Contacts of the helix formed by residues 10 - 38 (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 SER 10 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5V ARG* 4.0 3.9 + - - +
8V TYR 3.7 1.6 + - - -
9V HIS* 1.3 82.5 + - - +
11V ASP* 1.3 64.3 + - - +
13V GLU* 3.4 19.0 + - - +
14V ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V HIS* 2.8 22.8 + - + +
10V SER* 1.3 73.8 - - - +
12V CYS* 1.3 63.3 + - - +
14V ALA* 3.4 6.3 + - - +
15V ALA* 2.9 28.6 + - - +
18V ARG* 4.6 2.1 + - - -
116V LEU* 3.6 21.9 - - + +
120V LYS* 3.1 21.9 + - - +
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Residues in contact with CYS 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V TYR* 4.1 10.3 - - + -
9V HIS* 3.1 25.0 + - + +
11V ASP* 1.3 79.9 - - - +
13V GLU* 1.3 56.5 - - - +
15V ALA* 3.1 3.7 + - - +
16V VAL* 2.9 36.0 + - - +
113V LEU* 4.3 0.8 - - - +
116V LEU* 4.0 25.1 - - - -
117V ALA* 4.3 7.9 - - - -
120V LYS* 4.1 15.9 - - - -
122V ASP* 5.0 4.9 - - - -
125V LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V ARG* 2.7 33.7 + - - -
8V TYR* 3.7 20.3 + - + -
9V HIS 3.1 7.9 + - - +
10V SER* 3.5 18.2 + - - +
12V CYS* 1.3 78.8 - - - +
14V ALA* 1.3 63.2 + - - +
16V VAL 3.3 0.5 + - - -
17V ASN* 3.1 22.7 + - - +
69V GLN* 3.2 27.4 + - - +
74V GLY* 3.8 2.7 - - - -
75V ARG* 2.9 33.0 + - - +
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Residues in contact with ALA 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V SER 3.1 17.2 + - - +
11V ASP* 3.7 7.4 - - - +
13V GLU* 1.3 78.0 - - - +
15V ALA* 1.3 59.6 + - - +
17V ASN* 3.5 10.1 + - - +
18V ARG* 3.1 39.1 + - - +
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Residues in contact with ALA 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V ASP 2.9 18.0 + - - +
12V CYS 3.5 1.3 - - - +
14V ALA* 1.3 75.7 - - - +
16V VAL* 1.3 61.0 + - - +
18V ARG* 3.3 24.3 + - - +
19V MET* 2.9 29.1 + - - +
113V LEU* 3.5 26.6 - - + +
116V LEU* 3.7 11.4 - - + -
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Residues in contact with VAL 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V TYR* 3.6 15.3 - - - +
12V CYS 2.9 19.1 + - - +
13V GLU 3.6 4.7 - - - +
15V ALA* 1.3 76.1 - - - +
17V ASN* 1.3 57.3 + - - +
19V MET* 3.2 7.0 + - - +
20V LEU* 2.9 29.8 + - + +
65V PHE* 3.9 34.1 - - + +
68V TYR* 4.6 4.5 - - + -
69V GLN* 3.5 22.2 - - + +
113V LEU* 4.3 12.1 - - + -
125V LEU* 4.3 23.6 - - + -
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Residues in contact with ASN 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V GLU* 3.1 15.6 + - - +
14V ALA* 3.6 12.2 - - - +
15V ALA 3.3 0.2 - - - -
16V VAL* 1.3 76.4 - - - +
18V ARG* 1.3 60.9 + - - +
20V LEU* 3.5 17.6 - - - +
21V ASN* 3.4 20.1 + - - +
69V GLN* 3.4 12.4 + - - +
75V ARG 3.2 19.2 + - - -
76V VAL* 3.3 10.2 - - - -
77V VAL* 3.1 47.1 + - + +
79V GLN* 4.6 9.4 + - - +
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Residues in contact with ARG 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V ASP 4.6 2.8 + - - -
