Contacts of the helix formed by residues 92 - 119 (chain B) in PDB entry 1MFR
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 THR 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.6 20.0 - - - -
44B LEU* 3.8 8.0 - - - +
47B VAL* 4.1 17.2 - - + +
51B PHE* 5.9 0.2 - - + -
91B ASN* 1.3 73.2 - - - +
93B LEU* 1.3 57.8 + - - +
95B ALA* 3.9 1.0 - - - +
96B MET* 3.0 38.9 + - + +
151B LEU* 4.1 7.6 - - + -
156B LEU* 4.0 6.7 - - - -
163B GLU* 2.8 30.9 + - - +
166B PHE* 3.8 34.5 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 2.9 10.8 + - - +
92B THR* 1.3 74.1 - - - +
94B GLU* 1.3 60.7 + - - +
96B MET* 3.3 1.2 + - - +
97B GLN* 2.9 52.3 + - + +
148B ILE* 3.9 29.6 - - + +
151B LEU* 3.9 23.1 - - + -
152B LYS* 4.3 16.6 - - + -
156B LEU* 3.4 18.2 - - + +
157B PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.0 39.8 + - - +
89B TRP 3.4 12.1 - - - +
90B GLY* 3.7 7.7 - - - -
91B ASN* 3.1 26.8 + - - +
92B THR 3.4 0.2 - - - -
93B LEU* 1.3 79.6 - - - +
95B ALA* 1.3 58.1 + - - +
97B GLN* 3.5 15.2 + - - +
98B ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B MET* 3.8 9.0 - - - +
37B PHE* 3.7 27.8 - - + -
51B PHE* 4.1 11.2 - - + -
89B TRP* 3.7 16.1 + - + -
91B ASN 3.0 18.4 + - - +
92B THR 3.9 2.5 - - - +
94B GLU* 1.3 76.3 - - - +
96B MET* 1.3 59.2 + - - +
98B ALA* 3.4 8.5 + - - +
99B ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.6 4.0 - - + -
50B PHE* 4.0 16.8 - - + -
51B PHE* 3.7 30.1 - - + -
92B THR* 3.0 26.1 + - + +
93B LEU 3.3 3.8 + - - +
95B ALA* 1.3 73.2 - - - +
97B GLN* 1.3 61.7 + - - +
99B ALA* 3.5 2.4 - - - +
100B LEU* 2.8 23.9 + - - +
144B ILE* 3.4 20.7 - - + +
147B PHE* 3.9 32.5 - - + -
148B ILE* 3.7 17.8 - - + +
151B LEU* 3.8 17.5 - - + -
166B PHE* 4.3 16.2 - - + -
171B VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 2.9 43.2 + - + +
94B GLU* 3.8 14.9 - - - +
96B MET* 1.3 72.2 - - - +
98B ALA* 1.3 65.3 + - - +
100B LEU* 3.3 3.8 + - + +
101B GLN* 3.1 25.5 + - - +
148B ILE* 4.0 20.9 - - + +
152B LYS* 4.1 21.7 + - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B MET* 4.0 4.3 - - + -
85B GLU* 5.4 3.8 - - - +
86B ARG* 5.6 2.9 - - - +
89B TRP* 3.8 32.3 - - + -
94B GLU 3.0 15.1 + - - +
95B ALA 3.5 9.0 - - - +
96B MET 3.3 0.2 - - - -
97B GLN* 1.3 76.1 - - - +
99B ALA* 1.3 57.6 + - - +
101B GLN* 3.4 7.0 + - - +
102B LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.9 27.1 + - + +
33B MET* 4.2 5.1 - - + +
51B PHE* 4.2 8.7 - - + -
95B ALA 2.9 17.5 + - - +
96B MET* 3.5 10.1 - - - +
97B GLN 3.2 0.2 - - - -
98B ALA* 1.3 75.1 - - - +
100B LEU* 1.3 59.1 + - - +
102B LEU* 3.2 5.6 + - - +
103B GLU* 2.9 34.4 + - - +
144B ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET 2.8 20.2 + - - +
97B GLN* 3.3 7.2 + - + +
99B ALA* 1.3 71.5 - - - +
101B GLN* 1.3 60.8 + - + +
103B GLU* 3.4 3.5 + - - +
104B LYS* 3.0 41.2 + - + +
141B ILE* 3.9 42.2 - - + +
144B ILE* 3.9 10.9 - - + +
145B GLY* 4.5 3.4 - - - +
148B ILE* 3.7 22.0 - - + -
3E GLN* 3.7 39.3 - - + +
4E VAL* 4.9 0.4 - - + -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN 3.1 12.5 + - - +
