Contacts of the helix formed by residues 96 - 118 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 1.3 70.9 - - - +
97C LEU* 1.3 57.4 + - - -
98C GLY 3.1 2.9 - - - -
99C LEU* 2.6 33.3 + - - +
100C PHE* 3.5 13.8 + - - -
262C THR* 3.1 20.0 + - - -
285C ARG* 6.1 0.4 - - - -
93F GLY 4.7 5.8 - - - -
95F ARG* 3.5 18.0 - - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PRO* 4.3 11.0 - - + -
49C CYS* 4.2 10.5 - - - -
50C MET* 3.6 32.2 - - + +
53C PHE* 3.7 31.0 - - + -
95C ARG 3.9 0.6 + - - -
96C GLY* 1.3 70.3 - - - -
98C GLY* 1.3 57.4 + - - +
100C PHE* 2.8 43.6 + - + +
101C ALA 3.5 2.9 + - - -
53F PHE* 4.0 30.3 - - + -
92F ILE* 4.0 18.3 + - + +
95F ARG 4.4 3.0 + - - -
97F LEU* 4.4 24.0 - - + +
98F GLY 5.1 0.9 - - - +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE* 3.6 30.7 - - - -
89C THR* 5.5 0.7 + - - -
92C ILE 4.2 4.0 + - - -
93C GLY* 3.9 19.1 - - - -
95C ARG 4.3 2.6 + - - -
96C GLY 2.9 1.6 + - - -
97C LEU* 1.3 79.6 - - - +
99C LEU* 1.3 59.5 + - - +
101C ALA* 3.4 13.7 + - - +
102C ILE* 3.4 16.8 + - - +
97F LEU* 5.2 0.8 - - - +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 3.6 24.5 - - + +
86C TYR* 4.3 7.9 - - + -
94C MET* 2.9 48.5 - - - +
95C ARG* 3.3 10.5 + - - +
96C GLY 2.6 17.7 + - - +
98C GLY* 1.3 71.0 - - - -
100C PHE* 1.3 57.9 + - - -
101C ALA 3.2 0.7 - - - -
102C ILE* 3.8 16.1 - - + +
103C SER* 2.8 31.4 + - - -
262C THR* 4.0 4.9 - - - +
263C THR* 3.7 11.2 - - + -
285C ARG 3.3 12.6 - - - +
286C CYS 3.6 17.3 - - - +
287C GLY* 3.7 9.2 + - - -
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 3.2 9.8 - - - +
44C ASP* 3.3 36.1 - - + +
45C GLY* 4.0 5.8 - - - -
50C MET* 3.8 2.2 - - + -
96C GLY* 3.6 17.0 - - - -
97C LEU* 2.8 33.4 + - + +
99C LEU* 1.3 77.4 - - - +
101C ALA* 1.3 56.8 + - - +
103C SER* 3.2 4.2 + - - -
104C GLY 3.0 25.3 + - - -
262C THR* 4.0 10.1 - - + -
284C ASN 3.7 11.2 - - - +
285C ARG* 3.3 58.3 - - + -
91F TRP 3.6 10.8 - - - -
92F ILE* 4.2 20.2 - - + -
93F GLY 5.9 0.7 - - - -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.9 25.6 - - + -
43C ALA* 4.2 0.9 - - - -
50C MET* 3.8 7.8 - - + +
53C PHE* 3.6 33.7 - - + -
66C ILE* 3.9 10.3 - - + -
97C LEU 3.5 1.2 + - - -
98C GLY 3.4 8.3 + - - +
99C LEU 3.2 0.4 - - - -
100C PHE* 1.3 79.1 - - - +
102C ILE* 1.3 60.8 - - - +
104C GLY 3.4 1.4 + - - -
105C ILE* 3.3 26.0 + - - +
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Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.5 22.2 - - + -
82C TYR* 3.8 22.4 - - + +
85C MET* 4.0 22.1 - - + +
86C TYR* 3.8 33.9 - - + +
89C THR* 4.0 10.8 - - - +
94C MET 5.6 2.5 - - - +
98C GLY 3.4 13.3 + - - +
99C LEU* 3.8 22.7 - - + +
100C PHE 3.3 0.4 - - - -
101C ALA* 1.3 77.7 - - - +
103C SER* 1.3 56.3 + - - +
105C ILE* 3.4 1.7 + - - +
106C ASP* 2.9 28.8 + - - +
287C GLY* 3.7 15.3 - - - +
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU 4.6 1.1 - - - -
99C LEU 2.8 13.1 + - - -
100C PHE 3.2 9.6 - - - -
102C ILE* 1.3 77.2 - - - +
