Contacts of the helix formed by residues 82 - 111 (chain O) in PDB entry 2X17
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 SER 82 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.3 10.9 + - - -
80O TRP* 3.9 2.3 - - - +
81O GLU* 1.3 79.2 - - - +
83O PRO* 1.4 75.5 - - - +
84O LEU* 3.6 12.4 + - - +
85O LYS* 3.2 27.1 + - - +
86O ALA* 3.2 20.1 + - - +
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Residues in contact with PRO 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.9 5.8 - - + +
31O PHE* 3.6 21.8 - - + -
34O LEU* 4.0 21.1 - - + -
36O LEU* 4.1 13.5 - - + -
39O PHE* 5.2 0.9 - - + -
82O SER* 1.4 88.7 - - - +
84O LEU* 1.3 60.0 + - - +
86O ALA* 3.4 4.8 + - + +
87O PHE* 3.3 20.4 + - - -
141O LEU* 3.6 25.5 - - + +
151O LEU* 4.4 17.0 - - + -
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Residues in contact with LEU 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O SER* 3.2 11.5 + - - +
83O PRO* 1.3 80.3 - - - +
85O LYS* 1.3 62.7 + - + +
87O PHE* 3.3 3.8 + - - +
88O GLU* 3.1 42.9 + - - +
138O LEU* 3.8 13.2 - - + +
141O LEU* 3.7 40.4 - - + +
142O LYS* 3.7 33.2 - - + +
145O LYS* 5.0 13.5 - - + -
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Residues in contact with LYS 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80O TRP* 3.9 8.8 - - + -
81O GLU* 4.2 31.9 - - + +
82O SER* 3.2 26.0 + - - +
84O LEU* 1.3 82.4 - - + +
86O ALA* 1.3 59.4 + - - +
88O GLU* 3.4 29.1 + - + +
89O ALA* 3.1 25.6 + - - +
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Residues in contact with ALA 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O MET* 3.4 18.0 - - + +
30O TYR* 4.3 6.5 - - + -
31O PHE* 4.0 22.0 - - + -
80O TRP* 3.9 28.9 - - + +
82O SER 3.2 12.8 + - - +
83O PRO 3.5 10.1 - - - +
84O LEU 3.2 0.2 - - - -
85O LYS* 1.3 78.0 - - - +
87O PHE* 1.3 57.0 + - - +
89O ALA* 3.3 1.6 + - - +
90O ALA* 3.0 21.8 + - - +
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Residues in contact with PHE 87 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O PHE* 3.8 13.2 - + - -
39O PHE* 3.7 30.5 - + - -
42O TRP* 4.3 13.2 - + - -
43O MET* 3.7 26.0 - - + -
83O PRO 3.3 8.2 + - - -
84O LEU 3.3 6.5 + - - +
86O ALA* 1.3 75.6 - - - +
88O GLU* 1.3 59.6 + - - +
89O ALA 3.2 0.4 - - - -
90O ALA* 3.7 4.9 - - + +
91O TYR* 2.9 29.8 + - - +
134O VAL* 3.8 32.6 - - + +
137O ILE* 3.7 39.5 - - + -
138O LEU* 3.4 14.0 - - + +
141O LEU* 3.6 25.1 - - + -
158O LEU* 5.0 1.3 - - + -
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Residues in contact with GLU 88 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O LEU* 3.1 28.4 + - - +
85O LYS* 3.4 42.2 + - - +
86O ALA 3.3 0.2 - - - -
87O PHE* 1.3 76.5 - - - +
89O ALA* 1.3 57.0 + - - +
91O TYR* 4.0 2.4 - - - +
92O GLU* 3.1 29.6 + - - +
138O LEU* 3.8 24.0 - - + -
142O LYS* 4.1 19.1 - - - -
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Residues in contact with ALA 89 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O LEU* 5.1 1.0 - - - +
