Contacts of the helix formed by residues 85 - 114 (chain R) in PDB entry 5C3I
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 GLN 85 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ARG 4.2 0.4 - - - -
84R PHE* 1.3 74.4 - - - +
86R SER* 1.3 65.5 + - - +
87R SER* 4.1 9.8 + - - +
88R ALA* 3.0 19.8 + - + +
89R VAL* 3.2 12.1 + - - +
80S THR* 4.0 12.3 - - + +
81S VAL 2.9 19.9 + - - +
82S THR* 3.4 29.6 - - - +
83S ALA* 3.6 6.2 + - - +
96T ALA* 4.4 10.3 - - + -
100T GLU 4.9 2.6 + - - -
102T VAL* 3.4 33.3 - - - +
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Residues in contact with SER 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ILE* 3.3 25.3 - - - +
86P GLU* 3.3 37.1 + - - +
87P LEU* 6.3 0.2 - - - -
84R PHE 3.6 2.2 + - - -
85R GLN* 1.3 72.3 - - - +
87R SER* 1.3 62.9 + - - +
89R VAL* 3.5 4.9 + - - +
90R MET* 3.4 19.8 + - - +
90T TYR* 4.5 6.3 - - - -
95T LEU* 3.9 19.7 - - - +
96T ALA* 5.2 0.6 - - - +
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Residues in contact with SER 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P ILE* 6.6 0.4 - - - -
85R GLN* 4.1 12.0 + - - +
86R SER* 1.3 80.2 + - - +
88R ALA* 1.3 61.2 + - - +
90R MET* 3.5 18.3 + - - +
91R ALA* 3.0 26.2 + - - +
83S ALA* 4.1 16.4 - - - +
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Residues in contact with ALA 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R PHE* 4.6 6.3 - - + -
85R GLN* 3.0 13.1 + - + +
87R SER* 1.3 79.5 + - - +
89R VAL* 1.3 63.5 + - - +
91R ALA* 3.2 12.5 + - - +
92R LEU* 3.2 12.8 + - - +
81S VAL 3.7 12.3 - - - +
82S THR 3.5 32.1 - - - +
83S ALA* 3.6 9.9 - - - +
86S VAL* 3.9 14.8 - - + +
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Residues in contact with VAL 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R PHE* 3.9 8.7 - - + -
68R GLN* 4.2 19.3 - - + -
71R VAL* 4.8 8.5 - - + -
84R PHE* 3.6 34.8 - - + -
85R GLN 3.2 6.1 + - - +
86R SER 3.7 7.0 - - - +
88R ALA* 1.3 74.3 - - - +
90R MET* 1.3 57.7 + - - +
92R LEU* 3.2 12.8 + - - +
93R GLN* 3.0 24.1 + - - +
90T TYR* 3.3 31.6 - - + -
95T LEU* 3.7 15.7 - - + -
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Residues in contact with MET 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R LYS* 4.2 20.2 - - - +
86R SER 3.4 12.6 + - - +
87R SER* 3.7 17.3 - - - +
88R ALA 3.2 0.6 - - - -
89R VAL* 1.3 76.0 - - - +
91R ALA* 1.3 60.2 + - - +
93R GLN* 3.8 4.9 - - + -
94R GLU* 3.1 56.8 + - + +
90T TYR* 3.4 23.0 + - + +
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Residues in contact with ALA 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R SER 3.0 14.8 + - - +
88R ALA* 3.2 12.3 + - - +
90R MET* 1.3 79.1 - - - +
92R LEU* 1.3 56.4 + - - +
94R GLU* 4.0 7.9 - - - +
95R ALA* 3.1 28.1 + - - +
83S ALA* 4.7 11.4 - - + +
86S VAL* 3.9 18.4 - - + -
87S VAL* 5.2 7.4 - - + -
90S LEU* 4.3 5.3 - - + +
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Residues in contact with LEU 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R PHE* 3.7 11.0 - - + -
71R VAL* 4.1 12.6 - - + -
84R PHE* 4.0 23.6 - - + -
88R ALA 3.2 10.4 + - - +
89R VAL* 3.2 9.2 + - - +
