Contacts of the helix formed by residues 96 - 118 (chain V) in PDB entry 3MQT
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 GLY 96 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93M GLY 4.7 6.1 - - - -
95M ARG* 3.5 17.8 - - - +
95V ARG* 1.3 73.3 - - - +
97V LEU* 1.3 56.3 + - - +
99V LEU* 2.7 34.0 + - - +
100V PHE* 3.5 15.1 + - - -
262V THR* 3.0 20.7 + - - +
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Residues in contact with LEU 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M CYS* 5.5 0.4 - - - -
53M PHE* 4.0 32.3 - - + -
92M ILE* 4.1 17.6 + - + +
95M ARG 4.4 3.0 + - - -
97M LEU* 4.3 25.2 - - + +
98M GLY 5.1 0.7 - - - +
46V PRO* 4.4 10.3 - - + -
49V CYS* 4.3 10.5 - - - -
50V MET* 3.6 32.2 - - + +
53V PHE* 4.0 26.2 - - + -
95V ARG 3.7 1.4 + - - -
96V GLY* 1.3 69.9 - - - -
98V GLY* 1.3 65.1 + - - +
100V PHE* 3.0 34.8 + - + +
101V ALA 3.5 2.9 + - - -
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Residues in contact with GLY 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M LEU* 5.1 0.8 - - - +
53V PHE* 3.7 29.0 - - - -
89V THR* 5.6 0.4 + - - -
92V ILE 4.2 5.2 + - - -
93V GLY* 4.0 18.2 - - - -
95V ARG 4.2 2.6 + - - -
96V GLY 3.1 1.2 + - - -
97V LEU* 1.3 78.7 - - - +
99V LEU* 1.3 62.9 + - - +
101V ALA* 3.4 7.1 + - - +
102V ILE* 3.3 23.9 + - - +
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Residues in contact with LEU 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82V TYR* 3.5 24.9 - - - +
86V TYR* 4.3 6.3 - - + -
94V MET* 3.1 49.6 - - - +
95V ARG* 3.4 9.0 - - - +
96V GLY 2.7 18.1 + - - +
98V GLY* 1.3 69.2 - - - -
100V PHE* 1.3 56.8 + - - -
102V ILE* 3.3 17.3 + - + +
103V SER* 2.7 31.9 + - - -
262V THR* 3.9 6.3 - - - -
263V THR* 3.6 12.8 - - + -
285V ARG 3.3 13.0 - - - +
286V CYS 3.6 17.5 - - - +
287V GLY* 3.8 7.9 + - - -
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Residues in contact with PHE 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M TRP 3.6 11.4 - - - -
92M ILE* 4.2 21.1 - - + -
93M GLY 5.9 0.4 - - - -
43V ALA* 3.2 10.3 - - - +
44V ASP* 3.3 37.0 - - + +
45V GLY* 3.9 4.7 - - - -
50V MET* 3.9 2.0 - - + -
96V GLY* 3.6 18.2 - - - -
97V LEU* 3.0 30.7 + - + +
99V LEU* 1.3 74.4 - - - +
101V ALA* 1.3 62.8 + - - +
103V SER* 3.2 4.5 + - - -
104V GLY 3.1 18.0 + - - -
262V THR* 4.0 12.1 - - + -
284V ASN 3.6 12.0 - - - +
285V ARG* 3.3 55.9 - - + -
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Residues in contact with ALA 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V PHE* 3.7 25.0 - - + -
43V ALA* 4.3 0.7 - - - -
50V MET* 3.8 8.6 - - + +
53V PHE* 3.5 32.1 - - + -
66V ILE* 4.0 8.1 - - + -
97V LEU 3.5 1.4 + - - -
98V GLY 3.4 11.8 + - - +
99V LEU 3.2 0.2 - - - -
100V PHE* 1.3 77.4 - - - +
102V ILE* 1.3 65.3 + - - +
103V SER 3.4 0.2 + - - -
104V GLY 3.4 1.7 + - - -
105V ILE* 3.4 26.0 + - - +
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Residues in contact with ILE 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66V ILE* 3.7 21.3 - - + -
82V TYR* 3.6 34.8 - - + -
85V MET* 4.0 23.5 - - + +
86V TYR* 3.8 35.7 - - + +
89V THR* 4.3 7.0 - - - +
93V GLY* 6.0 0.2 - - - -
94V MET 5.7 1.8 - - - +
98V GLY 3.3 12.7 + - - +
99V LEU* 3.3 24.9 + - + +
101V ALA* 1.3 76.2 - - - +
103V SER* 1.3 58.0 + - - +
105V ILE* 3.4 3.1 + - - +
106V ASP* 2.9 27.4 + - - +
287V GLY* 3.9 3.4 - - - +
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Residues in contact with SER 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V GLU 4.3 2.0 - - - -