14V ALA* 3.1 21.0 + - - +
15V ALA* 3.4 34.1 - - - +
16V VAL 3.1 0.2 - - - -
17V ASN* 1.3 79.7 - - - +
19V MET* 1.3 64.7 + - - +
21V ASN* 3.4 7.6 + - + +
22V LEU* 3.1 20.1 + - - +
79V GLN* 4.8 17.5 - - - +
116V LEU* 5.4 2.4 - - - +
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Residues in contact with MET 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V ALA 2.9 15.7 + - - +
16V VAL* 3.5 6.5 - - - +
18V ARG* 1.3 76.4 - - - +
20V LEU* 1.3 63.4 + - - +
22V LEU* 3.2 12.9 + - - +
23V GLU* 2.9 28.3 + - + +
65V PHE* 3.4 29.4 - - + -
106V VAL* 4.6 3.1 - - - +
109V ALA* 3.1 50.0 - - + +
110V LEU* 3.5 21.8 - - + +
113V LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 5.1 0.2 - - - +
16V VAL* 2.9 16.5 + - + +
17V ASN* 3.5 19.5 - - - +
19V MET* 1.3 78.0 - - - +
21V ASN* 1.3 62.4 + - + +
23V GLU* 3.3 8.5 + - - +
24V LEU* 3.1 42.7 + - + +
62V ALA* 3.7 16.8 - - + +
65V PHE* 4.2 14.3 - - + +
66V MET* 3.8 35.2 - - + +
69V GLN* 5.8 0.7 - - + +
76V VAL* 4.0 19.1 - - + -
77V VAL 5.6 0.2 - - - +
78V LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 4.5 3.2 + - - +
17V ASN 3.4 8.7 + - - +
18V ARG 3.6 8.5 - - - +
19V MET 3.2 0.6 - - - -
20V LEU* 1.3 82.1 - - + +
22V LEU* 1.3 60.8 + - - +
24V LEU* 3.1 8.7 + - - +
25V TYR* 2.8 30.0 + - - +
79V GLN* 3.5 44.3 + - - +
80V ASP 3.2 27.3 + - - +
81V ILE* 4.3 10.1 - - - +
82V LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V ARG 3.1 13.3 + - - +
19V MET* 3.2 15.7 + - - +
21V ASN* 1.3 77.4 + - - +
23V GLU* 1.3 57.4 + - - +
25V TYR* 3.2 24.3 + - + +
26V ALA* 2.9 26.7 + - - +
102V LEU* 5.4 1.3 - - + -
105V THR* 4.4 16.6 - - + +
106V VAL* 3.9 30.2 - - + +
109V ALA* 3.7 31.0 - - + -
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Residues in contact with GLU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V MET* 2.9 19.3 + - + +
20V LEU 3.4 9.4 - - - +
21V ASN 3.2 0.2 - - - -
22V LEU* 1.3 77.1 - - - +
24V LEU* 1.3 58.3 + - - +
26V ALA* 3.3 5.1 + - - +
27V SER* 2.9 27.5 + - - -
58V GLU* 2.7 20.5 - - - +
61V HIS* 3.4 18.8 - - + +
62V ALA* 3.8 14.1 - - + +
65V PHE* 4.1 18.7 - - + -
106V VAL* 4.0 15.6 - - - +
110V LEU* 4.9 2.4 - - - +
133V TYR* 3.7 14.9 - - - -
176V MG 2.4 30.8 - - - -
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Residues in contact with LEU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR* 3.6 37.9 - - + +
20V LEU* 3.1 32.1 + - + +
21V ASN* 3.5 9.9 - - - +
23V GLU* 1.3 75.5 - - - +
25V TYR* 1.3 57.5 + - - +
27V SER* 3.5 6.8 - - - +
28V TYR* 3.0 27.4 + - - +
59V ARG* 4.9 17.5 - - + -
62V ALA* 3.7 17.9 - - + -
63V GLU* 6.4 0.4 - - + -
66V MET* 5.1 6.7 - - + -
78V LEU* 4.8 0.2 - - + -
81V ILE* 3.7 23.5 - - + +
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Residues in contact with TYR 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ASN* 2.8 18.1 + - - +
22V LEU* 3.4 27.4 - - + +
23V GLU 3.2 0.2 - - - -
24V LEU* 1.3 72.7 - - - +
