Contacts of the helix formed by residues 92 - 119 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V PHE* 3.6 20.2 - - - -
44V LEU* 3.8 7.8 - - - +
47V VAL* 4.1 18.0 - - + +
91V ASN* 1.3 73.2 - - - +
93V LEU* 1.3 59.8 + - - +
95V ALA* 3.9 1.0 - - - +
96V MET* 3.0 39.1 + - + +
151V LEU* 4.1 7.4 - - + -
156V LEU* 4.0 6.7 - - - -
163V GLU* 2.8 30.9 + - + +
166V PHE* 3.8 34.5 - - + -
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Residues in contact with LEU 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91V ASN* 2.9 10.5 + - - +
92V THR* 1.3 74.8 - - - +
94V GLU* 1.3 61.6 + - - +
96V MET* 3.3 1.1 + - - +
97V GLN* 2.9 52.8 + - - +
148V ILE* 3.9 29.8 - - + +
151V LEU* 3.9 23.6 - - + -
152V LYS* 4.3 16.4 - - + -
156V LEU* 3.4 17.6 - - + +
157V PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86V ARG* 3.0 39.6 + - - +
89V TRP 3.4 12.6 - - - +
90V GLY* 3.7 8.3 - - - -
91V ASN* 3.1 27.8 + - - +
92V THR 3.4 0.2 - - - -
93V LEU* 1.3 80.2 - - - +
95V ALA* 1.3 57.8 + - - +
97V GLN* 3.5 14.0 + - - +
98V ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V MET* 3.8 9.7 - - - +
37V PHE* 3.7 27.4 - - + -
51V PHE* 4.1 10.5 - - + -
89V TRP* 3.7 16.7 + - + -
91V ASN 3.0 17.3 + - - +
92V THR 3.9 2.2 - - - +
94V GLU* 1.3 76.3 - - - +
96V MET* 1.3 60.5 + - - +
98V ALA* 3.4 7.9 + - - +
99V ALA* 2.9 27.5 + - - +
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Residues in contact with MET 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47V VAL* 4.6 4.3 - - + -
50V PHE* 4.0 15.7 - - + -
51V PHE* 3.7 30.5 - - + -
92V THR* 3.0 27.1 + - + +
93V LEU 3.7 3.8 - - - +
95V ALA* 1.3 73.0 - - - +
97V GLN* 1.3 60.5 + - - +
99V ALA* 4.1 1.8 - - - -
100V LEU* 2.8 24.3 + - - +
144V ILE* 3.4 20.6 - - + +
147V PHE* 3.9 34.1 - - + -
148V ILE* 3.7 17.9 - - + +
151V LEU* 3.8 16.8 - - + -
166V PHE* 4.3 16.4 - - + -
171V VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93V LEU* 2.9 42.2 + - + +
94V GLU* 3.8 14.7 - - + +
96V MET* 1.3 73.2 - - - +
98V ALA* 1.3 65.3 + - - +
100V LEU* 3.3 4.2 + - + +
101V GLN* 3.1 25.5 + - - +
148V ILE* 4.0 21.9 - - + +
152V LYS* 4.1 22.0 + - - -
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Residues in contact with ALA 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V MET* 4.0 3.6 - - + -
85V GLU* 5.4 4.3 - - - +
86V ARG* 5.6 2.7 - - - +
89V TRP* 3.8 32.8 - - + -
94V GLU 3.0 15.3 + - - +
95V ALA 3.5 8.5 - - - +
97V GLN* 1.3 75.8 - - - +
99V ALA* 1.3 57.7 + - - +
101V GLN* 3.4 7.3 + - - +
102V LEU* 3.0 27.5 + - - +
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Residues in contact with ALA 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V TYR* 3.9 27.6 - - + +
33V MET* 4.5 5.4 - - + -
51V PHE* 4.2 7.9 - - + -
95V ALA 2.9 17.7 + - - +
96V MET* 3.5 10.1 - - - +
98V ALA* 1.3 74.9 - - - +
100V LEU* 1.3 60.0 + - - +
102V LEU* 3.2 6.4 + - - +
103V GLU* 2.9 35.0 + - - +
144V ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.7 38.1 - - + +
4B VAL* 4.9 0.9 - - + -
96V MET 2.8 20.2 + - - +
97V GLN* 3.3 6.7 + - + +
99V ALA* 1.3 72.4 - - - +
101V GLN* 1.3 59.4 + - + +
103V GLU* 3.4 4.1 + - + +
104V LYS* 3.0 41.1 + - + +
141V ILE* 3.9 41.3 - - + +
144V ILE* 3.9 12.5 - - + +
145V GLY* 4.5 2.7 - - - +
148V ILE* 3.7 22.0 - - + -
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Residues in contact with GLN 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97V GLN 3.1 12.0 + - - +
98V ALA* 3.7 8.7 - - - +
100V LEU* 1.3 76.5 - - + +
102V LEU* 1.3 60.2 + - - +
