Contacts of the helix formed by residues 96 - 118 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ARG* 1.3 74.1 - - - +
97E LEU* 1.3 60.2 + - - -
99E LEU* 2.8 27.1 + - - +
100E PHE* 3.3 16.2 - - - -
262E THR* 3.0 21.1 + - - -
93H GLY 4.7 6.3 - - - -
95H ARG* 3.5 17.4 - - - +
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PRO* 4.3 10.8 - - + -
49E CYS* 4.2 9.4 - - - -
50E MET* 3.6 33.8 - - + +
53E PHE* 3.9 25.6 - - + -
95E ARG 3.8 1.4 + - - -
96E GLY* 1.3 70.9 - - - -
98E GLY* 1.3 65.3 + - - +
100E PHE* 2.9 34.9 + - + +
101E ALA 3.5 3.6 + - - -
53H PHE* 3.9 31.6 - - + -
92H ILE* 3.9 20.4 + - + +
95H ARG 4.4 2.2 + - - -
97H LEU* 4.2 24.6 - - + +
98H GLY 5.2 1.1 - - - +
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Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E PHE* 3.7 28.3 - - - -
66E ILE* 4.7 0.2 - - - +
89E THR* 5.6 0.4 + - - -
92E ILE 4.2 5.6 + - - -
93E GLY* 4.0 17.0 - - - -
95E ARG 4.4 1.2 + - - -
96E GLY 3.3 1.2 - - - -
97E LEU* 1.3 78.7 - - - +
99E LEU* 1.3 64.3 + - - +
101E ALA* 3.3 13.9 + - - +
102E ILE* 3.4 17.1 + - - +
97H LEU* 5.0 1.6 - - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 3.8 22.0 - - - +
86E TYR* 4.4 5.2 - - + -
93E GLY* 4.0 0.4 - - - -
94E MET* 3.2 47.6 - - - +
95E ARG* 3.5 4.0 - - - +
96E GLY 2.8 16.7 + - - +
98E GLY* 1.3 69.6 - - - -
100E PHE* 1.3 58.1 + - - +
101E ALA 3.2 0.2 - - - -
102E ILE* 3.4 18.4 + - + +
103E SER* 2.7 32.9 + - - -
262E THR* 3.8 16.2 - - - -
263E THR* 4.0 7.2 - - + -
285E ARG 3.4 12.6 - - - +
286E CYS 3.9 13.7 - - - +
287E GLY* 3.9 8.1 - - - -
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Residues in contact with PHE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA* 3.3 10.1 - - - +
44E ASP* 3.4 34.5 - - + +
45E GLY* 4.0 6.1 - - - -
50E MET* 3.8 2.5 - - + -
96E GLY* 3.3 21.5 - - - -
97E LEU* 2.9 32.2 + - + +
99E LEU* 1.3 75.4 - - - +
101E ALA* 1.3 63.0 + - - +
103E SER* 3.3 3.3 + - - -
104E GLY 3.1 18.7 + - - -
262E THR* 4.0 9.4 - - + -
284E ASN 3.6 12.3 - - - +
285E ARG* 3.4 54.3 - - + -
91H TRP 3.7 11.0 - - - -
92H ILE* 4.3 19.1 - - + -
93H GLY 5.9 0.2 - - - -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PHE* 3.9 24.5 - - + -
43E ALA* 4.4 0.4 - - - -
50E MET* 3.9 8.7 - - + +
53E PHE* 3.7 30.5 - - + -
66E ILE* 3.9 9.9 - - + -
97E LEU 3.5 2.0 + - - -
98E GLY 3.3 11.1 + - - +
99E LEU 3.2 0.4 - - - -
100E PHE* 1.3 79.1 - - - +
102E ILE* 1.3 61.2 + - - +
104E GLY* 3.3 2.1 + - - -
105E ILE* 3.3 26.5 + - - +
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Residues in contact with ILE 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ILE* 3.4 22.0 - - + -
82E TYR* 3.7 34.5 - - + +
85E MET* 4.0 22.4 - - + +
86E TYR* 4.0 31.2 - - + +
89E THR* 4.0 11.4 - - - +
93E GLY* 6.0 0.2 - - - -
94E MET 5.7 1.1 - - - +
98E GLY 3.4 12.8 + - - +
99E LEU* 3.9 24.2 - - + +
100E PHE 3.3 0.4 - - - -
101E ALA* 1.3 76.6 - - - +
103E SER* 1.3 57.2 + - - +
105E ILE* 3.3 1.7 + - - +
106E ASP* 2.8 28.9 + - - +
287E GLY* 3.8 3.4 - - - +
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Residues in contact with SER 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E GLU 4.5 1.1 - - - -
99E LEU 2.7 20.5 + - - -
100E PHE 3.3 2.4 + - - -
102E ILE* 1.3 74.9 - - - +
