Contacts of the helix formed by residues 72 - 94 (chain W) in PDB entry 1P7G
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 ASP 72 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71W ILE* 1.3 72.4 - - - +
73W ILE* 1.3 63.5 + - - +
74W ARG* 3.5 12.0 + - - +
75W ALA* 3.2 30.3 + - + +
76W VAL* 3.0 25.3 + - + +
60X LYS* 4.7 9.5 + - - -
75X ALA* 4.5 7.3 - - + +
79X ASP* 4.3 14.4 - - - +
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Residues in contact with ILE 73 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V GLU* 4.1 26.0 - - + +
131V GLN* 3.6 33.0 - - + +
132V ALA* 3.9 23.3 - - + +
135V ASN* 3.7 21.8 - - + +
157V GLN* 4.5 0.2 - - - +
61W LEU* 4.3 8.5 - - + -
64W PHE* 5.4 0.4 - - + -
71W ILE* 3.2 27.2 + - + +
72W ASP* 1.3 72.8 + - - +
74W ARG* 1.3 62.9 + - - +
76W VAL* 3.8 0.6 - - - +
77W LEU* 2.9 58.9 + - + +
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Residues in contact with ARG 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135V ASN* 3.0 37.7 + - + +
136V VAL 4.6 0.2 - - - -
137V GLU* 3.9 28.2 + - - +
157V GLN* 3.2 31.5 + - - +
159V GLU* 5.0 0.2 - - - -
72W ASP* 3.3 8.7 + - - +
73W ILE* 1.3 82.2 - - + +
75W ALA* 1.3 64.0 + - - +
77W LEU* 3.9 0.5 - - - -
78W ARG* 3.0 63.3 + - - +
79X ASP* 2.7 37.6 + - - -
83X HIS* 4.9 10.3 - - - -
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Residues in contact with ALA 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72W ASP* 3.2 23.6 + - + +
74W ARG* 1.3 78.4 - - - +
76W VAL* 1.3 60.8 + - + +
78W ARG 3.3 0.5 + - - -
79W ASP* 3.0 28.1 + - - +
72X ASP* 5.2 2.2 - - - +
75X ALA* 3.5 31.6 - - + -
424X BME 3.2 28.8 - - + +
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Residues in contact with VAL 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57W ALA* 3.7 29.7 - - + +
60W LYS* 4.3 20.6 - - + +
61W LEU* 4.0 13.9 - - + -
71W ILE* 3.5 35.2 - - + -
72W ASP* 3.0 20.0 + - + +
73W ILE* 4.0 2.2 - - - +
75W ALA* 1.3 79.8 - - + +
77W LEU* 1.3 57.6 + - + +
79W ASP* 3.4 9.3 + - - +
80W LEU* 2.9 26.3 + - - +
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Residues in contact with LEU 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128V GLU* 5.0 1.6 - - - +
132V ALA* 3.8 27.1 - - + -
155V ILE* 3.2 31.2 - - + +
156V LEU* 3.9 4.5 - - + +
157V GLN* 3.7 34.8 + - + +
164V MSE 4.7 2.3 - - - +
61W LEU* 4.3 13.9 - - + -
73W ILE* 2.9 37.4 + - + +
74W ARG 4.2 2.2 - - - +
76W VAL* 1.3 75.1 - - - +
78W ARG* 1.3 61.0 + - - +
80W LEU* 3.9 18.2 - - + +
81W SER* 2.9 30.0 + - - -
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Residues in contact with ARG 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137U GLU* 4.4 4.2 - - - +
137V GLU* 2.9 29.3 + - - -
157V GLN* 4.8 0.4 - - - +
159V GLU* 2.7 28.3 + - - -
164V MSE 3.6 26.6 - - + +
74W ARG* 3.0 50.7 + - + +
75W ALA 3.6 4.0 - - - +
77W LEU* 1.3 77.9 - - - +
79W ASP* 1.3 63.9 + - - +
81W SER* 3.4 1.7 + - - -
82W PHE* 3.1 24.9 + - - +
162W ASN* 4.4 2.4 + - - -
78X ARG* 3.6 47.5 - - - +
79X ASP* 4.6 3.4 + - - -
160X LYS* 3.7 4.8 - - - +
424X BME 3.4 17.0 - - - -
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Residues in contact with ASP 79 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137U GLU* 4.3 5.8 - - - +
53W GLY 5.5 0.2 - - - +
57W ALA* 4.4 10.1 - - + -
60W LYS* 4.5 12.0 + - - +
75W ALA* 3.0 19.9 + - - +
76W VAL* 3.5 11.7 - - - +
78W ARG* 1.3 77.0 - - - +
80W LEU* 1.3 63.1 + - - +
82W PHE* 3.4 1.9 + - - +
83W HIS* 3.0 39.7 + - + +
72X ASP* 4.0 7.3 - - - +
74X ARG* 2.7 31.1 + - - -
424X BME 3.1 22.6 - - - +