26V ALA* 1.3 63.1 + - - +
28V TYR* 3.2 3.6 + - - +
29V THR* 2.9 48.0 + - - -
81V ILE* 4.0 9.6 - - + +
82V LYS* 3.4 37.2 - - + +
83V LYS 3.8 11.9 - - - -
84V PRO* 4.1 1.6 - - + -
85V GLU* 3.8 25.6 + - - +
102V LEU* 4.1 17.3 - - + -
105V THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V LEU 2.9 13.8 + - - +
23V GLU* 3.5 9.4 - - - +
25V TYR* 1.3 76.4 - - - +
27V SER* 1.3 62.4 + - - +
29V THR* 3.3 3.1 + - - -
30V TYR* 3.1 31.3 + - + -
58V GLU* 4.2 15.9 - - + -
102V LEU* 3.9 26.0 - - + +
103V GLU* 6.2 0.7 - - - +
106V VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V GLU 2.9 16.2 + - - -
24V LEU* 3.5 11.6 - - - +
25V TYR 3.2 0.2 - - - -
26V ALA* 1.3 77.1 - - - +
28V TYR* 1.3 61.8 + - - +
30V TYR 3.1 2.4 + - - -
31V SER* 3.0 19.2 + - - -
55V SER* 2.9 38.5 + - - +
58V GLU* 3.8 13.1 - - - +
59V ARG* 3.6 16.7 - - - +
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Residues in contact with TYR 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L ASN* 4.4 2.6 + - - -
24L LEU* 3.7 27.1 - - + +
66L MET* 5.6 0.7 - - + -
78L LEU* 3.3 38.3 - - + +
79L GLN 2.9 31.1 + - - -
81L ILE* 3.8 23.6 - - + +
24V LEU 3.0 18.4 + - - +
25V TYR 3.2 6.0 + - - +
27V SER* 1.3 77.8 + - - +
29V THR* 1.3 61.3 + - - +
31V SER* 3.2 15.8 - - - -
32V SER* 3.2 18.7 + - - -
81V ILE* 4.0 13.2 - - + -
82V LYS 3.6 18.2 - - - +
83V LYS* 4.0 4.0 - - - -
84V PRO* 3.7 17.6 - - + +
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Residues in contact with THR 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V TYR* 2.9 30.9 + - + -
26V ALA 3.6 8.7 - - - -
27V SER 3.2 0.2 - - - -
28V TYR* 1.3 75.7 - - - +
30V TYR* 1.3 62.1 + - - +
32V SER* 3.2 6.9 + - - -
33V MET* 3.2 39.2 + - + +
84V PRO* 3.4 21.3 - - - +
85V GLU 5.0 0.4 + - - +
89V TRP* 4.0 15.9 - - + -
102V LEU* 3.7 26.2 - - + -
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Residues in contact with TYR 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26V ALA* 3.1 23.4 + - + -
27V SER 3.1 6.5 + - - +
29V THR* 1.3 73.1 - - - +
31V SER* 1.3 59.4 + - - +
33V MET* 3.2 12.8 + - + +
34V TYR* 2.8 29.1 + - - +
50V PHE* 5.9 0.4 - + - -
51V PHE* 3.6 46.8 - + - +
54V HIS* 3.9 29.6 + + + -
55V SER* 3.7 7.6 - - - -
58V GLU* 4.0 13.2 - - + -
99V ALA* 3.9 24.1 + - + +
102V LEU* 3.9 17.2 - - + +
103V GLU* 2.8 41.8 + - - +
144V ILE* 4.3 2.8 - - + +
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Residues in contact with SER 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU* 6.1 0.3 - - - +
63L GLU* 4.9 5.5 + - - +
66L MET* 3.4 29.2 - - - +
78L LEU* 4.8 2.5 - - - -
27V SER 3.0 12.5 + - - -
28V TYR* 3.2 24.9 - - - -
30V TYR* 1.3 75.1 - - - +
32V SER* 1.3 61.0 + - - +
34V TYR* 3.4 11.9 + - - +
35V ALA* 3.1 22.7 + - - +
55V SER* 3.8 12.9 + - - -
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Residues in contact with SER 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L LEU* 3.4 17.4 - - - +
28V TYR 3.2 5.1 + - - -
29V THR 3.2 11.8 + - - -