104C GLY* 1.3 63.8 + - - +
106C ASP* 3.4 1.7 + - - +
107C MET* 2.9 25.3 + - - +
283C TYR 3.5 9.7 - - - +
284C ASN 3.4 21.3 - - - -
285C ARG 3.0 8.7 - - - -
287C GLY 2.8 39.3 + - - -
288C GLY* 3.3 4.1 + - - +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 3.8 10.2 - - - +
41C GLY* 3.7 8.0 - - - -
42C GLU 3.3 30.7 + - - -
43C ALA* 3.9 6.3 - - - -
100C PHE 3.0 12.1 + - - -
101C ALA 3.4 3.1 + - - -
102C ILE 3.4 0.2 - - - -
103C SER* 1.3 75.5 - - - +
105C ILE* 1.3 63.1 + - - +
107C MET* 3.4 3.9 + - - +
108C ALA* 3.1 18.9 + - - +
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 4.2 10.5 - - + -
12C PHE* 3.8 25.8 - - + -
29C VAL* 3.8 12.1 - - + +
31C VAL* 4.5 7.4 - - + -
66C ILE* 3.8 33.2 - - + +
67C LYS* 5.0 2.5 - - - +
70C VAL* 4.4 13.2 - - + -
85C MET* 3.6 31.9 - - - -
101C ALA 3.3 8.5 + - - +
102C ILE 3.9 1.8 - - - +
103C SER 3.3 0.4 - - - -
104C GLY* 1.3 72.4 - - - +
106C ASP* 1.3 67.6 + - - +
108C ALA* 3.1 4.7 + - - +
109C LEU* 2.9 38.2 + - + +
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Residues in contact with ASP 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 4.8 5.0 - - - +
82C TYR* 4.3 9.6 + - - +
85C MET* 4.2 8.2 - - + +
102C ILE* 2.9 18.9 + - + +
103C SER 3.6 4.0 - - - +
105C ILE* 1.3 79.1 - - - +
107C MET* 1.3 61.8 + - - +
109C LEU* 3.3 19.5 + - - +
110C TYR* 3.2 26.6 + - - -
287C GLY 3.7 12.1 - - - +
288C GLY 3.5 0.2 - - - -
289C VAL 3.0 28.2 + - - -
290C THR* 2.7 35.3 + - - -
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU 4.2 0.7 - - - -
41C GLY* 3.9 2.7 - - - -
42C GLU 3.8 21.8 - - - +
103C SER 2.9 14.0 + - - +
104C GLY 3.5 5.4 - - - +
106C ASP* 1.3 78.0 + - - +
108C ALA* 1.3 62.0 + - - +
110C TYR* 3.2 19.6 + - - +
111C ASP 3.3 8.1 + - - -
283C TYR* 4.0 32.8 - - + +
284C ASN* 4.1 1.8 - - + -
289C VAL* 4.9 12.3 - - + +
315C ILE* 3.8 30.7 - - - +
316C THR* 3.9 16.2 - - - +
319C ALA* 4.0 20.6 - - + -
369C LEU* 3.8 21.0 - - + +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.8 4.7 - - + +
31C VAL* 3.7 23.1 - - + -
39C GLY* 3.6 9.2 - - - +
40C LEU 3.6 15.3 - - - -
41C GLY* 3.5 16.7 - - - +
104C GLY 3.1 9.7 + - - +
105C ILE 3.1 8.6 + - - +
107C MET* 1.3 76.4 - - - +
109C LEU* 1.3 57.9 + - - +
111C ASP* 3.3 2.6 + - - +
112C LEU* 2.8 30.8 + - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.3 31.4 - - + -
31C VAL* 3.9 20.0 - - + -
70C VAL* 4.3 11.4 - - + -
75C PRO* 4.0 18.3 - - + +
78C PHE* 3.8 9.6 - - + -
81C ASN* 4.4 17.0 - - + +
85C MET* 4.3 14.6 - - + -
105C ILE* 2.9 35.0 + - + +
106C ASP* 3.7 11.4 - - - +
107C MET 3.2 0.4 - - - -
108C ALA* 1.3 75.0 - - - +
110C TYR* 1.3 58.7 + - - +
112C LEU* 4.4 2.9 - - + +
113C ALA* 2.8 34.1 + - - +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 3.5 49.2 - + - +
106C ASP* 3.2 32.8 + - - -
107C MET* 3.2 7.4 + - - +
109C LEU* 1.3 73.7 - - - +
111C ASP* 1.3 64.8 + - - +
114C GLY* 3.1 20.8 + - - -
121C ALA* 4.2 16.2 - - + +
124C LEU* 4.0 22.3 - - + +