27O MET* 4.2 6.8 - - + +
80O TRP* 3.4 30.1 - - + +
85O LYS 3.1 11.7 + - - +
86O ALA 3.5 7.0 - - - +
87O PHE 3.2 0.2 - - - -
88O GLU* 1.3 76.7 - - - +
90O ALA* 1.3 61.2 + - - +
92O GLU* 3.7 9.1 + - - +
93O HIS* 3.2 22.2 + - - +
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Residues in contact with ALA 90 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O TYR* 3.8 19.9 + - + +
27O MET* 3.8 18.4 - - + +
43O MET* 4.8 5.8 - - + -
86O ALA 3.0 15.3 + - - +
87O PHE* 3.7 10.1 - - + +
88O GLU 3.3 0.2 - - - -
89O ALA* 1.3 75.9 - - - +
91O TYR* 1.3 58.3 + - - +
93O HIS* 3.2 6.7 + - - +
94O GLU* 2.9 32.4 + - - +
134O VAL* 4.1 13.7 - - + -
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Residues in contact with TYR 91 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87O PHE 2.9 17.8 + - - +
88O GLU* 4.0 4.0 - - - +
90O ALA* 1.3 74.4 - - - +
92O GLU* 1.3 60.5 + - - +
94O GLU* 3.4 3.6 + - + +
95O LYS* 3.1 52.2 + - - +
131O GLU* 3.8 40.0 + - + -
134O VAL* 3.8 10.3 - - + +
135O LYS* 3.5 47.3 - - + +
138O LEU* 3.6 20.6 - - + -
1P MET* 3.4 26.1 - - + +
65P ASN* 4.6 3.8 + - - +
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Residues in contact with GLU 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O GLU 3.1 19.8 + - - +
89O ALA* 4.0 8.9 - - - +
90O ALA 3.3 0.2 - - - -
91O TYR* 1.3 78.1 - - - +
93O HIS* 1.3 55.9 - - - +
95O LYS* 3.5 17.1 + - - +
96O PHE* 3.1 24.1 + - - +
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Residues in contact with HIS 93 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O TYR* 3.6 30.6 - + - -
20O SER* 3.0 34.7 + - - -
23O LEU* 3.6 24.7 - - + +
24O TYR* 4.4 11.0 - - - +
89O ALA 3.2 18.9 + - - +
90O ALA* 3.5 5.6 - - - +
91O TYR 3.2 0.4 - - - -
92O GLU* 1.3 76.8 - - - +
94O GLU* 1.3 59.8 + - - +
95O LYS 3.3 0.2 - - - -
96O PHE* 3.2 30.8 + + - +
97O ILE* 2.9 35.8 + - + +
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Residues in contact with GLU 94 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O SER* 5.3 0.5 + - - -
24O TYR* 2.6 25.9 + - - +
50O GLU* 4.1 3.6 - - - +
90O ALA 2.9 20.1 + - - +
91O TYR* 3.4 9.4 + - - +
93O HIS* 1.3 80.2 - - - +
95O LYS* 1.3 57.7 + - - +
97O ILE* 4.5 6.1 - - - +
98O SER* 2.9 32.2 + - - -
127O GLN* 3.0 26.6 + - - +
130O GLU* 3.0 38.9 - - - +
131O GLU* 3.7 17.3 + - + +
134O VAL* 4.0 18.4 - - + -
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Residues in contact with LYS 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O TYR* 3.1 46.0 + - + +
92O GLU* 3.7 18.1 - - - +
93O HIS 3.3 0.2 - - - -
94O GLU* 1.3 75.4 - - - +
96O PHE* 1.3 59.6 + - - +
98O SER* 3.9 2.1 - - - -
99O LYS* 3.1 29.1 + - - +
131O GLU* 3.9 24.7 - - - +
1P MET* 5.0 19.2 - - + +
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Residues in contact with PHE 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O ARG* 4.2 32.8 - - + -
19O TYR* 6.1 0.9 - + - -
92O GLU 3.1 13.9 + - - +
93O HIS* 3.2 37.6 + + - +