30V TYR 3.2 0.2 - - - -
31V SER* 1.3 73.1 - - - +
33V MET* 1.3 60.6 + - - +
35V ALA* 3.2 7.2 + - - +
36V PHE* 2.9 28.1 + - - +
84V PRO* 3.2 29.4 - - - +
86V ARG 4.0 6.6 + - - -
87V ASP* 5.1 7.0 + - - +
89V TRP* 3.4 17.5 + - - -
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Residues in contact with MET 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29V THR* 3.2 33.5 + - + +
30V TYR* 3.5 16.4 - - + +
32V SER* 1.3 76.8 - - - +
34V TYR* 1.3 66.0 + - - +
36V PHE* 3.3 0.7 + - - +
37V PHE* 3.0 32.6 + - + -
51V PHE* 3.8 41.3 - - + -
89V TRP* 3.7 43.3 - - + +
95V ALA* 3.8 24.2 - - + +
98V ALA* 4.0 7.9 - - + +
99V ALA* 4.2 9.0 - - - +
102V LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L GLU* 5.1 12.1 + - + -
66L MET* 4.5 24.2 - - + -
67L LYS* 3.4 36.9 - - + +
70L ASN* 6.3 0.2 - - - -
30V TYR 2.8 14.0 + - - +
31V SER* 3.4 14.4 - - - +
33V MET* 1.3 77.6 - - - +
35V ALA* 1.3 71.9 + - - +
36V PHE 3.3 0.2 + - - -
37V PHE 3.4 0.5 + - - -
38V ASP* 3.2 29.8 + - + +
48V ALA* 3.2 40.2 - - + +
49V GLU* 3.6 19.5 + - - -
51V PHE* 4.0 2.4 - - - +
52V LYS* 3.7 42.7 + - + +
55V SER* 5.8 0.2 - - - +
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Residues in contact with ALA 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L MET* 4.4 13.9 - - + -
70L ASN* 3.1 26.6 + - - +
76L VAL* 4.2 32.1 - - + -
31V SER 3.1 11.2 + - - +
32V SER* 3.6 9.4 - - - +
34V TYR* 1.3 84.5 - - - +
36V PHE* 1.3 62.7 + - - +
38V ASP* 4.4 0.9 - - - -
39V ARG* 3.5 10.4 + - - +
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Residues in contact with PHE 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32V SER 2.9 17.0 + - - +
33V MET 3.5 5.2 - - - +
34V TYR 3.1 0.4 - - - -
35V ALA* 1.3 77.7 - - - +
37V PHE* 1.3 85.9 + + - +
39V ARG* 3.3 52.2 - - - +
42V VAL* 3.3 35.3 - - + +
87V ASP 4.5 3.4 - - - +
88V GLU* 3.8 12.1 - - + -
89V TRP* 3.6 33.4 - - + -
90V GLY* 3.5 41.1 - - - -
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Residues in contact with PHE 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33V MET* 3.0 27.0 + - + +
34V TYR 3.4 0.6 + - - -
36V PHE* 1.3 91.9 - + - +
38V ASP* 1.3 60.7 + - - +
39V ARG 3.2 0.4 - - - -
42V VAL* 3.5 22.2 - - + -
43V ALA* 3.5 7.5 + - - -
44V LEU* 3.2 48.7 + - + +
45V HIS* 4.3 0.5 + - - -
47V VAL* 3.9 11.7 - - + -
48V ALA* 3.7 15.0 - - + -
51V PHE* 3.7 20.9 - + - -
89V TRP* 4.8 0.2 - - + -
91V ASN* 3.5 24.5 - - - -
92V THR* 3.6 28.0 - - - -
95V ALA* 3.7 22.4 - - + -
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Residues in contact with ASP 38 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L LYS* 3.2 42.7 + - - +
70L ASN* 3.1 31.9 + - - +
142M LYS* 3.0 31.3 + - - -
34V TYR* 3.2 29.2 + - + +
35V ALA* 4.3 1.1 - - - -
36V PHE 3.2 0.4 - - - -
37V PHE* 1.3 75.2 - - - +
39V ARG* 1.3 62.2 + - - +
45V HIS* 3.4 23.4 + - - -
48V ALA* 4.1 3.1 - - + +
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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