Contacts of the helix formed by residues 71 - 96 (chain A) in PDB entry 1RJG
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 PHE 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 4.0 13.9 - - - -
70A SER* 1.3 74.2 + - - +
72A PRO* 1.3 75.6 - - + +
73A VAL* 3.2 11.4 - - + +
74A MET* 3.2 20.3 + - + +
75A ASN* 2.8 29.3 + - - -
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.7 7.8 + - - +
70A SER 4.6 0.9 - - - +
71A PHE* 1.3 98.8 - - + +
73A VAL* 1.3 62.8 + - + +
75A ASN* 3.4 9.6 + - - +
76A TYR* 3.2 28.4 + - - -
306A GLN* 3.8 33.4 - - + +
307A PHE 5.2 5.2 - - - +
308A LEU* 3.9 18.8 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.2 8.9 - - + -
72A PRO* 1.3 77.1 - - + +
74A MET* 1.3 65.2 + - + +
76A TYR* 3.3 15.5 + - - +
77A GLY 3.4 3.3 + - - -
308A LEU* 3.7 24.2 - - + -
310A GLU 5.7 1.1 - - - +
313A GLU* 3.8 59.2 - - + +
314A LEU* 4.0 4.0 - - - +
317A MET* 3.3 34.2 - - + +
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 4.7 10.5 - - - -
69A SER 5.8 0.2 - - - +
70A SER* 3.5 23.3 - - - +
71A PHE* 3.2 24.7 + - + +
73A VAL* 1.3 80.4 - - + +
75A ASN* 1.3 58.6 + - - +
76A TYR 3.3 0.2 - - - -
77A GLY* 3.6 2.1 + - - -
78A THR* 3.0 28.6 + - - -
317A MET* 4.4 17.9 - - - -
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 4.5 2.3 - - - +
18A ALA* 3.3 28.1 + - - +
19A ALA* 4.0 3.8 + - - +
22A VAL* 4.4 7.3 - - - +
24A TYR* 3.3 33.4 - - + +
70A SER* 3.0 24.0 + - - -
71A PHE 2.8 25.7 + - - -
72A PRO 3.8 2.9 - - - +
73A VAL 3.2 0.8 - - - -
74A MET* 1.3 75.5 - - - +
76A TYR* 1.3 60.9 + - - +
78A THR* 3.6 7.6 + - - -
79A TYR* 3.2 25.3 + - - +
306A GLN* 3.7 15.6 + - - +
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.3 27.6 - + - -
72A PRO 3.2 21.8 + - - +
73A VAL 3.6 3.8 - - - +
74A MET 3.3 0.2 - - - -
75A ASN* 1.3 77.0 - - - +
77A GLY* 1.3 60.9 + - - +
79A TYR* 3.3 7.1 + + - +
80A LEU* 3.2 31.8 + - + +
290A PHE* 3.7 30.5 - + - -
299A ARG 4.7 0.9 + - - -
302A LEU* 3.3 42.9 + - + +
303A ARG* 3.9 10.4 + - - +
306A GLN 4.2 6.1 + - - -
308A LEU* 3.8 31.9 - - + +
311A LEU* 5.5 2.1 - - + +
314A LEU* 3.4 33.9 - - + -
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL 3.4 9.6 + - - -
74A MET 3.6 4.0 + - - -
75A ASN 3.4 0.4 - - - -
76A TYR* 1.3 79.1 - - - +
78A THR* 1.3 56.4 + - - +
80A LEU 4.1 0.2 - - - -
81A ARG* 3.3 25.7 + - - +
231A TYR* 4.2 6.1 + - - -
286A MET* 5.8 0.2 - - - +
314A LEU* 4.4 1.0 - - - +
317A MET* 4.5 2.0 - - - -
318A GLN* 3.5 36.8 - - - +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS* 3.2 53.5 + - + +
16A LYS* 4.0 12.3 - - + +
19A ALA* 4.1 7.9 - - + -
25A LEU* 4.4 0.6 - - + +
74A MET 3.0 18.2 + - - -
75A ASN* 3.9 7.5 + - - -
76A TYR 3.2 0.4 - - - -
77A GLY* 1.3 75.1 - - - +
79A TYR* 1.3 63.1 + - - +
80A LEU 3.3 0.2 - - - -
81A ARG* 3.4 11.8 + - + +
82A THR* 2.9 37.1 + - - +
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 5.5 0.2 - - - -
24A TYR* 3.4 37.0 - + + -
25A LEU* 3.7 14.4 - - + -
27A SER* 4.1 2.7 - - - -
30A LEU* 3.2 17.4 - - + +
75A ASN 3.2 18.7 + - - +
76A TYR* 3.3 7.2 + + - +