95O LYS* 1.3 75.4 - - - +
97O ILE* 1.3 69.2 + - + +
99O LYS* 3.5 9.1 + - + +
100O SER* 3.2 23.2 + - - -
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Residues in contact with ILE 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O GLN* 4.1 8.3 - - - +
16O ARG* 4.0 26.9 - - + +
17O GLU* 4.0 18.4 - - - +
20O SER* 3.5 25.4 - - - +
50O GLU* 5.8 1.6 - - - +
93O HIS* 2.9 31.7 + - + +
94O GLU* 3.9 9.9 - - - +
96O PHE* 1.3 84.9 - - + +
98O SER* 1.3 58.2 + - - +
100O SER* 2.7 18.8 + - - +
101O ILE* 3.0 17.6 + - + +
127O GLN* 3.6 30.5 - - + +
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Residues in contact with SER 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O GLU 2.9 16.2 + - - -
95O LYS* 3.9 4.3 - - - -
96O PHE 3.4 0.2 - - - -
97O ILE* 1.3 75.4 - - - +
99O LYS* 1.3 56.7 + - - +
101O ILE* 3.2 10.4 + - - +
102O TYR* 3.0 51.0 + - - -
127O GLN* 3.2 26.7 + - - +
131O GLU* 2.8 28.2 + - - -
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Residues in contact with LYS 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O LYS 3.1 19.5 + - - +
96O PHE* 3.7 10.5 - - + +
97O ILE 3.3 0.2 - - - -
98O SER* 1.3 76.8 - - - +
100O SER* 1.3 56.6 + - - +
102O TYR* 3.2 18.5 + - + +
103O GLU* 3.0 49.4 + - + +
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Residues in contact with SER 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O GLN* 3.1 22.1 + - - +
16O ARG* 4.0 25.7 + - - -
96O PHE* 3.2 14.5 + - - -
97O ILE* 2.7 23.9 + - - -
99O LYS* 1.3 76.4 - - - +
101O ILE* 1.3 58.9 + - - +
103O GLU* 3.9 13.7 - - - +
104O LEU* 3.3 30.7 + - - +
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Residues in contact with ILE 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O GLN* 3.8 33.0 - - + +
17O GLU* 4.7 1.8 - - - +
57O PHE* 4.1 10.3 - - + -
97O ILE* 3.0 25.5 + - + +
98O SER* 3.5 11.7 - - - +
100O SER* 1.3 76.3 - - - +
102O TYR* 1.3 60.4 + - + +
104O LEU* 3.4 4.3 + - + +
105O ALA* 3.0 26.7 + - - +
120O LEU* 4.3 12.0 - - + +
123O PHE* 4.1 31.0 - - + +
124O ILE* 3.8 31.9 - - + +
127O GLN* 4.6 7.4 - - + -
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Residues in contact with TYR 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98O SER* 3.0 37.3 + - - -
99O LYS* 3.4 18.8 - - + +
101O ILE* 1.3 81.4 - - + +
103O GLU* 1.3 57.7 + - + +
105O ALA* 3.2 7.5 + - - +
106O ALA* 2.8 29.7 + - - +
124O ILE* 4.5 9.4 - - + -
131O GLU* 5.1 0.3 + - - -
64P ARG* 3.1 18.9 + - - -
112P LYS 5.4 3.4 - - - -
113P ASP* 5.1 1.5 + - - -
114P TYR* 3.6 46.1 - + + -
115P SER* 2.5 31.4 + - - -
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Residues in contact with GLU 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O ARG* 5.9 1.0 + - - -
99O LYS* 3.0 46.5 + - + +
100O SER* 4.0 11.1 - - - +
101O ILE 3.3 0.4 - - - -
102O TYR* 1.3 77.6 - - + +
104O LEU* 1.3 57.3 + - - +
106O ALA* 3.9 7.4 - - - +
107O LEU* 3.1 27.9 + - - +