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Residues in contact with LEU 80 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154V LEU* 4.4 19.5 - - + -
155V ILE 4.5 2.2 - - - +
156V LEU* 4.4 15.9 - - + -
54W ALA* 4.0 23.1 - - + +
57W ALA* 3.7 13.4 - - + +
58W LEU* 4.4 12.6 - - + -
61W LEU* 3.7 27.8 - - + -
76W VAL 2.9 18.4 + - - +
77W LEU* 3.9 15.3 - - + +
78W ARG 3.3 0.2 - - - -
79W ASP* 1.3 77.0 - - - +
81W SER* 1.3 57.5 + - - +
83W HIS* 5.1 1.6 - - - -
84W LEU* 2.8 51.8 + - + +
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Residues in contact with SER 81 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156V LEU* 4.6 11.7 - - - -
157V GLN 5.5 0.2 - - - -
164V MSE 2.7 39.5 + - - -
77W LEU 2.9 20.2 + - - -
78W ARG 3.8 2.7 - - - -
80W LEU* 1.3 77.0 - - - +
82W PHE* 1.3 62.1 + - - +
84W LEU* 4.1 3.3 - - - +
85W ASN* 2.9 32.5 + - - +
162W ASN* 2.9 21.5 + - - +
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Residues in contact with PHE 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137U GLU* 3.4 51.8 - - + +
138U GLY 4.7 2.7 - - - -
50W TYR* 3.5 36.3 - + - -
78W ARG 3.1 13.6 + - - +
79W ASP 3.7 2.0 - - - +
80W LEU 3.3 0.2 - - - -
81W SER* 1.3 78.3 - - - +
83W HIS* 1.3 80.2 + + - +
85W ASN 3.5 0.2 + - - -
86W GLY* 3.0 22.2 + - - -
160W LYS* 4.3 8.5 - - + -
161W HIS* 3.6 23.9 + - - +
162W ASN* 3.4 23.2 - - - +
178W TRP* 3.7 25.8 - + - -
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Residues in contact with HIS 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49W GLY 3.7 3.8 + - - -
50W TYR* 3.3 37.5 - + - +
53W GLY* 3.3 32.7 + - - -
54W ALA* 3.2 21.1 - - - +
79W ASP* 3.0 32.0 + - + +
80W LEU 4.3 0.2 - - - +
82W PHE* 1.3 93.0 - + - +
84W LEU* 1.3 68.6 + - - +
86W GLY* 2.9 1.6 + - - +
87W HIS* 2.8 24.9 + - - +
74X ARG* 4.8 15.3 - - - -
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Residues in contact with LEU 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147V GLU* 3.9 12.1 - - + -
154V LEU* 3.7 28.5 - - + -
156V LEU* 5.3 5.4 - - + -
166V ALA* 4.2 19.3 - - + -
18W TYR* 3.5 43.5 - - + +
54W ALA* 4.0 7.6 - - + +
80W LEU* 2.8 35.1 + - + +
81W SER* 4.1 3.1 - - - +
83W HIS* 1.3 72.7 - - - +
85W ASN* 1.3 58.0 + - - +
87W HIS* 3.3 4.7 + - + +
88W ILE* 2.8 47.9 + - + +
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Residues in contact with ASN 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165V HIS 2.8 21.3 + - - +
166V ALA* 3.5 5.4 - - - +
167V ALA* 2.8 38.0 - - - +
81W SER* 2.9 28.2 + - - +
84W LEU* 1.3 74.6 - - - +
86W GLY* 1.3 66.8 + - - +
88W ILE* 4.2 4.0 - - - +
89W LEU* 2.9 28.4 + - - +
161W HIS* 3.4 25.8 - - + +
162W ASN* 3.0 11.5 - - - +
165W HIS* 3.5 10.9 + - - +
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Residues in contact with GLY 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50W TYR* 3.9 11.0 - - - -
82W PHE 3.0 9.4 + - - -
83W HIS 2.9 7.3 + - - -
85W ASN* 1.3 75.6 - - - +
87W HIS* 1.3 57.7 + - - +
89W LEU* 4.3 0.2 - - - +
90W HIS* 2.8 37.9 + - - +
161W HIS* 3.5 32.0 - - - +
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Residues in contact with HIS 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149V LEU* 3.3 21.6 - - + +
150V GLU* 5.3 0.8 + - - -
18W TYR* 3.2 45.4 - + + +
19W THR 3.2 25.8 + - - -
21W PRO* 4.0 3.1 - - + -
47W HIS* 3.0 32.3 + - - -
50W TYR* 3.8 8.7 - - + +
51W VAL* 3.5 15.1 - - + +
54W ALA* 5.3 1.3 - - + -
83W HIS 2.8 11.5 + - - +
84W LEU* 3.5 10.5 - - + +
86W GLY* 1.3 76.7 - - - +
88W ILE* 1.3 57.4 + - - +
91W SER* 2.7 49.1 + - - -