91R ALA* 1.3 76.6 - - - +
93R GLN* 1.3 59.3 + - - +
95R ALA* 3.4 6.8 + - + +
96R CYS* 2.9 33.1 + - - +
61S PHE* 6.4 0.9 - - + -
62S LEU* 4.1 17.5 - - + -
65S VAL* 3.8 29.6 - - + -
66S ILE* 4.0 24.7 - - + +
69S ALA* 5.8 0.9 - - + -
86S VAL* 3.7 20.2 - - + -
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Residues in contact with GLN 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R ILE* 2.8 36.0 + - - +
63R ARG 3.7 11.3 + - - -
64R LYS* 3.8 14.0 - - - +
67R PHE* 3.4 31.8 - - + +
89R VAL 3.0 6.9 + - - +
90R MET* 4.1 5.6 - - + +
91R ALA 3.3 0.4 - - - -
92R LEU* 1.3 74.5 - - - +
94R GLU* 1.3 65.7 + - - +
96R CYS* 3.2 1.2 + - - +
97R GLU* 2.9 49.1 + - + +
90T TYR* 2.5 44.6 + - - +
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Residues in contact with GLU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R MET* 3.1 50.3 + - + +
91R ALA* 4.0 7.1 - - - +
93R GLN* 1.3 75.5 - - - +
95R ALA* 1.3 57.1 + - - +
97R GLU* 4.2 4.7 - - - +
98R ALA* 3.0 33.0 + - - +
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Residues in contact with ALA 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R ALA 3.1 18.9 + - - +
92R LEU* 3.6 8.1 - - + +
93R GLN 3.1 0.2 - - - -
94R GLU* 1.3 74.9 - - - +
96R CYS* 1.3 55.5 + - - +
98R ALA* 3.7 3.6 - - - +
99R TYR* 2.7 35.9 + - - +
61S PHE* 4.2 6.9 - - + -
90S LEU* 3.5 36.6 - - + -
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Residues in contact with CYS 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R ILE* 4.6 3.6 - - + -
67R PHE* 3.9 11.2 - - + -
92R LEU* 2.9 20.5 + - - +
93R GLN 3.8 3.4 - - - +
95R ALA* 1.3 72.9 - - - +
97R GLU* 1.3 61.1 + - - +
99R TYR* 3.5 0.9 - - - +
100R LEU* 3.0 35.3 + - - +
58S LEU* 3.7 17.5 - - + -
61S PHE* 3.6 26.2 - - - -
62S LEU* 3.4 38.8 - - - -
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Residues in contact with GLU 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R LEU 5.7 0.2 + - - -
61R LEU* 2.9 46.8 + - + +
62R ILE* 3.2 29.3 + - + +
93R GLN* 2.9 52.9 + - + +
94R GLU* 4.2 4.0 - - - +
96R CYS* 1.3 75.7 - - - +
98R ALA* 1.3 57.8 + - - +
100R LEU* 3.4 0.5 + - - -
101R VAL* 2.9 37.4 + - - +
37S LEU* 4.1 7.3 - - - +
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Residues in contact with ALA 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R GLU 3.0 22.1 + - - +
95R ALA* 3.9 4.3 - - - +
97R GLU* 1.3 72.9 - - - +
99R TYR* 1.3 65.1 + - - +
101R VAL* 4.3 5.1 - - - +
102R GLY* 3.2 18.4 + - - -
131R ARG* 5.6 0.7 + - - -
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Residues in contact with TYR 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ALA 2.7 22.8 + - - +
96R CYS 3.5 3.4 - - - +
98R ALA* 1.3 75.4 - - - +
100R LEU* 1.3 75.4 + - + +
102R GLY* 3.7 0.9 - - - -
103R LEU* 2.9 43.5 + - + +
128R ARG* 3.6 13.9 - - - +
131R ARG* 4.6 21.6 + - + +
133R GLU* 3.2 22.1 + - - -
57S VAL* 3.3 35.3 - - + +
58S LEU* 5.5 0.9 - - + -
61S PHE* 3.6 50.0 - + + -
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Residues in contact with LEU 100 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R ILE* 4.6 2.9 - - + -
96R CYS 3.0 18.5 + - - +
