3.0 35.4 + - + +
84P ILE* 3.7 7.0 - - - +
86P PHE* 1.3 75.4 - - + +
88P ILE* 1.3 58.9 + - + +
90P GLU* 3.0 10.8 + - - +
91P VAL* 2.8 37.3 + - + +
240P TRP* 3.9 32.1 - - + +
241P TYR* 4.0 24.2 - - + +
244P PHE* 4.0 26.2 - - + -
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Residues in contact with ILE 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G ALA* 4.2 23.3 - - - +
2G SER* 4.2 13.7 - - - +
102G PEK 5.0 5.2 - - + -
196N LEU* 4.1 8.1 - - + -
197N LEU* 3.6 30.5 - - + -
84P ILE* 3.1 35.8 + - + +
85P LEU* 3.4 22.4 - - + +
87P ILE* 1.3 76.6 - - + +
89P SER* 1.3 62.9 + - - +
91P VAL* 3.1 11.5 + - + +
92P LEU* 3.0 25.5 + - + +
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Residues in contact with SER 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158N ILE* 4.1 11.8 - - - +
196N LEU* 3.8 28.7 - - - -
200N PRO* 3.4 22.6 - - - +
85P LEU 3.2 6.8 + - - -
86P PHE* 2.7 27.8 + - - -
88P ILE* 1.3 79.5 - - - +
90P GLU* 1.3 60.9 + - - +
92P LEU* 3.4 1.6 + - - -
93P PHE 3.1 18.0 + - - -
301P DCW 3.4 18.3 - - - +
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Residues in contact with GLU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P PHE* 3.0 24.4 + - + +
87P ILE* 3.0 9.3 + - - +
89P SER* 1.3 77.0 - - - +
91P VAL* 1.3 61.9 + - - +
93P PHE* 3.3 5.2 - - - +
94P PHE* 3.3 25.6 + - - -
207P HIS* 3.3 6.8 - - - +
241P TYR* 2.8 30.0 + - - -
244P PHE* 3.6 15.5 - - + -
301P DCW 1.4 75.6 + - + +
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Residues in contact with VAL 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA 5.1 4.0 - - - +
102G PEK 4.2 42.9 - - + +
87P ILE* 2.8 26.0 + - + +
88P ILE* 3.1 10.5 + - - +
90P GLU* 1.3 74.7 - - - +
92P LEU* 1.3 70.1 + - + +
94P PHE* 3.0 9.2 + - - +
95P THR* 2.9 31.5 + - - +
244P PHE* 3.6 26.7 - - + -
308P PGV 4.7 10.5 - - + -
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Residues in contact with LEU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ALA* 4.5 13.2 - - + +
196N LEU 4.7 0.4 - - - +
197N LEU* 3.4 49.8 - - + +
200N PRO* 3.7 21.3 - - + -
201N VAL* 3.9 20.5 + - + +
237N PHE* 5.2 5.4 - - + -
88P ILE* 3.0 22.7 + - + +
89P SER* 3.4 3.3 + - - +
91P VAL* 1.3 83.1 - - + +
93P PHE* 1.3 65.8 + - - +
95P THR* 3.0 27.8 + - + +
96P GLY 3.3 4.0 + - - -
308P PGV 4.3 18.4 - - + -
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Residues in contact with PHE 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200N PRO* 3.4 22.8 - - + +
203N ALA* 3.8 12.1 - - + -
204N ALA* 3.5 29.6 - - - +
207N THR* 4.4 4.5 - - - -
89P SER 3.1 12.6 + - - +
90P GLU 3.3 12.3 - - - +
91P VAL 3.1 0.2 - - - -
92P LEU* 1.3 77.1 - - - +
94P PHE* 1.3 66.0 + + - +
96P GLY 3.1 10.6 + - - -
97P PHE* 3.5 38.0 - + - -
203P PHE* 4.1 33.4 - + + -
207P HIS* 5.1 11.0 - + - -
301P DCW 3.7 33.9 - - + -
305P PEK 4.1 13.0 - - + -
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Residues in contact with PHE 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 4.6 6.1 - - + -