104E GLY* 1.3 59.3 + - - +
106E ASP* 3.7 0.9 - - - +
107E MET* 3.0 30.0 + - - +
283E TYR 3.5 10.7 - - - +
284E ASN 3.3 28.9 - - - -
285E ARG 3.0 8.1 - - - -
287E GLY 2.8 32.2 + - - -
288E GLY* 3.6 4.6 - - - +
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Residues in contact with GLY 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 3.7 13.9 - - - +
41E GLY* 3.7 8.5 - - - -
42E GLU 3.4 30.3 + - - -
43E ALA* 4.0 1.3 - - - -
100E PHE 3.1 11.4 + - - -
101E ALA 3.3 3.1 + - - -
102E ILE 3.3 0.4 - - - -
103E SER* 1.3 78.3 - - - +
105E ILE* 1.3 61.2 + - - +
107E MET* 3.6 3.1 - - - +
108E ALA* 3.2 19.2 + - - +
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Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 4.3 9.6 - - + -
12E PHE* 3.8 27.8 - - + -
29E VAL* 3.9 9.4 - - + -
31E VAL* 4.2 16.4 - - + -
66E ILE* 3.8 37.5 - - + +
67E LYS* 5.0 2.2 - - - +
70E VAL* 4.4 13.5 - - + -
85E MET* 3.8 23.8 - - + -
101E ALA 3.3 14.8 + - - +
104E GLY* 1.3 73.1 - - - +
106E ASP* 1.3 64.6 + - - +
108E ALA* 3.2 3.5 + - - +
109E LEU* 3.0 33.9 + - + +
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Residues in contact with ASP 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E PHE* 4.7 4.0 - - - +
82E TYR* 4.3 9.4 + - + +
85E MET* 4.3 7.7 - - + +
102E ILE* 2.8 23.1 + - + +
103E SER 3.7 2.5 - - - +
105E ILE* 1.3 71.0 - - - +
107E MET* 1.3 61.1 + - - +
109E LEU* 3.0 23.7 + - - +
110E TYR* 3.2 22.5 + - - -
287E GLY 3.6 12.1 - - - +
288E GLY 3.2 1.2 - - - -
289E VAL* 2.7 31.5 + - - -
290E THR* 2.4 37.9 + - - -
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU 4.0 0.2 - - - -
41E GLY* 3.7 9.2 - - - -
42E GLU 3.6 28.0 - - - +
103E SER 3.0 13.9 + - - +
104E GLY 3.6 5.8 - - - +
106E ASP* 1.3 76.0 + - - +
108E ALA* 1.3 60.3 + - - +
109E LEU 3.2 0.7 + - - -
110E TYR* 3.2 18.4 + - - +
111E ASP 3.3 8.7 + - - -
283E TYR* 3.8 40.2 - - + +
289E VAL* 4.9 12.3 - - + +
315E ILE* 4.0 15.7 - - - +
316E THR* 4.0 13.2 - - - +
319E ALA* 4.0 20.2 - - + -
369E LEU* 3.8 20.3 - - + +
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Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 3.6 5.4 - - + +
31E VAL* 3.6 21.9 - - + +
39E GLY* 3.4 24.7 - - - +
40E LEU 3.4 12.3 + - - -
41E GLY 3.5 13.2 - - - +
104E GLY 3.2 7.2 + - - +
105E ILE 3.2 5.2 + - - +
107E MET* 1.3 78.6 - - - +
109E LEU* 1.3 58.3 + - - +
111E ASP* 3.4 0.8 + - - -
112E LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ILE* 3.7 27.1 - - + -
31E VAL* 3.8 22.7 - - + -
70E VAL* 4.3 7.4 - - + -
75E PRO* 3.9 15.8 - - + +
78E PHE* 3.7 11.9 - - + -
81E ASN* 4.2 30.5 - - + +
85E MET* 4.2 17.0 - - + -
105E ILE* 3.0 26.0 + - + +
106E ASP* 3.0 14.0 + - - +
108E ALA* 1.3 74.5 - - - +
110E TYR* 1.3 60.7 + - - +
112E LEU* 4.0 2.2 - - - +
113E ALA* 2.9 32.2 + - - +
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Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 3.4 49.1 - + - +
106E ASP* 3.2 24.8 + - - -
107E MET* 3.2 7.9 + - - +
109E LEU* 1.3 75.5 - - - +
111E ASP* 1.3 62.9 + - - +
114E GLY* 3.1 20.6 + - - -
121E ALA* 4.0 17.2 - - + +
124E LEU* 4.1 16.2 + - + +
125E MET* 4.1 34.5 - - + -
289E VAL* 3.6 27.4 - - + -
290E THR* 2.9 36.1 + - - +
293E LEU* 3.9 10.2 - - - +
368E GLY* 3.9 3.5 - - - -
