Contacts of the helix formed by residues 72 - 94 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60W LYS* 4.6 10.9 + - - -
75W ALA* 5.2 2.2 - - + +
79W ASP* 4.0 7.4 - - - +
71X ILE* 1.3 71.1 - - - +
73X ILE* 1.3 63.1 + - - +
74X ARG* 3.3 8.3 + - - +
75X ALA* 3.0 30.8 + - + +
76X VAL* 3.1 16.0 + - + +
424X BME 2.7 30.2 - - - +
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Residues in contact with ILE 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128U GLU* 3.9 26.5 - - + +
131U GLN* 3.3 35.4 - - + +
132U ALA* 3.8 15.7 - - + +
135U ASN* 3.5 18.4 - - + +
157U GLN* 4.5 0.2 - - - +
61X LEU* 4.0 16.4 - - + -
64X PHE* 5.3 0.2 - - + -
71X ILE* 3.0 25.7 + - + +
72X ASP* 1.3 73.1 + - - +
74X ARG* 1.3 67.0 + - - +
76X VAL 3.9 0.4 - - - +
77X LEU* 3.0 62.5 + - + +
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Residues in contact with ARG 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135U ASN* 2.7 53.4 + - + +
136U VAL 4.7 0.4 + - - -
137U GLU* 3.9 31.3 + - - +
157U GLN* 3.3 31.1 + - - +
79W ASP* 2.7 28.1 + - - +
83W HIS* 4.8 10.9 - - - -
72X ASP* 3.2 10.2 + - - +
73X ILE* 1.3 81.4 - - - +
75X ALA* 1.3 63.9 + - - +
77X LEU 4.1 0.2 - - - -
78X ARG* 3.1 49.8 + - - +
424X BME 3.2 18.5 + - - +
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Residues in contact with ALA 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72W ASP* 4.5 9.0 - - - +
75W ALA* 3.5 30.1 - - + -
72X ASP* 3.0 28.0 + - + +
74X ARG* 1.3 78.5 - - - +
76X VAL* 1.3 64.6 + - + +
78X ARG* 3.3 2.9 + - - +
79X ASP* 3.2 29.0 + - - +
424X BME 3.3 12.9 - - - -
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Residues in contact with VAL 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X ALA* 3.8 21.4 - - + +
60X LYS* 4.1 21.5 - - + +
61X LEU* 3.7 34.1 - - + -
71X ILE* 3.6 31.4 - - + -
72X ASP* 3.1 8.8 + - + +
73X ILE 4.1 2.0 - - - +
75X ALA* 1.3 78.9 - - + +
77X LEU* 1.3 57.2 + - - +
79X ASP* 3.3 9.1 + - - +
80X LEU* 2.9 25.8 + - - +
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Residues in contact with LEU 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128U GLU* 5.0 1.6 - - - +
132U ALA* 3.9 17.5 - - + -
155U ILE* 3.4 29.2 - - + +
156U LEU* 4.2 4.4 - - + +
157U GLN* 4.1 29.5 + - + +
164U MSE 5.1 2.2 - - - -
61X LEU* 4.1 32.5 - - + -
73X ILE* 3.0 41.6 + - + +
74X ARG 4.4 1.3 - - - +
76X VAL* 1.3 75.2 - - - +
78X ARG* 1.3 59.6 + - - +
80X LEU* 3.8 7.7 - - + +
81X SER* 2.9 32.1 + - - -
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Residues in contact with ARG 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137U GLU* 3.1 33.5 + - - +
157U GLN* 4.7 2.3 - - - +
159U GLU* 3.4 28.5 + - - -
164U MSE 3.7 26.2 - - + -
137V GLU* 4.3 4.3 - - - +
78W ARG* 3.6 37.8 - - - +
160W LYS* 3.7 5.3 - - - +
74X ARG* 3.1 36.9 + - + +
75X ALA 3.6 4.3 - - - +
76X VAL 3.3 0.2 - - - -
77X LEU* 1.3 77.6 - - - +
79X ASP* 1.3 63.3 + - - +
81X SER* 3.7 2.1 - - - -
82X PHE* 3.1 23.6 + - - +
162X ASN* 4.1 3.3 + - - -
424X BME 2.8 52.9 - - - +
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Residues in contact with ASP 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137V GLU* 4.1 6.9 - - - +
72W ASP* 4.3 13.7 - - - +
74W ARG* 2.7 35.3 + - - -
78W ARG* 4.6 3.8 + - - -
57X ALA* 4.6 8.7 - - + -
60X LYS* 4.5 12.3 + - - +
75X ALA 3.2 16.2 + - - +
76X VAL* 3.5 10.3 - - - +
78X ARG* 1.3 75.6 - - - +
80X LEU* 1.3 64.7 + - - +
82X PHE* 3.3 1.6 + - - +
83X HIS* 2.9 40.9 + - + +