90P GLU 3.3 17.9 + - - -
91P VAL* 3.0 9.4 + - - +
93P PHE* 1.3 81.6 - + - +
95P THR* 1.3 66.4 + - - +
97P PHE* 2.9 26.9 + + + +
98P PHE* 2.9 32.7 + + + -
200P ALA* 3.9 23.6 - - + -
203P PHE* 4.1 7.9 - - + -
204P HIS* 3.8 17.7 - + + -
207P HIS* 3.6 45.5 - + - -
244P PHE* 4.1 11.4 - + - -
248P VAL* 3.8 32.1 - - + -
252P LEU* 5.3 2.0 - - + -
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Residues in contact with THR 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 4.4 14.5 - - + +
201N VAL* 5.1 5.2 - - + -
91P VAL* 2.9 21.2 + - - +
92P LEU* 3.0 27.4 + - + +
94P PHE* 1.3 76.8 - - - +
96P GLY* 1.3 55.8 + - - +
98P PHE* 3.2 8.2 + - - +
99P TRP* 2.8 34.0 + - + +
308P PGV 3.8 46.6 - - + +
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Residues in contact with GLY 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201N VAL* 4.8 6.5 - - - +
204N ALA* 3.8 13.2 - - - -
208N MET* 3.6 14.4 - - - +
234N LEU* 3.9 18.8 - - - +
92P LEU 3.3 3.6 + - - -
93P PHE 3.1 9.0 + - - -
94P PHE 3.1 1.0 - - - -
95P THR* 1.3 80.1 - - - +
97P PHE* 1.3 56.5 + - - +
99P TRP* 3.3 4.6 + - - +
100P ALA* 3.0 22.5 + - - +
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Residues in contact with PHE 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204N ALA* 4.1 14.1 - - + -
207N THR* 4.5 4.9 - - + -
208N MET* 3.4 36.1 - - + -
219N PHE* 5.0 4.0 - + - -
93P PHE* 3.5 52.9 - + - -
94P PHE* 2.9 22.0 + + + +
96P GLY* 1.3 74.3 - - - +
98P PHE* 1.3 61.3 + - + +
100P ALA* 3.1 4.4 + - - +
101P PHE* 2.9 27.0 + - - +
196P THR* 5.5 1.9 - - - +
199P VAL* 3.7 23.1 - - + -
200P ALA* 4.7 23.3 - - + +
203P PHE* 3.9 25.4 - + - -
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Residues in contact with PHE 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 3.6 42.2 - - + -
94P PHE* 2.9 41.9 + + + -
95P THR 3.8 5.6 - - - +
97P PHE* 1.3 78.7 - - + +
99P TRP* 1.3 62.2 + - - +
101P PHE* 3.4 7.6 + + + +
102P TYR* 3.0 44.5 + + + -
200P ALA* 6.1 0.7 - - + -
248P VAL* 4.2 5.6 - - + -
251P PHE* 3.5 44.0 - + + -
252P LEU* 3.6 31.4 - - + -
255P SER* 4.0 16.8 - - - -
256P ILE* 5.6 1.8 - - + -
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Residues in contact with TRP 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201N VAL* 4.7 4.3 - - + -
230N LEU* 4.2 10.0 - - + +
233N HIS* 3.7 30.7 - - + +
234N LEU* 3.7 19.7 - - + -
237N PHE* 3.7 42.6 - + + -
288N TRP* 3.9 15.7 - + - -
95P THR* 2.8 20.9 + - + +
96P GLY* 3.3 7.4 - - - +
98P PHE* 1.3 78.4 - - - +
100P ALA* 1.3 56.2 + - - +
102P TYR* 3.3 3.7 + - - +
103P HIS* 2.9 27.3 + - + +
304P CHD 2.9 34.9 + - + +
308P PGV 3.7 52.7 - - + +
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Residues in contact with ALA 100 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208N MET* 3.7 27.4 - - + -
219N PHE* 4.2 13.7 - - + -
230N LEU* 3.7 24.1 - - + +
96P GLY 3.0 12.5 + - - +
97P PHE* 3.4 8.5 - - - +
99P TRP* 1.3 77.6 - - - +