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Residues in contact with LEU 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O MET* 4.1 19.8 - - - +
9O ALA* 3.7 37.2 - - + +
10O LEU* 4.1 11.4 - - + -
13O GLN* 3.7 37.5 - - + +
16O ARG* 5.2 2.0 - - - +
57O PHE* 4.4 2.7 - - + -
100O SER 3.3 20.4 + - - +
101O ILE* 3.7 5.8 - - + +
102O TYR 3.3 0.2 - - - -
103O GLU* 1.3 75.4 - - - +
105O ALA* 1.3 60.0 + - - +
107O LEU* 3.4 6.2 + - + +
108O ALA* 3.0 23.6 + - - +
120O LEU* 3.5 30.8 - - + +
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Residues in contact with ALA 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O ILE 3.0 14.5 + - - +
102O TYR* 3.2 10.3 + - - +
104O LEU* 1.3 77.4 - - - +
106O ALA* 1.3 56.0 + - - +
108O ALA 3.4 0.7 + - - -
109O GLU* 3.1 33.0 + - - +
117O ARG* 3.6 19.7 - - - +
120O LEU* 3.7 11.2 - - + +
124O ILE* 4.5 9.0 - - + -
114P TYR* 4.0 25.1 - - + -
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Residues in contact with ALA 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O TYR 2.8 15.0 + - - +
103O GLU* 3.9 8.3 - - - +
105O ALA* 1.3 73.9 - - - +
107O LEU* 1.3 60.1 + - - +
109O GLU* 3.4 4.9 + - - +
110O GLU* 3.1 30.3 + - - +
112P LYS* 6.4 1.8 - - + -
114P TYR* 3.4 22.4 + - + +
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Residues in contact with LEU 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O ARG* 3.8 28.5 - - - +
6O MET* 3.7 28.5 - - + +
9O ALA* 3.7 29.6 - - + -
103O GLU 3.1 19.6 + - - +
104O LEU* 3.5 7.6 - - + +
105O ALA 3.3 0.4 - - - -
106O ALA* 1.3 77.2 - - - +
108O ALA* 1.3 56.3 + - - +
110O GLU* 3.6 4.7 + - - +
111O GLU* 3.1 41.1 + - + +
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Residues in contact with ALA 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O MET* 3.6 17.4 - - + +
104O LEU 3.0 17.0 + - - +
105O ALA 3.7 5.6 - - - +
107O LEU* 1.3 75.7 - - - +
109O GLU* 1.3 59.4 + - - +
112O LYS 3.1 7.4 + - - -
113O ASP* 2.9 46.6 + - - +
116O THR* 4.3 6.3 - - + -
117O ARG* 3.9 20.9 - - + +
120O LEU* 4.5 0.7 - - + -
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Residues in contact with GLU 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O ALA 3.1 15.4 + - - +
106O ALA* 3.8 4.9 - - - +
107O LEU 3.4 0.2 - - - -
108O ALA* 1.3 76.8 - - - +
110O GLU* 1.3 61.2 + - - +
112O LYS* 3.6 9.1 + - - +
117O ARG* 3.0 34.3 + - + +
109P GLU* 6.0 2.1 - - - +
114P TYR* 2.9 38.5 + - - -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O ALA 3.1 17.7 + - - +
107O LEU* 3.6 5.4 + - - +
109O GLU* 1.3 76.8 - - - +
111O GLU* 1.3 63.5 + - + +
112O LYS* 3.4 0.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O SER* 2.7 32.8 + - - -
5O ARG* 3.9 31.0 + - - +
6O MET* 3.6 18.2 + - - +
107O LEU* 3.1 25.2 + - + +
108O ALA 3.4 3.3 + - - +
109O GLU 3.3 0.2 - - - -
110O GLU* 1.3 80.2 - - + +
112O LYS* 1.3 66.2 + - - +
113O ASP* 3.1 12.1 + - + +
----------------------------------------------------------
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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