78A THR* 1.3 78.9 - - - +
80A LEU* 1.3 66.6 + - + +
82A THR* 4.2 0.5 - - - -
83A VAL* 3.1 47.7 + - + +
290A PHE* 5.9 0.4 - + - -
294A ILE* 3.7 24.6 - - + +
298A GLU* 2.7 35.2 + - - +
301A ARG* 4.1 2.2 - - - -
302A LEU* 3.5 36.8 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 3.2 20.0 + - + +
77A GLY 4.3 0.2 - - - +
79A TYR* 1.3 81.1 - - + +
81A ARG* 1.3 61.1 + - - +
83A VAL* 4.2 3.6 - - - -
84A GLY* 3.2 20.5 + - - -
85A ILE 4.5 0.2 + - - -
286A MET* 3.1 44.0 - - + +
289A ILE* 4.0 7.1 - - + +
290A PHE* 3.7 32.5 - - + -
294A ILE* 3.5 35.7 - - + -
314A LEU* 4.9 4.7 - - + -
318A GLN* 3.6 24.7 - - + +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 5.3 2.4 + - - -
12A ALA* 4.1 17.6 - - - +
15A CYS* 5.6 7.9 - - - +
16A LYS* 6.5 1.3 - - - +
77A GLY 3.3 19.4 + - - +
78A THR* 3.5 13.9 - - - +
80A LEU* 1.3 78.8 - - - +
82A THR* 1.3 60.6 + - - +
85A ILE* 3.3 32.2 + - - +
201A GLU* 3.5 20.3 + - - +
202A CYS* 3.1 38.2 - - - +
231A TYR* 3.5 42.3 - - + +
286A MET* 4.2 0.6 - - - +
321A TYR* 6.0 2.4 - - - -
335A SAH 3.1 27.9 + - - +
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.6 21.4 - - + +
25A LEU* 3.4 19.7 - - + +
31A GLN* 3.5 22.0 - - - +
41A TYR* 3.7 17.0 - - + +
78A THR* 2.9 18.1 + - - +
79A TYR 4.2 1.6 - - - -
81A ARG* 1.3 78.3 - - - +
83A VAL* 1.3 60.0 + - - +
84A GLY 3.3 0.4 - - - -
85A ILE 3.7 0.2 + - - -
86A ASP* 2.9 39.1 + - - +
111A ARG* 3.6 14.4 + - + +
201A GLU* 5.3 1.3 + - - -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 22.9 - - + -
27A SER* 4.4 2.7 - - - -
30A LEU* 3.5 38.0 - - + +
31A GLN* 4.2 15.0 - - + -
79A TYR* 3.1 36.7 + - + +
80A LEU* 4.2 2.7 - - - -
82A THR* 1.3 72.5 - - - +
84A GLY* 1.3 62.7 + - - +
85A ILE 3.5 0.2 - - - -
86A ASP* 3.9 8.7 - - - +
87A ALA* 3.2 27.5 + - - +
289A ILE* 6.2 0.2 - - + -
293A GLN* 5.0 0.3 - - - +
294A ILE* 3.8 17.5 - - + -
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU 3.2 20.0 + - - -
83A VAL* 1.3 80.1 - - - +
85A ILE* 1.3 63.3 + - - +
87A ALA* 3.8 5.7 + - - +
88A ALA* 3.8 10.4 + - - +
286A MET* 5.1 0.2 - - - -
289A ILE* 4.9 6.3 - - - -
293A GLN* 4.3 12.4 - - - +
294A ILE* 6.4 0.2 - - - -
323A LEU* 3.8 26.4 - - - +
325A LYS* 5.6 0.2 - - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 3.3 15.9 + - - +
82A THR 3.7 1.0 + - - -
84A GLY* 1.3 75.3 - - - +
86A ASP* 1.3 63.8 + - - +
88A ALA* 3.1 15.1 + - - +
89A ILE* 3.2 28.0 + - + +
111A ARG* 3.5 26.5 - - - +
199A ILE* 4.4 9.9 - - + -
201A GLU* 3.2 43.3 - - + +
229A ILE* 3.9 20.2 - - + +
230A SER 5.4 0.9 - - - +
231A TYR* 4.3 15.7 - - + -
323A LEU* 3.7 20.2 - - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 5.8 0.2 - - - -
31A GLN* 3.1 34.6 - - + +
41A TYR* 5.9 0.2 - - - -
82A THR* 2.9 32.5 + - - +
83A VAL* 4.2 7.0 - - - -
84A GLY 3.5 0.2 - - - -
85A ILE* 1.3 76.6 - - - +
87A ALA* 1.3 58.6 + - - +
89A ILE* 3.2 11.3 + - - +
90A LEU* 3.0 41.6 + - + +
111A ARG* 3.4 27.7 + - - +
115A LEU* 4.9 8.7 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.1 8.0 + - + +
83A VAL 3.2 19.3 + - - +
84A GLY 4.0 6.1 - - - +
85A ILE 3.2 0.6 - - - -