101P PHE* 1.3 61.7 + - - +
103P HIS* 3.4 1.6 + - - +
104P SER* 3.1 29.6 + - - -
196P THR* 4.4 3.3 - - + +
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Residues in contact with PHE 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97P PHE 2.9 13.3 + - - +
98P PHE* 3.7 10.8 - + + +
100P ALA* 1.3 78.1 - - - +
102P TYR* 1.3 78.4 + + - +
104P SER* 3.4 1.2 + - - -
105P SER* 2.8 42.4 + - - -
116P TRP* 4.0 23.8 - + - -
193P TYR* 5.8 1.8 - + - -
196P THR* 3.8 30.9 - - - +
255P SER* 3.6 28.7 - - - -
256P ILE* 3.8 35.0 - - + -
259P TRP* 3.6 26.9 - + - -
260P GLY* 3.8 9.6 - - - -
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Residues in contact with TYR 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PEK 5.3 9.0 - - + -
98P PHE* 3.0 37.7 + + + +
99P TRP* 4.0 2.7 - - - +
101P PHE* 1.3 83.7 - + - +
103P HIS* 1.3 65.8 + - - +
105P SER* 3.5 1.3 - - - -
106P LEU* 3.0 50.5 + - + +
254P VAL* 5.7 1.4 - - - +
255P SER* 2.6 39.8 + - - -
259P TRP* 3.8 35.2 - + - -
308P PGV 3.5 18.1 - - + +
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Residues in contact with HIS 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227N ASP* 2.8 36.6 + - + +
229N ILE* 5.1 1.8 - - + -
230N LEU* 3.8 38.6 - - + +
233N HIS* 4.6 4.7 - + - -
99P TRP 2.9 18.2 + - - +
100P ALA 3.6 4.7 - - - +
101P PHE 3.3 0.2 - - - -
102P TYR* 1.3 79.0 - - - +
104P SER* 1.3 66.7 + - - +
106P LEU* 4.7 0.5 - - - +
107P ALA* 3.7 21.2 + - - +
304P CHD 2.6 38.2 + - - +
308P PGV 3.3 21.8 + - - +
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Residues in contact with SER 104 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219N PHE 4.8 2.1 + - - -
225N GLY 4.4 7.4 + - - +
226N GLY* 5.0 1.4 - - - -
227N ASP* 5.6 0.7 + - - +
230N LEU* 4.5 9.9 - - - +
100P ALA 3.1 14.6 + - - -
101P PHE 3.9 2.0 - - - -
103P HIS* 1.3 82.1 - - - +
105P SER* 1.3 60.7 + - - +
107P ALA 3.7 4.6 - - - +
108P PRO* 3.6 21.1 - - - +
112P LEU* 4.7 1.6 - - - +
116P TRP* 3.9 10.9 - - - -
192P VAL* 3.2 41.4 - - - +
196P THR* 4.9 2.0 - - - -
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Residues in contact with SER 105 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P PHE* 2.8 30.7 + - - -
102P TYR* 3.5 7.8 - - - -
104P SER* 1.3 74.7 - - - +
106P LEU* 1.3 59.9 + - - +
107P ALA 3.4 0.2 - - - -
108P PRO* 3.7 13.7 - - - +
116P TRP* 3.5 46.9 - - - +
259P TRP* 3.3 29.8 - - - -
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P TYR* 3.0 40.9 + - + +
105P SER* 1.3 77.1 + - - +
107P ALA* 1.3 59.7 + - - +
108P PRO* 3.6 5.5 - - - +
259P TRP* 3.6 31.6 - - + -
308P PGV 4.1 58.9 - - + +
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Residues in contact with ALA 107 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P HIS* 3.7 11.8 + - - +
104P SER* 3.7 7.6 - - - +
106P LEU* 1.3 79.9 - - - +
108P PRO* 1.4 66.6 - - - +
109P THR* 3.3 10.9 + - - +
308P PGV 3.9 42.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il