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Residues in contact with LEU 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154U LEU* 4.0 24.5 - - + -
155U ILE 4.5 1.6 - - - +
156U LEU* 3.8 23.1 - - + -
18X TYR* 5.9 0.2 - - + -
54X ALA* 3.8 25.8 - - + +
57X ALA* 3.9 14.1 - - + +
58X LEU* 4.0 17.9 - - + +
61X LEU* 4.0 20.6 - - + -
76X VAL 2.9 17.0 + - - +
77X LEU* 3.8 10.8 - - + +
79X ASP* 1.3 75.9 - - - +
81X SER* 1.3 59.4 + - - +
83X HIS* 4.9 1.8 - - - -
84X LEU* 2.8 45.3 + - + +
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Residues in contact with SER 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156U LEU* 4.8 11.6 - - - +
157U GLN 5.5 0.9 - - - -
164U MSE 2.5 40.4 + - - -
166U ALA* 6.3 0.7 - - - -
77X LEU 2.9 18.3 + - - -
78X ARG 3.7 2.2 - - - -
80X LEU* 1.3 78.2 - - - +
82X PHE* 1.3 63.8 + - - +
84X LEU* 4.1 2.8 - - - +
85X ASN* 2.9 32.1 + - - +
162X ASN* 3.0 20.0 + - - +
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Residues in contact with PHE 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137V GLU* 3.2 48.2 - - + +
138V GLY 4.7 2.5 - - - -
50X TYR* 3.8 15.5 - + - -
78X ARG 3.1 11.7 + - - +
79X ASP 3.6 2.5 - - - +
81X SER* 1.3 80.2 - - - +
83X HIS* 1.3 89.0 + + - +
85X ASN* 3.7 2.6 - - - +
86X GLY* 2.9 24.1 + - - -
160X LYS* 4.2 11.0 - - + -
161X HIS* 3.7 19.3 - - - +
162X ASN* 3.3 24.1 - - - +
178X TRP* 3.6 36.1 - + - -
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Residues in contact with HIS 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74W ARG* 4.9 11.0 - - - -
49X GLY 4.1 2.7 + - - -
50X TYR* 3.4 28.8 - + - +
53X GLY* 3.4 31.7 + - - -
54X ALA* 3.3 21.5 - - - +
79X ASP* 2.9 32.6 + - + +
80X LEU 4.2 0.2 - - - +
82X PHE* 1.3 102.8 - + - +
84X LEU* 1.3 65.8 + - - +
86X GLY* 3.2 1.4 + - - +
87X HIS* 2.9 23.7 + - - +
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Residues in contact with LEU 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U GLU* 3.7 12.8 - - + -
154U LEU* 3.6 31.0 - - + -
156U LEU* 5.5 2.9 - - + -
166U ALA* 4.3 14.6 - - + -
18X TYR* 3.6 42.0 - - + +
54X ALA* 4.1 7.5 - - + +
80X LEU* 2.8 32.5 + - + +
81X SER* 4.1 2.5 - - - +
83X HIS* 1.3 73.8 - - - +
85X ASN* 1.3 58.5 + - - +
87X HIS* 3.2 5.9 + - + +
88X ILE* 2.8 53.8 + - + +
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Residues in contact with ASN 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165U HIS 2.8 19.2 - - - +
166U ALA* 3.6 7.0 - - - +
167U ALA* 2.8 35.9 - - - +
81X SER* 2.9 27.0 + - - +
82X PHE 3.7 1.1 - - - +
84X LEU* 1.3 76.3 - - - +
86X GLY* 1.3 65.5 + - - +
88X ILE* 4.3 3.7 - - - +
89X LEU* 2.8 29.5 + - - +
161X HIS* 3.2 26.9 - - - +
162X ASN* 3.3 5.2 - - - +
165X HIS* 3.2 19.0 + - - -
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Residues in contact with GLY 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X TYR* 4.0 11.1 - - - -
82X PHE 2.9 12.6 + - - -
83X HIS 3.2 3.7 + - - -
85X ASN* 1.3 76.4 - - - +
87X HIS* 1.3 61.1 + - - +
90X HIS* 2.7 32.6 + - - -
161X HIS* 3.1 34.7 - - - +
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Residues in contact with HIS 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U LEU* 3.4 20.4 - - + +
18X TYR* 3.4 43.9 - + + +
19X THR 3.4 23.6 + - - -
21X PRO* 3.9 3.6 - - + -
47X HIS* 3.1 28.0 + - - +
50X TYR* 3.9 6.6 - - + +
51X VAL* 3.7 15.2 - - + +
54X ALA* 5.2 1.6 - - + -
83X HIS 2.9 12.6 + - - +
84X LEU* 3.4 11.4 - - + +
86X GLY* 1.3 73.6 - - - +
88X ILE* 1.3 67.5 + - - +
90X HIS 3.1 2.3 + - - -
91X SER* 2.9 42.4 + - - -