99V LEU 2.7 19.2 + - - -
100V PHE 3.2 8.7 + - - -
102V ILE* 1.3 73.6 - - - +
104V GLY* 1.3 66.6 + - - +
106V ASP* 3.8 0.3 - - - +
107V MET* 2.9 27.2 + - - +
283V TYR 3.6 7.6 - - - +
284V ASN* 3.4 24.9 - - - -
285V ARG 3.2 8.1 - - - -
287V GLY 2.8 32.8 + - - -
288V GLY* 3.8 3.6 - - - +
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Residues in contact with GLY 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V VAL* 3.7 15.7 - - - +
41V GLY* 3.8 5.0 - - - -
42V GLU 3.3 28.1 + - - -
43V ALA* 4.0 2.5 - - - -
100V PHE 3.1 8.9 + - - -
101V ALA 3.4 2.4 + - - -
102V ILE 3.4 0.2 - - - -
103V SER* 1.3 81.0 - - - +
105V ILE* 1.3 61.4 + - - +
107V MET* 3.4 3.3 + - - +
108V ALA* 3.1 22.0 + - - +
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Residues in contact with ILE 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V VAL* 4.2 8.7 - - + -
12V PHE* 3.9 20.6 - - + -
29V VAL* 3.8 10.8 - - + -
31V VAL* 4.3 9.9 - - + -
66V ILE* 3.5 46.2 - - + +
67V LYS* 5.1 2.7 - - - +
70V VAL* 4.3 14.6 - - + -
85V MET* 3.6 22.7 - - - -
101V ALA 3.4 8.7 + - - +
102V ILE 3.9 0.9 - - - +
104V GLY* 1.3 71.5 - - - +
106V ASP* 1.3 67.7 + - - +
108V ALA* 3.0 4.3 + - - +
109V LEU* 2.9 43.8 + - + +
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Residues in contact with ASP 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78V PHE* 4.6 4.2 - - - +
82V TYR* 4.2 9.4 + - - +
85V MET* 4.1 8.0 - - + +
102V ILE* 2.9 19.5 + - + +
103V SER 3.8 2.2 - - - +
105V ILE* 1.3 75.7 - - - +
107V MET* 1.3 61.2 + - - +
109V LEU* 3.2 22.3 + - - +
110V TYR* 3.2 24.6 + - - -
287V GLY 3.7 15.5 - - - +
288V GLY 3.5 0.5 - - - -
289V VAL 3.0 14.4 + - - -
290V THR* 2.6 48.6 + - - -
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Residues in contact with MET 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V LEU 4.0 2.3 - - - +
41V GLY* 3.7 9.6 - - - -
42V GLU 3.6 30.7 - - - +
103V SER 2.9 15.5 + - - +
104V GLY 3.6 4.5 - - - +
106V ASP* 1.3 76.2 + - - +
108V ALA* 1.3 62.0 + - - +
109V LEU 3.3 0.5 + - - -
110V TYR* 3.3 18.2 + - - +
111V ASP 3.4 8.0 + - - -
283V TYR* 3.8 38.6 - - + +
284V ASN* 4.3 0.7 - - + -
289V VAL* 4.9 11.0 - - + +
315V ILE* 4.0 16.4 - - - +
316V THR* 4.0 12.8 - - - +
319V ALA* 4.1 20.9 - - + -
369V LEU* 3.9 18.3 - - + +
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Residues in contact with ALA 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V VAL* 3.8 5.8 - - + +
31V VAL* 3.8 18.8 - - + -
39V GLY* 3.5 16.3 - - - +
40V LEU 3.5 14.3 + - - -
41V GLY 3.6 16.4 - - - +
104V GLY 3.1 10.2 + - - +
105V ILE 3.0 9.7 + - - +
107V MET* 1.3 76.5 - - - +
109V LEU* 1.3 59.0 + - - +
111V ASP* 3.2 3.5 + - - +
112V LEU* 2.9 25.7 + - - +
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Residues in contact with LEU 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 3.4 30.3 - - + -
31V VAL* 3.8 19.5 - - + -
70V VAL* 4.5 4.5 - - + -
75V PRO* 4.0 18.4 - - + +
78V PHE* 3.9 9.7 - - + -
81V ASN* 4.2 29.8 - - + +
85V MET* 4.4 8.3 - - + -
105V ILE* 2.9 33.9 + - + +
106V ASP* 3.2 13.4 + - - +
108V ALA* 1.3 75.0 - - - +
110V TYR* 1.3 59.3 + - - +
112V LEU* 3.9 2.8 - - + +
113V ALA* 2.9 32.7 + - - +
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Residues in contact with TYR 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78V PHE* 3.4 50.5 - + - +
106V ASP* 3.2 25.5 + - - -
107V MET* 3.3 7.5 + - - +
108V ALA 3.3 0.4 - - - -
109V LEU* 1.3 74.8 - - - +
111V ASP* 1.3 65.6 + - - +
114V GLY* 3.1 21.7 + - - -