104V LYS* 3.2 10.7 + - - +
105V THR* 2.9 34.2 + - - +
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Residues in contact with LEU 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V LEU* 5.4 1.6 - - + -
25V TYR* 4.1 27.8 - - + -
26V ALA* 3.9 25.6 - - + +
29V THR* 3.7 27.8 - - + -
30V TYR* 3.9 33.2 - - + +
98V ALA 3.0 17.2 + - - +
99V ALA* 3.2 6.3 + - - +
101V GLN* 1.3 76.4 - - - +
103V GLU* 1.3 59.8 + - + +
105V THR* 3.4 10.6 + - + -
106V VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V ALA* 6.2 0.8 - - - +
30V TYR* 2.8 29.3 + - - +
54V HIS* 3.6 14.2 + - - -
58V GLU* 3.4 12.6 - - - +
99V ALA 2.9 14.2 + - - +
100V LEU* 3.8 5.2 - - - +
102V LEU* 1.3 76.6 - - - +
104V LYS* 1.3 58.4 + - - +
106V VAL* 3.3 5.6 + - - +
107V ASN* 2.8 25.6 + - - +
137V GLN* 3.0 28.8 + - - +
140V ASP* 4.4 7.0 - - + -
141V ILE* 3.9 15.3 - - + -
144V ILE* 3.9 13.9 - - + -
177V MG 2.9 28.0 - - - -
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Residues in contact with LYS 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER 5.0 0.6 + - - -
3B GLN* 2.9 29.5 + - - +
4B VAL 4.4 5.8 - - - +
5B ARG 3.5 17.2 + - - -
6B GLN* 3.1 45.0 + - + +
100V LEU* 3.0 29.3 + - + +
101V GLN* 3.7 9.4 - - - +
103V GLU* 1.3 74.7 - - - +
105V THR* 1.3 57.1 + - - +
107V ASN* 4.1 0.2 - - - -
108V GLN* 2.9 25.5 + - - +
141V ILE* 4.2 11.2 - - + -
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Residues in contact with THR 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V LEU* 4.6 19.7 - - + -
25V TYR* 6.5 0.2 - - + -
101V GLN* 2.9 20.7 + - - +
102V LEU* 3.5 12.3 - - + +
104V LYS* 1.3 77.7 - - - +
106V VAL* 1.3 61.8 + - - +
108V GLN* 3.4 6.7 + - - +
109V ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V MET* 4.6 2.0 - - - +
22V LEU* 3.9 29.4 - - + +
23V GLU* 4.0 10.3 - - - +
26V ALA* 4.2 24.2 - - + -
58V GLU* 4.9 0.7 - - - +
102V LEU* 3.1 19.7 + - + +
103V GLU* 3.7 10.1 - - - +
105V THR* 1.3 72.1 - - - +
107V ASN* 1.3 66.3 + - - +
109V ALA* 3.2 3.1 + - - +
110V LEU* 3.0 31.2 + - + +
137V GLN* 3.9 11.9 - - - +
176V MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 3.1 38.9 + - - +
103V GLU 2.8 21.2 + - - +
104V LYS 3.6 0.2 - - - +
106V VAL* 1.3 73.4 - - - +
108V GLN* 1.3 57.8 + - - +
110V LEU* 3.1 9.5 + - - +
111V LEU* 2.9 43.7 + - - +
134V LEU* 4.8 8.3 - - - +
137V GLN* 3.6 22.6 - - - +
138V VAL* 5.0 9.4 - - - +
141V ILE* 3.9 17.2 - - + +
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Residues in contact with GLN 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 3.6 20.3 + - - +
7B ASN* 5.8 2.6 - - - +
104V LYS 2.9 17.7 + - - +
105V THR* 3.6 6.7 - - - +
107V ASN* 1.3 78.3 - - - +
109V ALA* 1.3 57.1 + - - +
111V LEU* 4.2 16.0 - - - +
112V ASP* 2.9 63.7 + - - +
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Residues in contact with ALA 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V MET* 3.1 20.3 - - + +
22V LEU* 3.7 22.0 - - + -
105V THR 3.1 14.1 + - - +
106V VAL 3.4 8.5 - - - +
108V GLN* 1.3 77.9 - - - +
110V LEU* 1.3 58.5 + - - +
112V ASP* 3.4 9.7 + - - +
113V LEU* 2.9 22.2 + - - +
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Residues in contact with LEU 110 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V MET* 3.7 25.1 - - + -
23V GLU* 4.9 1.6 - - - +
65V PHE* 4.0 21.3 - - + -
106V VAL* 3.0 26.0 + - + +
107V ASN* 3.1 6.9 + - - +
109V ALA* 1.3 74.8 - - - +
111V LEU* 1.3 59.9 + - - +
113V LEU* 3.4 3.0 + - - +
114V HIS* 2.9 26.3 + - - +
129V LEU* 4.2 14.3 - - + +
133V TYR* 3.9 32.1 - - + -
