Contacts of the helix formed by residues 85 - 114 (chain E) in PDB entry 3MGR
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E PHE* 1.3 75.4 - - - +
86E SER* 1.3 66.3 + - - +
87E SER* 3.9 14.9 + - - +
88E ALA* 2.9 19.0 + - + +
89E VAL 3.4 3.6 + - - -
80F THR* 3.9 12.3 - - + +
81F VAL 3.0 17.5 + - - +
82F THR* 3.3 25.0 - - - +
83F ALA* 3.1 21.3 + - - +
28I C 5.7 2.8 + - - -
29I A 5.1 7.7 + - - -
-25J C 5.7 3.0 - - - -
-24J C 3.3 27.8 + - - +
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLN* 5.4 6.1 - - - -
72E ARG* 6.4 0.2 - - - +
84E PHE 3.6 3.2 + - - -
85E GLN* 1.3 73.8 - - - +
87E SER* 1.3 58.8 + - - +
89E VAL* 3.2 12.6 + - - +
90E MET* 3.2 29.6 + - - +
-24J C 3.1 18.6 + - - -
-23J A 6.1 0.4 - - - -
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLN* 3.9 12.1 + - - +
86E SER* 1.3 78.0 + - - +
88E ALA* 1.3 61.8 + - - +
90E MET* 3.8 9.9 - - - -
91E ALA* 3.0 27.4 + - - +
83F ALA* 3.4 19.8 - - - +
100F PHE* 3.6 17.8 - - - -
-24J C 5.0 0.2 + - - -
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Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E PHE* 4.3 8.3 - - + -
85E GLN 2.9 13.9 + - - +
87E SER* 1.3 79.6 + - - +
89E VAL* 1.3 61.2 + - - +
91E ALA* 3.5 3.0 + - - +
92E LEU* 3.2 29.6 + - - +
81F VAL 3.5 23.1 - - - +
82F THR 3.5 6.3 - - - +
83F ALA* 3.5 22.0 - - - +
86F VAL* 3.9 9.2 - - + +
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E LYS 5.5 0.7 - - - +
67E PHE* 3.8 11.9 - - + -
68E GLN* 4.0 50.5 - - + +
71E VAL* 4.7 8.3 - - + -
72E ARG* 5.0 2.9 - - + +
84E PHE* 3.9 32.8 - - + -
85E GLN 4.0 4.0 - - - +
86E SER* 3.2 10.8 + - - +
88E ALA* 1.3 79.3 - - - +
90E MET* 1.3 62.9 + - + +
92E LEU* 3.4 9.4 + - - +
93E GLN* 3.1 25.4 + - - +
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Residues in contact with MET 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 3.7 29.4 - - + -
64E LYS* 3.8 32.8 - - + +
86E SER* 3.2 18.2 + - - +
87E SER* 3.6 3.8 + - - +
88E ALA 3.3 0.2 - - - -
89E VAL* 1.3 81.2 - - - +
91E ALA* 1.3 58.5 + - - +
93E GLN* 3.2 8.3 + - - +
94E GLU* 2.9 37.5 + - + +
100F PHE* 3.9 21.5 - - + -
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E SER 3.0 18.9 + - - +
88E ALA* 3.7 6.5 - - - +
89E VAL 3.4 0.2 - - - -
90E MET* 1.3 76.0 - - - +
92E LEU* 1.3 55.5 + - - +
94E GLU 3.6 0.2 + - - -
95E ALA* 3.1 30.3 + - - +
83F ALA* 4.8 4.5 - - + +
86F VAL* 3.8 17.9 - - + -
87F VAL* 4.9 0.9 - - + -
97F LEU* 3.4 25.2 - - + +
100F PHE* 3.8 20.3 - - + -
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 3.7 11.7 - - + -
71E VAL* 3.6 32.5 - - + -
84E PHE* 4.3 10.8 - - + -
88E ALA 3.2 20.5 + - - +
89E VAL* 3.5 7.4 - - - +
90E MET 3.3 0.2 - - - -
91E ALA* 1.3 77.5 - - - +
93E GLN* 1.3 56.1 + - - +
95E ALA* 3.8 4.4 - - - +
96E SER* 2.6 38.1 + - - -
61F PHE* 4.9 2.1 - - + -
62F LEU* 4.5 7.9 - - + -
65F VAL* 3.8 30.1 - - + -
66F ILE* 4.1 18.8 - - + +
69F ALA* 5.6 0.4 - - + -
86F VAL* 3.9 19.7 - - + -