98B ALA* 3.7 9.0 - - - +
100B LEU* 1.3 76.1 - - + +
102B LEU* 1.3 60.2 + - - +
104B LYS* 3.2 10.3 + - - +
105B THR* 2.9 34.4 + - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 5.4 2.0 - - + -
25B TYR* 4.1 27.8 - - + -
26B ALA* 3.9 25.4 - - + +
29B THR* 3.7 28.3 - - + -
30B TYR* 3.9 33.0 - - + +
33B MET* 5.2 0.2 - - + -
98B ALA 3.0 18.0 + - - +
99B ALA* 3.2 5.6 + - - +
101B GLN* 1.3 75.8 - - - +
103B GLU* 1.3 58.8 + - + +
105B THR* 3.4 10.2 + - + -
106B VAL* 3.1 35.2 + - + +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 6.5 0.4 - - - -
30B TYR* 2.8 28.4 + - - +
54B HIS* 3.6 13.9 + - - -
58B GLU* 3.4 12.4 - - - +
99B ALA 2.9 14.8 + - - +
100B LEU* 3.8 5.4 - - - +
102B LEU* 1.3 76.3 - - - +
104B LYS* 1.3 59.8 + - - +
106B VAL* 3.3 5.7 + - - +
107B ASN* 2.8 25.6 + - - +
137B GLN* 3.0 29.3 + - - +
140B ASP* 4.4 6.7 - - + -
141B ILE* 3.9 14.6 - - + -
144B ILE* 3.9 15.0 - - + -
177B MG 2.9 27.1 - - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.0 29.7 + - + +
101B GLN* 3.2 9.8 + - - +
103B GLU* 1.3 74.7 - - - +
105B THR* 1.3 57.3 + - - +
107B ASN* 4.1 0.4 - - - -
108B GLN* 2.9 25.8 + - - +
141B ILE* 4.2 10.5 - - + -
2E SER 4.9 0.6 + - - -
3E GLN* 2.9 30.9 + - - +
4E VAL 4.4 5.4 - - - +
5E ARG 3.5 17.2 + - - -
6E GLN* 3.0 45.1 + - + +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.6 19.3 - - + -
25B TYR* 6.5 0.7 - - + -
101B GLN* 2.9 20.9 + - - +
102B LEU* 3.5 13.2 - - + +
103B GLU 3.2 0.2 - - - -
104B LYS* 1.3 77.7 - - - +
106B VAL* 1.3 62.6 + - - +
108B GLN* 3.4 7.0 + - - +
109B ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 5.1 1.8 - - - -
22B LEU* 3.9 29.2 - - + +
23B GLU* 4.0 10.5 - - - +
26B ALA* 4.2 24.5 - - + -
58B GLU* 4.9 0.7 - - - +
102B LEU* 3.1 20.3 + - + +
103B GLU* 3.7 9.9 - - - +
105B THR* 1.3 72.2 - - - +
107B ASN* 1.3 65.7 + - - +
109B ALA* 3.2 3.5 + - - +
110B LEU* 3.0 30.2 + - + +
137B GLN* 3.9 11.9 - - - +
176B MG 3.8 21.8 - - - -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU 2.8 21.4 + - - +
104B LYS 3.6 0.2 - - - +
106B VAL* 1.3 72.4 - - - +
108B GLN* 1.3 56.9 + - - +
110B LEU* 3.1 10.1 + - - +
111B LEU* 2.9 42.5 + - - +
134B LEU* 4.8 8.5 - - - +
137B GLN* 3.6 22.4 - - - +
138B VAL* 5.0 9.9 - - - +
141B ILE* 3.9 16.8 - - + +
6E GLN* 3.0 41.3 + - - +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS 2.9 18.5 + - - +
105B THR* 3.6 7.0 - - - +
107B ASN* 1.3 77.3 - - - +
109B ALA* 1.3 57.1 + - - +
111B LEU* 3.4 16.8 + - - +
112B ASP* 2.9 63.1 + - - +
6E GLN* 3.6 20.1 + - - +
7E ASN* 5.8 2.2 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 3.1 20.8 - - + +
22B LEU* 3.7 22.2 - - + -
105B THR 3.1 14.8 + - - +
106B VAL 3.2 8.3 + - - +
108B GLN* 1.3 76.9 - - - +
110B LEU* 1.3 57.3 + - - +
112B ASP* 3.4 9.9 + - - +
113B LEU* 2.9 22.7 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 3.7 24.0 - - + -
23B GLU* 4.9 1.8 - - - +
65B PHE* 4.0 21.3 - - + -
106B VAL* 3.0 24.4 + - + +
107B ASN* 3.1 7.2 + - - +
109B ALA* 1.3 75.2 - - - +