97R GLU 4.1 1.3 - - - +
99R TYR* 1.3 95.9 - - + +
101R VAL* 1.3 60.6 + - - +
103R LEU* 3.2 18.3 + - + +
104R PHE* 2.8 39.0 + - + -
29S ILE* 5.1 0.4 - - + -
37S LEU* 3.6 33.0 - - + -
54S THR* 4.1 26.2 - - + -
57S VAL* 4.3 8.5 - - + -
58S LEU* 3.5 34.1 - - + +
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Residues in contact with VAL 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R LEU* 3.6 26.7 - - + -
97R GLU 2.9 25.3 + - - +
98R ALA* 4.3 4.9 - - - +
100R LEU* 1.3 69.1 - - - +
102R GLY* 1.3 61.1 + - - +
104R PHE* 3.2 7.8 + - - +
105R GLU* 2.9 42.2 + - - +
37S LEU* 3.8 14.1 - - + +
40S ARG* 3.6 39.5 - - + +
41S GLY* 3.9 0.5 - - - -
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Residues in contact with GLY 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ALA 3.2 14.1 + - - -
99R TYR 3.7 3.4 - - - -
101R VAL* 1.3 78.4 - - - +
103R LEU* 1.3 59.0 + - - +
105R GLU* 3.3 11.5 + - - +
106R ASP 3.1 14.2 + - - -
131R ARG* 2.8 26.2 + - - -
98S TYR* 3.3 20.8 + - - -
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Residues in contact with LEU 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R TYR* 2.9 24.7 + - + +
100R LEU* 3.2 24.0 + - + +
102R GLY* 1.3 77.0 - - - +
104R PHE* 1.3 53.2 + - + +
106R ASP* 3.3 6.4 - - - +
107R THR* 2.7 34.0 + - - +
124R ILE* 4.0 20.6 - - + -
127R ALA* 3.6 37.0 - - + +
128R ARG* 3.9 7.6 - - + +
131R ARG* 3.8 18.8 - - - +
54S THR* 6.2 0.4 - - + -
57S VAL* 3.8 28.3 - - + -
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Residues in contact with PHE 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R LEU* 2.8 26.9 + - + +
101R VAL 3.6 4.7 - - - +
103R LEU* 1.3 77.4 - - + +
105R GLU* 1.3 59.1 + - - +
107R THR* 3.2 8.8 + - - -
108R ASN* 2.8 29.3 + - - +
119R ILE* 3.9 20.2 - - + -
124R ILE* 4.8 7.2 - - + -
34S ILE* 4.1 8.3 - - + -
37S LEU* 3.7 17.5 - - + +
38S ALA* 3.5 45.8 - - + -
41S GLY* 3.9 15.7 - - - -
43S VAL* 3.9 14.1 - - + +
50S ILE* 4.0 12.3 - - + -
54S THR* 3.8 32.5 - - + -
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145Q ARG* 4.4 8.0 + - - +
101R VAL* 2.9 30.7 + - - +
102R GLY* 3.4 8.2 - - - +
104R PHE* 1.3 73.2 - - - +
106R ASP* 1.3 59.2 + - - +
108R ASN* 3.2 5.4 + - - +
109R LEU* 2.9 29.5 + - - +
40S ARG 4.8 3.2 - - - +
41S GLY* 3.5 24.2 + - - +
98S TYR* 3.0 32.6 + - - -
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Residues in contact with ASP 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Q TYR* 3.0 31.5 + - - +
145Q ARG* 2.6 35.4 + - - +
102R GLY 3.1 3.9 + - - +
103R LEU 3.3 10.8 - - - +
105R GLU* 1.3 78.5 - - - +
107R THR* 1.3 52.3 + - - +
109R LEU* 3.3 5.6 + - - +
110R CYS* 2.7 37.2 + - - +
127R ALA* 3.5 8.6 - - + +
130R ILE* 3.7 7.6 - - - +
131R ARG* 2.7 39.3 + - - -
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Residues in contact with THR 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R LEU 2.7 22.0 + - - -
104R PHE* 3.2 12.7 + - - -
106R ASP* 1.3 77.2 - - - +
108R ASN* 1.3 56.9 + - - +
110R CYS* 3.6 6.3 - - - +
111R ALA* 3.0 30.0 + - - +
119R ILE* 3.6 36.0 - - + +
120R MET 4.8 0.2 - - - +
123R ASP* 3.3 34.0 + - + +