369E LEU* 4.6 4.0 - - + -
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Residues in contact with ASP 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E TYR 4.2 0.2 - - - +
39E GLY* 3.3 4.9 - - - -
40E LEU* 2.6 53.0 + - - +
107E MET 3.3 3.2 + - - +
108E ALA 3.6 2.2 - - - +
110E TYR* 1.3 76.1 - - - +
112E LEU* 1.3 58.7 + - - +
115E LYS* 2.8 49.3 + - - +
367E PRO 4.3 0.3 - - - +
368E GLY* 3.4 9.2 - - - -
369E LEU* 2.8 39.3 + - + +
370E GLY 4.0 4.2 + - - -
371E ILE* 4.5 8.1 + - - +
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Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.1 7.2 - - + -
31E VAL* 3.8 33.9 - - + +
33E ASP* 4.0 13.0 - - + +
37E VAL* 3.6 39.9 - - + +
38E TYR 3.9 4.7 - - - -
39E GLY* 3.6 10.0 - - - -
75E PRO* 3.9 25.1 - - + -
108E ALA 2.9 18.9 + - - +
109E LEU* 4.0 3.6 - - + +
110E TYR 3.3 0.2 - - - -
111E ASP* 1.3 74.3 - - - +
113E ALA* 1.3 61.6 + - - +
115E LYS* 3.1 2.4 + - - -
116E GLN* 2.8 35.5 + - + +
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Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PRO* 3.7 25.3 - - - +
76E LEU* 4.1 11.0 - - + +
78E PHE* 3.9 5.2 - - + -
109E LEU 2.9 22.7 + - - +
112E LEU* 1.3 73.6 - - - +
114E GLY* 1.3 57.2 + - - +
116E GLN* 3.2 12.8 + - - +
117E LEU* 3.0 34.7 + - - +
124E LEU* 3.8 16.8 - - + -
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Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR 3.1 16.8 + - - -
113E ALA* 1.3 76.0 - - - +
115E LYS* 1.3 60.9 + - - +
117E LEU 3.3 0.5 + - - -
118E GLY* 3.0 21.1 + - - -
119E VAL* 3.1 26.0 + - - -
121E ALA 5.2 0.4 - - - -
124E LEU* 3.5 12.8 - - - +
367E PRO* 3.8 0.5 - - - +
368E GLY* 3.4 13.5 - - - -
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 3.8 20.2 - - + +
38E TYR* 2.8 53.6 + - - +
40E LEU* 5.6 1.0 - - - +
111E ASP* 2.8 41.7 + - - +
112E LEU 3.6 4.5 - - - +
114E GLY* 1.3 72.7 - - - +
116E GLN* 1.3 62.9 + - - +
118E GLY* 3.5 7.6 + - - -
367E PRO* 4.1 25.8 - - + +
368E GLY 3.6 0.2 - - - +
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Residues in contact with GLN 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ALA* 2.9 36.6 + - - +
33E ASP* 2.8 36.2 + - - +
37E VAL* 4.7 4.9 - - + -
74E ASP* 4.4 5.4 - - - +
75E PRO* 3.4 27.1 - - - +
76E LEU* 5.9 0.5 - - - +
112E LEU* 2.8 26.9 + - + +
113E ALA* 3.2 8.3 + - - +
115E LYS* 1.3 75.0 - - - +
117E LEU* 1.3 66.3 + - + +
118E GLY 3.5 0.3 + - - -
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Residues in contact with LEU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E LEU* 4.0 26.5 - - + -
113E ALA* 3.0 20.2 + - + +
116E GLN* 1.3 80.0 - - + +
118E GLY* 1.3 61.7 + - - +
119E VAL* 3.6 20.1 + - + +
124E LEU* 4.0 26.7 - - + -
76G LEU* 5.4 0.4 - - + -
117G LEU* 4.3 44.6 - - + +
119G VAL* 5.4 4.5 - - + -
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Residues in contact with GLY 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLY 3.0 6.7 + - - -
115E LYS 3.5 6.3 + - - -
116E GLN 3.3 4.0 + - - -
117E LEU* 1.3 79.3 - - - +
119E VAL* 1.3 60.7 + - - +
120E PRO* 4.6 2.3 - - - +
365E ASP 5.2 0.9 - - - +
367E PRO* 4.1 19.7 - - - +
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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