111B LEU* 1.3 60.6 + - - +
113B LEU* 3.4 3.8 + - + +
114B HIS* 2.9 26.5 + - - +
129B LEU* 4.2 13.5 - - + +
133B TYR* 3.9 32.1 - - + -
134B LEU* 3.9 15.3 - - + +
137B GLN* 3.7 31.4 - - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 2.9 43.0 + - - +
108B GLN* 3.7 20.0 - - - +
110B LEU* 1.3 74.3 - - - +
112B ASP* 1.3 60.8 + - - +
114B HIS* 3.2 6.1 + - - +
115B LYS* 3.0 26.9 + - - +
134B LEU* 4.6 15.0 - - + -
6E GLN* 4.5 4.0 - - + -
7E ASN* 3.7 33.2 - - + +
123E PRO* 3.7 34.5 - - + +
124E HIS* 5.4 4.0 - - + +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 2.9 48.5 + - - +
109B ALA* 3.4 9.9 - - - +
111B LEU* 1.3 76.4 - - - +
113B LEU* 1.3 60.7 + - - +
115B LYS* 3.3 8.5 + - - +
116B LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS 4.3 9.2 - - - +
15B ALA* 3.5 31.2 - - + +
16B VAL* 4.3 16.8 - - + -
19B MET* 3.7 34.5 - - + -
65B PHE* 4.5 2.2 - - + -
109B ALA 2.9 16.3 + - - +
110B LEU* 3.7 5.2 - - + +
111B LEU 3.3 0.2 - - - -
112B ASP* 1.3 76.0 - - - +
114B HIS* 1.3 59.3 + - - +
116B LEU* 3.4 10.3 + - + +
117B ALA* 3.0 25.8 + - - +
125B LEU* 4.4 10.1 - - + -
129B LEU* 3.9 26.5 - - + -
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU 2.9 14.9 + - - +
111B LEU* 3.3 13.0 - - - +
112B ASP 3.1 0.2 - - - -
113B LEU* 1.3 75.2 - - - +
115B LYS* 1.3 61.5 + - - +
117B ALA* 3.3 4.2 + - - +
118B THR* 2.9 42.3 + - - -
126B CYS* 3.6 32.0 + - + +
129B LEU* 3.8 17.7 - - + +
130B GLU* 2.9 24.9 + - - -
134B LEU* 4.2 7.2 - - + -
121E VAL* 6.0 1.6 - - - +
123E PRO* 3.5 35.6 - - + +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU 3.0 13.4 + - - +
112B ASP* 3.3 11.6 + - - +
114B HIS* 1.3 74.7 + - - +
116B LEU* 1.3 61.6 + - - +
118B THR* 3.2 9.9 + - + +
119B ASP* 2.9 29.6 + - + +
121E VAL* 4.3 25.1 - - + -
123E PRO* 5.9 0.2 - - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.6 39.7 - - + +
12B CYS* 4.0 11.0 - - - -
15B ALA* 3.7 20.2 - - + -
18B ARG* 5.4 2.2 - - - +
112B ASP 3.0 13.6 + - - +
113B LEU* 3.6 11.2 - - + +
114B HIS 3.3 0.2 - - - -
115B LYS* 1.3 76.8 - - - +
117B ALA* 1.3 56.6 + - - +
119B ASP* 3.3 5.6 + - + +
120B LYS* 2.9 49.9 + - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 4.3 10.3 - - - -
113B LEU 3.0 14.9 + - - +
114B HIS* 3.5 9.6 - - - +
116B LEU* 1.3 73.1 - - - +
118B THR* 1.3 64.9 + - - +
120B LYS 3.5 0.9 + - - +
121B VAL 3.1 3.5 + - - -
122B ASP* 2.9 34.8 + - + +
125B LEU* 3.9 28.0 - - + -
126B CYS* 3.6 17.9 - - - +
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B HIS* 2.9 31.2 + - - -
115B LYS* 3.5 11.0 - - + +
117B ALA* 1.3 76.8 - - - +
119B ASP* 1.3 63.0 + - - +
121B VAL* 3.1 18.2 + - - +
126B CYS* 3.5 15.7 - - - -
121E VAL* 6.4 2.2 - - + -
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LYS 2.9 17.3 + - - +
116B LEU* 3.6 9.2 - - + +
118B THR* 1.3 78.6 - - - +
120B LYS* 1.3 72.3 + - + +
121B VAL* 3.2 9.6 + - - +
----------------------------------------------------------
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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