121V ALA* 4.2 13.8 - - + +
124V LEU* 4.0 23.3 - - + +
125V MET* 4.1 18.2 - - + -
289V VAL* 3.5 35.0 - - + -
290V THR* 2.7 38.5 + - - +
293V LEU* 3.9 10.2 - - + +
368V GLY* 4.0 3.8 - - - -
369V LEU* 4.7 5.8 - - + -
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Residues in contact with ASP 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V TYR 4.2 0.3 - - - +
39V GLY* 3.3 4.7 - - - -
40V LEU* 2.7 44.7 + - - +
107V MET 3.4 2.0 + - - +
108V ALA 3.2 9.3 + - - +
110V TYR* 1.3 79.9 - - - +
112V LEU* 1.3 61.6 + - - +
115V LYS* 3.1 45.8 + - - +
367V PRO 4.4 0.2 - - - +
368V GLY* 3.5 1.7 - - - -
369V LEU* 2.9 45.2 + - + +
370V GLY 4.1 3.3 + - - -
371V ILE* 4.6 7.0 + - - +
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Residues in contact with LEU 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 4.0 7.6 - - + -
31V VAL* 3.8 30.7 - - + +
33V ASP* 4.0 13.0 - - + +
37V VAL* 3.6 39.3 - - + +
38V TYR 4.0 5.2 - - - -
39V GLY* 3.6 11.2 - - - +
75V PRO* 3.8 28.5 - - + -
108V ALA 2.9 16.6 + - - +
109V LEU* 3.9 5.2 - - + +
110V TYR 3.4 0.2 - - - -
111V ASP* 1.3 77.8 - - - +
113V ALA* 1.3 58.0 + - - +
115V LYS* 3.2 3.4 + - - +
116V GLN* 2.9 39.4 + - + +
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Residues in contact with ALA 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75V PRO* 3.9 25.4 - - + +
76V LEU* 3.9 13.9 - - + +
78V PHE* 4.1 2.7 - - + -
109V LEU 2.9 18.3 + - - +
112V LEU* 1.3 74.2 - - - +
114V GLY* 1.3 64.5 + - - +
116V GLN* 3.3 12.2 + - - +
117V LEU* 3.0 29.0 + - + +
124V LEU* 3.8 15.3 - - + -
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Residues in contact with GLY 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110V TYR 3.1 11.7 + - - -
113V ALA* 1.3 75.7 - - - +
115V LYS* 1.3 52.1 + - - +
118V GLY* 2.8 14.2 + - - -
119V VAL* 2.7 50.7 + - - -
124V LEU* 3.4 14.1 - - - +
367V PRO* 3.8 0.5 - - - +
368V GLY* 3.5 11.4 - - - -
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Residues in contact with LYS 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V VAL* 4.0 17.7 - - + +
38V TYR* 2.6 53.3 + - - +
111V ASP* 3.1 37.0 + - - +
112V LEU 3.2 4.2 + - - +
114V GLY* 1.3 72.7 - - - +
116V GLN* 1.3 66.1 + - - +
118V GLY* 3.3 9.9 + - - -
367V PRO* 3.9 29.1 - - + +
371V ILE 6.0 1.6 - - - -
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Residues in contact with GLN 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V ALA* 3.0 38.5 + - - +
33V ASP* 2.5 36.4 + - - +
37V VAL* 4.8 5.8 - - + -
74V ASP* 4.3 3.5 - - - +
75V PRO* 3.1 27.9 - - - +
76V LEU* 5.9 0.3 - - - +
112V LEU* 2.9 22.8 + - + +
113V ALA* 3.6 8.7 - - - +
115V LYS* 1.3 79.4 - - - +
117V LEU* 1.3 67.5 + - + +
118V GLY 3.7 0.2 + - - -
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Residues in contact with LEU 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N LEU* 4.0 50.6 - - + +
119N VAL* 5.5 4.7 - - + -
76V LEU* 4.1 27.8 - - + -
113V ALA 3.0 20.6 + - - +
116V GLN* 1.3 83.9 - - + +
118V GLY* 1.3 63.0 + - - +
119V VAL* 3.6 21.3 + - + +
124V LEU* 4.3 17.7 - - + -
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Residues in contact with GLY 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114V GLY 2.8 9.5 + - - -
115V LYS 3.3 7.2 + - - -
116V GLN 3.3 3.4 + - - -
117V LEU* 1.3 80.6 - - - +
119V VAL* 1.3 60.3 + - - +
120V PRO* 4.6 1.7 - - - +
365V ASP 5.6 0.7 - - - +
367V PRO* 4.2 18.9 - - - +
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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