86A ASP* 1.3 77.5 - - - +
88A ALA* 1.3 60.8 + - - +
90A LEU* 3.6 8.2 + - - +
91A GLU* 3.4 32.9 + - - +
293A GLN* 4.4 13.2 - - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 3.8 7.9 + - - +
85A ILE 3.1 9.2 + - - +
87A ALA* 1.3 77.3 - - - +
89A ILE* 1.3 63.8 + - - +
91A GLU* 3.8 10.4 + - - +
92A PHE 3.6 10.7 + - - -
227A LEU* 3.4 19.8 - - + +
229A ILE* 4.0 17.9 - - + -
325A LYS* 4.0 32.3 - - + +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.2 28.0 + - + +
86A ASP* 3.2 12.5 + - - +
88A ALA* 1.3 76.2 - - - +
90A LEU* 1.3 59.3 + - + +
92A PHE* 3.3 3.5 + - - +
93A LEU* 3.0 48.6 + - + +
101A VAL* 5.6 3.4 - - + -
111A ARG* 3.7 31.9 - - - +
115A LEU* 4.2 15.7 - - + -
197A ILE* 3.9 17.9 - - + -
199A ILE* 3.9 15.0 - - + -
229A ILE* 3.5 14.1 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 3.5 24.2 - - - +
31A GLN* 3.6 15.9 - - - +
32A ARG* 3.7 24.7 - - - +
86A ASP* 3.0 28.8 + - + +
87A ALA* 4.0 6.5 - - - +
88A ALA 3.4 0.2 - - - -
89A ILE* 1.3 76.9 - - + +
91A GLU* 1.3 63.4 + - + +
93A LEU* 4.5 3.6 - - - +
94A VAL* 3.1 35.2 + - + +
115A LEU* 4.9 7.2 - - + -
118A MET* 3.8 29.6 - - + -
119A PHE* 4.0 17.3 - - + -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.4 21.3 + - - +
88A ALA* 4.1 8.5 - - - +
89A ILE 3.3 0.6 - - - -
90A LEU* 1.3 78.8 - - + +
92A PHE* 1.3 61.2 + - - +
94A VAL* 4.5 2.7 - - - +
95A ALA* 3.5 24.1 + - - +
325A LYS* 5.5 4.3 + - - -
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 3.6 1.0 + - - -
89A ILE 3.3 8.5 + - - +
91A GLU* 1.3 79.7 - - - +
93A LEU* 1.3 57.2 + - - +
94A VAL 3.3 1.1 - - - -
95A ALA* 4.1 0.9 - - - -
96A ASN* 3.2 38.0 + - - +
99A VAL* 4.0 8.5 - - + +
195A PRO* 3.7 31.6 - - + -
196A THR 4.0 5.4 - - - -
197A ILE* 3.4 30.5 - - + -
225A HIS* 5.5 1.6 - - + -
226A GLY* 4.1 26.0 - - - -
227A LEU* 3.6 41.1 - - + -
327A GLN* 4.4 17.5 - - + -
329A HIS* 5.2 5.6 - + - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.0 31.0 + - + +
90A LEU 3.6 1.1 + - - +
92A PHE* 1.3 73.6 - - - +
94A VAL* 1.3 57.4 + - - +
96A ASN 2.8 20.1 - - - +
97A GLU* 4.2 4.6 - - - +
99A VAL* 3.5 37.9 - - + -
101A VAL* 5.1 0.9 - - + -
115A LEU* 3.6 31.4 - - + -
119A PHE* 3.3 47.4 - - + -
122A LEU* 3.7 21.5 - - + -
197A ILE* 4.0 7.2 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 6.0 7.2 - - - +
90A LEU* 3.1 22.4 + - + +
91A GLU* 4.5 3.1 - - - +
93A LEU* 1.3 79.0 - - - +
95A ALA* 1.3 64.1 + - - +
96A ASN* 3.2 3.2 + - - -
97A GLU* 5.1 1.4 + - - +
119A PHE* 4.3 15.3 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU 3.5 18.8 + - - +
92A PHE* 4.8 0.9 - - + -
94A VAL* 1.3 80.0 - - - +
96A ASN* 1.3 76.6 + - - +
----------------------------------------------------------
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.2 34.7 + - + +
93A LEU 2.8 21.7 - - - +
94A VAL 4.5 1.6 - - - -
95A ALA* 1.3 92.7 - - - +
97A GLU* 1.3 60.6 + - - +
98A LYS 5.0 0.7 - - - +
99A VAL* 3.0 26.2 - - + +
195A PRO* 4.0 27.3 - - + +
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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