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Residues in contact with GLN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 3.9 18.8 - - + +
62E ILE* 2.8 35.6 + - - +
63E ARG 4.4 0.2 + - - -
64E LYS* 3.3 24.1 - - - +
67E PHE* 3.5 43.8 - - + +
89E VAL* 3.1 11.2 + - - +
90E MET* 3.2 14.5 + - - +
92E LEU* 1.3 75.4 - - - +
94E GLU* 1.3 59.3 + - - +
96E SER* 3.8 0.3 - - - -
97E GLU* 2.9 57.4 + - + +
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Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 4.5 2.1 - - - +
103C ALA* 3.5 8.2 - - + -
104C GLN* 3.0 54.7 + - - +
60E LEU* 3.5 26.8 - - + +
90E MET* 2.9 25.6 + - + +
91E ALA 3.9 3.1 - - - +
93E GLN* 1.3 72.1 - - - +
95E ALA* 1.3 62.4 + - - +
97E GLU* 4.0 1.0 - - - +
98E ALA* 3.1 24.8 + - - +
97F LEU* 4.5 10.5 - - + -
100F PHE* 3.8 26.2 - - + -
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 5.2 3.1 + - - +
91E ALA 3.1 16.0 + - - +
92E LEU* 3.9 4.9 - - - +
94E GLU* 1.3 80.7 - - - +
96E SER* 1.3 55.8 + - - +
98E ALA* 3.5 4.1 + - - +
99E TYR* 2.9 30.1 + - - +
61F PHE* 3.9 7.0 - - + -
90F LEU* 3.6 37.0 - - + -
95F ARG* 5.0 4.5 + - + +
97F LEU* 4.5 10.0 - - + +
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Residues in contact with SER 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 5.5 1.1 - - - -
67E PHE* 3.6 11.1 - - - -
92E LEU 2.6 27.8 + - - -
93E GLN 3.3 3.3 + - - -
95E ALA* 1.3 73.9 - - - +
97E GLU* 1.3 60.1 + - - +
99E TYR* 3.6 2.8 + - - +
100E LEU* 3.0 34.8 + - - +
58F LEU* 3.7 19.3 - - - -
61F PHE* 3.5 15.9 - - - -
62F LEU* 3.3 25.6 - - - +
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Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLU 4.7 0.2 - - - +
60E LEU* 3.5 20.5 - - + +
61E LEU* 2.7 31.9 + - - +
62E ILE* 2.9 41.5 + - + +
93E GLN* 2.9 40.1 + - + +
94E GLU 4.2 2.7 - - - +
96E SER* 1.3 74.3 - - - +
98E ALA* 1.3 58.7 + - - +
100E LEU* 3.3 1.2 + - - -
101E VAL* 2.9 36.9 + - + +
37F LEU* 3.7 17.7 - - + +
40F ARG* 4.8 2.4 + - - +
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C THR* 3.7 30.7 - - + +
94E GLU 3.1 18.9 + - - +
95E ALA 4.1 2.2 - - - +
97E GLU* 1.3 72.1 - - - +
99E TYR* 1.3 65.5 + - - +
101E VAL* 4.2 6.0 - - - +
102E ALA* 3.3 24.8 + - - +
95F ARG* 4.1 5.0 + - - +
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Residues in contact with TYR 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ALA 2.9 19.1 + - - +
96E SER 3.6 4.7 - - - +
98E ALA* 1.3 77.5 - - - +
100E LEU* 1.3 78.3 + - + +
102E ALA* 3.9 1.8 - - - +
103E LEU* 3.0 34.7 + - + +
128E ARG* 3.6 3.3 + - - -
131E ARG* 3.7 20.2 + - - -
133E GLU* 2.5 30.5 + - - -
57F VAL* 3.5 31.9 + - + +
58F LEU* 5.9 0.2 - - + -
61F PHE* 3.6 50.4 - + + +
95F ARG* 3.7 30.0 - - - +
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 4.6 4.0 - - + -
96E SER 3.0 22.5 + - - +
97E GLU 3.3 3.5 + - - +
99E TYR* 1.3 96.4 - - + +
101E VAL* 1.3 62.8 + - - +
103E LEU* 3.3 8.9 + - + +
104E PHE* 2.9 39.6 + - + -
29F ILE* 5.5 1.8 - - + -
37F LEU* 4.0 26.5 - - + -