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Residues in contact with ILE 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147V GLU* 4.4 12.8 - - + +
149V LEU* 4.6 15.5 - - + -
166V ALA* 4.5 3.1 - - + -
167V ALA* 3.8 40.6 - - + +
168V ASP* 4.9 4.7 - - + +
169V ALA* 6.0 0.2 - - + -
84W LEU* 2.8 60.6 + - + +
85W ASN* 3.9 13.7 - - - +
87W HIS* 1.3 73.9 - - - +
89W LEU* 1.3 61.7 + - - +
91W SER* 3.4 13.5 + - - -
92W ILE* 3.4 26.6 + - + +
220W LEU* 5.4 9.3 - - + +
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Residues in contact with LEU 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ALA* 4.0 14.6 - - + -
85W ASN 2.9 17.1 + - - +
88W ILE* 1.3 74.1 - - - +
90W HIS* 1.3 61.0 + - - +
92W ILE* 3.3 7.7 + - + +
93W PHE* 2.9 27.5 + - - +
141W TRP* 3.6 48.8 - - + +
143W ILE* 4.7 8.1 - - + -
158W ILE* 4.5 1.1 - - + -
161W HIS* 3.3 27.4 - - - +
165W HIS* 3.6 24.0 - - + +
171W VAL* 4.3 22.2 - - + -
174W ALA* 4.7 2.7 - - + +
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Residues in contact with HIS 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42W HIS* 2.7 41.4 + + - -
47W HIS* 3.3 34.8 - + + +
50W TYR* 3.6 25.6 - + - -
86W GLY 2.8 28.4 + - - +
89W LEU* 1.3 76.5 - - - +
91W SER* 1.3 61.5 + - - +
92W ILE 3.3 0.7 + - - -
93W PHE* 3.3 13.9 + + - +
94W TRP* 3.0 39.5 + + - +
141W TRP* 3.6 23.4 - + - -
161W HIS* 3.6 8.3 - - - -
176W ASP* 3.6 2.4 + - - -
180W HIS* 4.5 1.5 + - - -
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Residues in contact with SER 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V LEU* 4.4 12.7 - - - +
21W PRO* 4.1 10.5 - - - +
47W HIS* 3.9 7.5 - - - -
87W HIS* 2.7 43.3 + - - -
88W ILE* 3.5 8.5 - - - -
89W LEU 3.2 0.4 - - - -
90W HIS* 1.3 77.7 - - - +
92W ILE* 1.3 56.3 + - - +
94W TRP* 4.6 3.5 - - - -
95W PRO* 3.0 22.9 - - - +
220W LEU* 6.1 0.7 - - - -
323W ACT 3.4 18.7 - - - +
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Residues in contact with ILE 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168V ASP* 4.0 16.6 - - - +
88W ILE* 3.4 21.1 - - + +
89W LEU* 3.3 9.3 + - + +
90W HIS 3.1 0.4 - - - -
91W SER* 1.3 78.3 - - - +
93W PHE* 1.3 67.0 + - - +
94W TRP 3.4 0.4 - - - -
95W PRO* 3.2 6.9 - - - +
96W ASN* 3.0 44.4 + - - +
171W VAL* 3.7 43.3 - - + +
172W LEU 4.8 0.4 - - - +
174W ALA* 4.7 2.2 - - + -
209W ARG* 3.9 17.5 - - - +
220W LEU* 4.3 17.5 - - + -
323W ACT 4.5 2.5 - - + -
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Residues in contact with PHE 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W ILE* 5.2 3.6 - - + -
39W MSE 5.8 0.7 - - - -
42W HIS* 3.7 19.7 - + - -
89W LEU 2.9 17.1 + - - +
90W HIS* 3.5 9.9 - + - +
92W ILE* 1.3 76.0 - - - +
94W TRP* 1.3 99.1 + + - +
96W ASN* 3.1 20.9 + - - +
97W MSE 3.3 37.1 + - + +
141W TRP* 3.7 16.2 - + + -
174W ALA* 3.4 21.9 - - - +
175W LEU* 4.0 2.7 - - + -
176W ASP* 3.4 24.0 - - + -
181W ALA* 5.6 0.2 - - + -
193W TYR* 3.8 17.7 - - - -
197W TRP* 4.1 10.5 - + - -
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Residues in contact with TRP 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W PRO* 4.5 11.2 - - + -
22W PRO 5.2 2.2 - - - +
23W LEU* 3.5 14.8 - - + -
24W PRO* 3.7 20.4 - - + -
25W TYR* 2.7 20.0 + - - -
39W MSE 3.6 22.0 - - + -
42W HIS* 3.4 35.7 - + + -
43W HIS* 3.4 38.5 - + + -
47W HIS* 3.0 26.5 + + - -
90W HIS* 3.0 37.4 + + - -
91W SER* 4.6 1.3 - - - -
93W PHE* 1.3 100.4 - + - +
95W PRO* 1.4 63.3 - - + +
97W MSE 2.9 25.5 + - + +
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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