134V LEU* 3.9 15.4 - - + +
137V GLN* 3.7 30.3 - - + +
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Residues in contact with LEU 111 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 4.6 4.0 - - + -
7B ASN* 3.8 32.3 - - + +
123B PRO* 3.7 35.3 - - + +
124B HIS* 5.3 4.7 - - + +
107V ASN* 2.9 43.9 + - - +
108V GLN* 3.7 20.0 - - - +
110V LEU* 1.3 75.2 - - - +
112V ASP* 1.3 59.9 + - - +
114V HIS* 3.2 6.3 + - - +
115V LYS* 3.0 27.5 + - - +
134V LEU* 4.6 15.7 - - + -
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Residues in contact with ASP 112 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108V GLN* 2.9 49.2 + - - +
109V ALA* 3.4 9.4 - - - +
111V LEU* 1.3 76.5 - - - +
113V LEU* 1.3 60.6 + - - +
115V LYS* 3.3 8.1 + - - +
116V LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V CYS* 4.3 8.5 - - - +
15V ALA* 3.5 31.4 - - + +
16V VAL* 4.3 17.7 - - + -
19V MET* 3.7 34.8 - - + -
65V PHE* 4.5 2.0 - - + -
109V ALA 2.9 16.1 + - - +
110V LEU* 3.7 5.4 - - + +
111V LEU 3.3 0.2 - - - -
112V ASP* 1.3 75.2 - - - +
114V HIS* 1.3 60.0 + - - +
116V LEU* 3.4 9.7 + - + +
117V ALA* 3.0 25.1 + - - +
125V LEU* 4.4 9.9 - - + -
129V LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 6.2 1.4 - - - +
123B PRO* 3.6 34.9 - - + +
110V LEU 2.9 14.7 + - - +
111V LEU* 3.3 13.2 - - - +
112V ASP 3.1 0.4 - - - -
113V LEU* 1.3 74.6 - - - +
115V LYS* 1.3 61.7 + - - +
117V ALA* 3.3 3.9 + - - +
118V THR* 2.9 43.1 + - - -
126V CYS* 3.6 32.6 + - + +
129V LEU* 3.8 18.3 - - + +
130V GLU* 2.9 25.2 + - - -
134V LEU* 4.2 6.7 - - + -
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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
----------------------------------------------------------
121B VAL* 4.3 24.9 - - + -
111V LEU 3.0 14.0 + - - +
112V ASP* 3.3 11.2 + - - +
114V HIS* 1.3 74.7 + - - +
116V LEU* 1.3 60.2 + - - +
118V THR* 3.2 9.4 + - + +
119V ASP* 2.9 29.7 + - - +
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Residues in contact with LEU 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V ASP* 3.6 40.2 - - + +
12V CYS* 4.0 11.4 - - - -
15V ALA* 3.7 19.7 - - + -
18V ARG* 5.4 2.5 - - - +
112V ASP 3.0 13.6 + - - +
113V LEU* 3.6 10.5 - - + +
114V HIS 3.3 0.2 - - - -
115V LYS* 1.3 77.2 - - - +
117V ALA* 1.3 57.1 + - - +
119V ASP* 3.3 5.6 + - + +
120V LYS* 2.9 50.8 + - + +
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Residues in contact with ALA 117 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V CYS* 4.3 11.4 - - - -
113V LEU 3.0 14.3 + - - +
114V HIS* 3.5 10.5 - - - +
116V LEU* 1.3 73.4 - - - +
118V THR* 1.3 65.2 + - - +
120V LYS 3.5 0.7 + - - -
121V VAL 3.1 3.6 + - - -
122V ASP* 2.9 34.9 + - + +
125V LEU* 3.9 27.8 - - + -
126V CYS* 3.6 17.7 - - - +
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Residues in contact with THR 118 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 6.5 1.3 - - + -
114V HIS* 2.9 31.2 + - - -
115V LYS* 3.5 10.5 - - + +
117V ALA* 1.3 76.2 - - - +
119V ASP* 1.3 61.9 + - - +
121V VAL* 3.1 18.7 + - - +
126V CYS* 3.5 15.3 - - - -
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Residues in contact with ASP 119 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115V LYS 2.9 16.6 + - - +
116V LEU* 3.6 9.4 - - + +
118V THR* 1.3 78.5 - - - +
120V LYS* 1.3 72.1 + - + +
121V VAL* 3.4 8.7 + - - +
----------------------------------------------------------
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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