124R ILE* 4.2 19.2 - - + +
127R ALA* 4.6 0.2 - - - +
43S VAL* 5.1 0.2 - - - -
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Residues in contact with ASN 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R PHE 2.8 14.1 + - - +
105R GLU* 3.3 10.8 + - - +
106R ASP 3.2 0.2 - - - -
107R THR* 1.3 77.1 - - - +
109R LEU* 1.3 57.6 + - - +
111R ALA* 4.1 1.2 - - - +
112R ILE* 3.1 37.0 + - - +
119R ILE* 4.7 7.7 - - - +
41S GLY 4.1 14.3 + - - +
42S GLY* 3.5 24.4 + - - +
43S VAL* 4.3 9.4 - - + +
44S LYS* 5.2 1.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 109 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Q TYR* 4.3 13.7 - - + -
140Q LEU* 4.0 14.8 - - + +
143Q ASN* 3.5 31.0 - - + +
145Q ARG* 3.4 36.8 - - - +
105R GLU 2.9 14.3 + - - +
106R ASP* 3.7 6.5 - - - +
108R ASN* 1.3 74.9 - - - +
110R CYS* 1.3 67.8 + - - +
112R ILE* 3.1 24.2 - - + +
113R HIS* 3.3 26.9 + - + +
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Residues in contact with CYS 110 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q VAL* 3.7 35.8 - - - +
112Q TYR* 3.6 29.8 - - + -
140Q LEU* 5.9 0.7 - - - -
106R ASP 2.7 23.0 + - - +
107R THR* 3.6 9.9 - - - +
109R LEU* 1.3 77.6 - - - +
111R ALA* 1.3 61.2 + - - +
113R HIS* 3.6 2.9 + - - +
114R ALA* 3.4 14.7 + - - +
123R ASP* 3.6 24.0 - - + +
126R LEU* 3.8 16.8 - - - -
----------------------------------------------------------
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Residues in contact with ALA 111 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R THR 3.0 18.2 + - - +
108R ASN 4.2 2.0 - - - +
110R CYS* 1.3 73.1 - - - +
112R ILE* 1.3 62.7 + - - +
113R HIS 3.2 1.8 - - - -
114R ALA 3.3 1.7 + - - -
115R LYS 3.3 4.0 + - - -
116R ARG* 3.0 65.7 + - + +
117R VAL 5.6 0.9 - - - -
118R THR 4.7 0.9 - - - +
119R ILE* 3.8 21.1 - - + +
123R ASP* 4.3 1.6 - - - +
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Residues in contact with ILE 112 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R ASN* 3.1 26.9 + - - +
109R LEU* 3.1 27.8 - - + +
111R ALA* 1.3 76.3 - - - +
113R HIS* 1.3 69.4 + - + +
115R LYS* 3.5 14.4 + - - +
116R ARG 4.3 5.4 + - - -
----------------------------------------------------------
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Residues in contact with HIS 113 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q VAL* 5.5 4.0 - - + -
114Q ASN* 3.8 34.3 + - + +
138Q ASN* 4.7 8.7 + - - -
140Q LEU* 3.4 39.6 - - + +
142Q SER* 6.0 1.3 - - - -
143Q ASN* 5.5 3.4 - - - -
109R LEU* 3.3 29.5 + - + +
110R CYS* 4.0 4.7 - - - +
111R ALA 3.2 0.4 - - - -
112R ILE* 1.3 85.5 - - + +
114R ALA* 1.3 56.9 + - - +
115R LYS* 3.1 17.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Q GLY* 5.6 3.4 - - - -
92Q VAL* 4.1 17.0 - - + +
114Q ASN* 4.9 5.2 - - - -
110R CYS 3.4 8.9 + - - +
111R ALA 3.3 3.7 + - - +
113R HIS* 1.3 76.3 - - - +
115R LYS* 1.3 69.6 + - - +
116R ARG* 3.2 41.8 + - - +
----------------------------------------------------------
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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).
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