54F THR* 4.1 27.6 - - + -
57F VAL* 4.5 6.5 - - + -
58F LEU* 4.1 41.3 - - + +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 3.7 29.8 - - + -
97E GLU* 2.9 24.2 + - + +
98E ALA* 4.2 5.8 - - - +
100E LEU* 1.3 74.3 - - - +
102E ALA* 1.3 62.1 + - - +
104E PHE* 3.2 7.0 + - - +
105E GLU* 3.1 24.7 + - - +
37F LEU* 3.8 35.0 - - + +
40F ARG* 3.9 20.4 - - + -
41F GLY* 3.8 19.6 - - - +
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ALA 3.3 18.0 + - - +
99E TYR* 4.0 2.7 - - - +
101E VAL* 1.3 79.4 - - - +
103E LEU* 1.3 60.6 + - - +
105E GLU* 3.5 21.0 + - - +
106E ASP* 3.3 18.5 + - - -
131E ARG* 3.3 17.6 + - - +
95F ARG* 5.1 7.0 - - - +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E TYR* 3.0 30.9 + - + +
100E LEU* 3.7 10.8 - - + +
101E VAL 3.2 0.2 - - - -
102E ALA* 1.3 74.8 - - - +
104E PHE* 1.3 58.7 + - + +
106E ASP* 3.2 4.3 + - - +
107E THR* 2.8 41.5 + - - +
124E ILE* 4.4 15.3 - - + +
127E ALA* 4.2 12.1 - - + -
128E ARG* 3.8 23.1 - - + -
131E ARG* 3.5 30.7 - - - +
57F VAL* 3.6 31.0 - - + -
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Residues in contact with PHE 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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100E LEU* 2.9 35.2 + - + -
101E VAL 3.5 6.3 - - - +
103E LEU* 1.3 79.7 - - + +
105E GLU* 1.3 51.6 + - - +
107E THR* 3.4 9.1 - - - -
108E ASN* 2.7 35.9 + - - +
119E ILE* 3.7 29.4 - - + -
124E ILE* 4.6 8.7 - - + -
34F ILE* 3.9 15.0 - - + -
37F LEU* 3.9 15.3 - - + -
38F ALA* 3.7 36.8 - - + -
41F GLY* 4.1 6.3 - - - -
43F VAL* 3.7 7.7 - - + +
50F ILE* 4.2 6.1 - - + -
54F THR* 3.6 38.4 - - + -
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.9 18.8 + - - +
107C VAL* 4.1 24.3 - - - +
101E VAL* 3.1 15.2 + - - +
102E ALA* 3.6 22.2 - - - +
104E PHE* 1.3 73.6 - - - +
106E ASP* 1.3 65.5 + - - +
108E ASN* 3.2 6.0 + - - +
109E LEU* 3.0 26.8 + - + +
40F ARG 4.9 0.5 - - - +
41F GLY* 3.4 25.2 + - - +
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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
----------------------------------------------------------
129A ARG* 2.7 36.5 + - - -
130A ILE* 4.1 21.0 - - + +
102E ALA 3.3 8.9 + - - +
103E LEU 3.2 7.9 + - - +
105E GLU* 1.3 74.1 - - - +
107E THR* 1.3 58.5 + - - +
109E LEU* 3.2 9.7 + - - +
110E CYS* 3.0 31.4 + - - -
127E ALA* 3.8 18.6 - - + -
131E ARG* 2.8 33.2 + - - +
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Residues in contact with THR 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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103E LEU* 2.8 33.6 + - - +
104E PHE* 3.4 10.9 - - + -
106E ASP* 1.3 72.7 - - - +
108E ASN* 1.3 55.1 + - - +
110E CYS* 3.1 11.2 + - - +
111E ALA* 2.9 25.3 + - - +
119E ILE* 3.6 27.8 - - + -
120E MET 4.6 0.2 - - - +
123E ASP* 3.5 24.2 - - + +
124E ILE* 3.6 35.6 - - + +
127E ALA* 4.1 0.6 - - - +
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Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 4.3 14.5 - - - +