125C MET* 4.2 27.8 - - + -
289C VAL* 3.6 22.7 - - + -
290C THR* 2.6 38.2 + - - +
293C LEU* 4.2 9.0 - - + +
368C GLY* 4.0 3.8 - - - -
369C LEU* 4.8 3.8 - - + -
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Residues in contact with ASP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY* 3.4 4.7 - - - -
40C LEU* 2.8 43.6 + - - +
107C MET 3.3 3.7 + - - +
108C ALA 3.3 8.5 + - - +
110C TYR* 1.3 79.3 - - - +
112C LEU* 1.3 63.3 + - - +
114C GLY 3.4 0.2 + - - -
115C LYS* 3.1 41.2 + - - +
368C GLY* 3.4 7.8 - - - -
369C LEU* 2.7 47.1 + - + +
370C GLY 4.0 2.9 + - - -
371C ILE* 4.5 8.0 + - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.1 7.2 - - + -
31C VAL* 3.8 32.3 - - + +
33C ASP* 3.9 16.2 - - + +
37C VAL* 3.5 40.8 - - + +
38C TYR 3.8 7.0 - - - -
39C GLY* 3.7 10.7 - - - +
75C PRO* 3.9 19.7 - - + -
108C ALA 2.8 20.2 + - - +
109C LEU* 4.0 4.3 - - + +
111C ASP* 1.3 70.2 - - - +
113C ALA* 1.3 67.4 + - - +
115C LYS* 3.0 4.6 + - - -
116C GLN* 2.9 35.1 + - - +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PRO* 3.9 21.7 - - - +
76C LEU* 4.1 9.4 - - + +
78C PHE* 3.8 23.1 - - + -
109C LEU 2.8 22.2 + - - +
112C LEU* 1.3 73.9 - - - +
114C GLY* 1.3 61.6 + - - +
116C GLN* 3.4 8.6 + - - +
117C LEU* 3.1 30.1 + - + +
124C LEU* 3.9 7.9 - - + -
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR 3.1 11.1 + - - -
111C ASP 3.7 1.6 - - - -
112C LEU 3.2 0.2 - - - -
113C ALA* 1.3 77.9 - - - +
115C LYS* 1.3 51.3 + - - +
117C LEU 3.4 0.3 + - - -
118C GLY* 2.7 30.0 + - - -
119C VAL* 2.9 32.6 + - - +
124C LEU* 3.5 12.8 - - - +
367C PRO* 3.8 0.7 - - - +
368C GLY* 3.5 12.1 - - - -
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 3.7 18.3 - - + +
38C TYR* 2.8 51.7 + - - +
40C LEU* 5.7 0.6 - - - +
111C ASP* 3.1 35.4 + - - +
112C LEU* 3.0 6.7 + - - +
114C GLY* 1.3 71.5 - - - +
116C GLN* 1.3 67.2 + - - +
118C GLY* 2.9 13.3 + - - -
367C PRO* 4.0 24.3 - - + +
371C ILE 5.8 5.3 + - - +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 3.0 37.6 + - + +
33C ASP* 2.7 36.7 + - - +
37C VAL* 4.7 6.2 - - + +
74C ASP* 4.3 4.0 - - - +
75C PRO* 3.4 28.5 - - - +
76C LEU* 6.0 0.3 - - - +
112C LEU* 2.9 23.8 + - + +
113C ALA* 3.7 8.0 - - - +
115C LYS* 1.3 76.3 - - - +
117C LEU* 1.3 68.4 + - + +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 5.2 0.7 - - + -
117A LEU* 4.2 44.8 - - + +
119A VAL* 5.8 4.3 - - + -
76C LEU* 4.3 22.7 - - + -
113C ALA* 3.1 19.9 + - - +
116C GLN* 1.3 85.9 - - + +
118C GLY* 1.3 63.0 + - - +
119C VAL* 3.6 20.2 + - + +
124C LEU* 3.9 27.1 - - + -
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Residues in contact with GLY 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLY 2.7 11.0 + - - -
115C LYS 2.9 11.2 + - - -
117C LEU* 1.3 79.1 - - - +
119C VAL* 1.3 59.4 + - - +
120C PRO* 4.7 1.0 - - - +
365C ASP 5.5 0.5 - - - +
367C PRO* 4.1 20.9 - - - +
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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