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Residues in contact with ILE 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147U GLU* 3.8 17.7 - - + +
149U LEU* 4.0 16.2 - - + -
166U ALA* 4.9 1.8 - - + -
167U ALA* 3.6 46.7 - - + +
168U ASP* 4.4 6.1 - - + +
84X LEU* 2.8 52.4 + - + +
85X ASN* 4.0 5.2 - - - +
87X HIS* 1.3 74.4 - - - +
89X LEU* 1.3 62.8 + - - +
91X SER* 3.2 15.0 + - - -
92X ILE* 3.3 27.0 + - + +
220X LEU* 5.1 8.1 - - + -
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Residues in contact with LEU 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167U ALA* 4.3 11.9 - - + -
85X ASN 2.8 22.1 + - - +
88X ILE* 1.3 73.5 - - - +
90X HIS* 1.3 58.9 + - - +
92X ILE* 3.3 6.5 + - + +
93X PHE* 2.9 26.3 + - - +
141X TRP* 3.4 53.3 - - + +
143X ILE* 4.5 8.5 - - + -
158X ILE* 4.6 1.3 - - + -
161X HIS* 3.5 23.1 - - - +
165X HIS* 3.8 26.2 - - + +
171X VAL* 4.4 21.3 - - + -
174X ALA* 4.6 4.7 - - + +
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Residues in contact with HIS 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X HIS* 2.7 37.7 + + - -
47X HIS* 3.4 32.3 - + + +
50X TYR* 3.6 24.8 - + - -
86X GLY 2.7 26.5 + - - +
87X HIS 3.1 1.6 + - - -
89X LEU* 1.3 72.1 - - - +
91X SER* 1.3 65.6 + - - +
92X ILE 3.0 1.8 - - - -
93X PHE* 3.1 15.2 + + - -
94X TRP* 2.9 43.2 + + - +
141X TRP* 3.3 25.9 - + - -
161X HIS* 3.8 7.0 - - - -
176X ASP* 3.3 5.1 + - - -
180X HIS* 4.5 1.7 + - - -
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Residues in contact with SER 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149U LEU* 4.5 8.6 - - - +
21X PRO* 3.9 13.7 - - - +
47X HIS* 3.8 5.1 + - - -
87X HIS* 2.9 39.7 + - - -
88X ILE* 3.2 12.7 + - - -
90X HIS* 1.3 75.8 - - - +
92X ILE* 1.3 57.7 + - - +
94X TRP* 4.2 3.6 - - - -
95X PRO* 3.0 24.5 - - - +
220X LEU* 6.2 0.2 - - - -
324X ACT 3.3 22.4 - - - +
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Residues in contact with ILE 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168U ASP* 4.0 15.9 - - - +
88X ILE* 3.3 27.3 + - + +
89X LEU* 3.7 9.0 - - - +
90X HIS 3.0 0.4 - - - -
91X SER* 1.3 78.3 - - - +
93X PHE* 1.3 60.7 + - - +
94X TRP 3.5 0.2 - - - -
95X PRO* 3.4 5.3 - - - +
96X ASN* 3.0 52.9 + - - +
171X VAL* 3.8 42.0 - - + +
172X LEU 4.6 0.7 - - - +
174X ALA* 4.8 2.7 - - + -
209X ARG* 3.9 18.2 - - - +
220X LEU* 4.1 16.4 - - + -
324X ACT 4.3 3.4 - - + -
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Residues in contact with PHE 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X ILE* 5.0 3.8 - - + -
39X MSE 5.9 1.1 - - - -
42X HIS* 3.9 27.6 - + - -
89X LEU 2.9 17.6 + - - +
90X HIS* 3.1 9.6 + + - +
92X ILE* 1.3 74.7 - - - +
94X TRP* 1.3 83.3 + + - +
96X ASN* 3.3 17.3 + - + +
97X MSE 3.4 39.8 - - + +
141X TRP* 3.8 13.5 - + + -
174X ALA* 2.9 30.0 - - - +
175X LEU* 4.0 3.6 - - + -
176X ASP* 3.4 18.8 - - + -
181X ALA* 5.4 0.2 - - + -
193X TYR* 3.6 22.0 - - - -
197X TRP* 4.0 14.4 - - - -
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Residues in contact with TRP 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X PRO* 4.7 7.6 - - + -
22X PRO 5.2 2.2 - - - +
23X LEU* 3.3 18.8 - - + -
24X PRO* 3.8 20.6 - - + -
25X TYR* 2.9 20.4 + - - +
39X MSE 3.7 28.0 - - + -
42X HIS* 3.6 32.5 - + + -
43X HIS* 3.7 36.9 - + + -
47X HIS* 2.7 29.0 + + - -
90X HIS* 2.9 41.2 + + + -
91X SER* 4.2 4.7 - - - -
93X PHE* 1.3 91.4 - + - +
95X PRO* 1.3 69.8 - - + +
97X MSE 3.0 16.2 + - + +
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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