115C LEU* 3.9 14.5 - - - +
104E PHE 2.7 20.7 + - - +
105E GLU* 3.3 8.1 - - - +
107E THR* 1.3 73.8 - - - +
109E LEU* 1.3 63.1 + - + +
111E ALA* 3.3 2.6 + - - +
112E ILE* 3.0 39.3 + - - +
117E VAL 4.6 7.6 - - - +
119E ILE* 3.8 16.1 - - - +
41F GLY 4.5 1.2 + - - +
42F GLY* 3.0 30.7 + - - -
43F VAL* 3.8 16.4 - - + +
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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
----------------------------------------------------------
126A LEU* 3.8 20.6 - - + +
129A ARG* 3.6 48.9 - - + +
130A ILE* 5.1 1.6 - - + -
112C GLN* 3.8 36.3 - - + +
105E GLU* 3.0 13.8 + - + +
106E ASP* 3.2 11.4 + - - +
108E ASN* 1.3 76.2 - - + +
110E CYS* 1.3 58.0 + - - +
112E ILE* 3.7 8.3 + - + +
113E HIS* 3.1 27.0 + - - +
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Residues in contact with CYS 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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113A HIS* 3.1 27.0 + - - +
126A LEU* 4.4 3.4 - - - -
130A ILE* 3.5 24.9 - - - -
106E ASP 3.0 16.2 + - - +
107E THR 3.3 8.7 - - - +
109E LEU* 1.3 75.1 - - - +
111E ALA* 1.3 65.5 + - - +
113E HIS* 3.5 6.0 - - - +
114E ALA 3.4 6.6 + - - -
123E ASP* 3.6 30.7 - - + +
126E LEU* 3.7 25.1 - - - -
127E ALA* 4.0 4.3 - - - -
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E THR 2.9 11.2 + - - +
108E ASN* 3.3 8.7 + - - +
110E CYS* 1.3 72.9 - - - +
112E ILE* 1.3 59.3 + - + +
114E ALA* 2.9 20.6 + - - +
115E LYS 3.3 0.2 + - - -
116E ARG* 3.0 29.2 + - - +
117E VAL 4.7 1.8 - - - -
118E THR 3.6 21.1 - - - +
119E ILE* 4.0 10.8 - - + -
123E ASP* 3.5 23.6 + - - +
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Residues in contact with ILE 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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112C GLN* 3.8 39.3 - - + +
114C VAL* 3.9 32.5 - - + -
115C LEU* 4.8 7.0 - - + -
108E ASN* 3.0 30.4 + - - +
109E LEU* 3.9 9.2 - - + +
111E ALA* 1.3 75.0 - - + +
113E HIS* 1.3 58.3 + - - +
115E LYS* 2.9 21.5 + - - +
116E ARG 3.4 14.8 - - - +
117E VAL* 5.4 0.4 - - - -
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Residues in contact with HIS 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A CYS* 3.0 24.2 + - - +
113A HIS* 4.7 4.5 - + - -
114A ALA* 3.8 15.6 - - + +
116A ARG* 3.6 10.9 + - - -
122A LYS* 3.7 35.4 + - + +
123A ASP* 2.7 31.7 + - - -
126A LEU* 3.5 27.0 - - + +
109E LEU 3.1 20.0 + - - +
110E CYS 3.5 7.6 - - - +
112E ILE* 1.3 77.6 - - - +
114E ALA* 1.3 56.8 + - - +
115E LYS* 3.1 9.9 + - - +
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 3.8 24.7 - - + +
114A ALA* 4.4 10.9 - - - +
115A LYS* 5.9 4.3 - - - -
110E CYS 3.4 0.6 + - - -
111E ALA 2.9 10.3 + - - +
113E HIS* 1.3 77.1 - - - +
115E LYS* 1.3 70.5 + - - +
116E ARG* 3.3 35.2 + - - +
----------------------------------------------------------
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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