Contacts of the helix formed by residues 10 - 38 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ARG* 4.0 4.4 + - - +
8J TYR 3.7 1.8 + - - -
9J HIS* 1.3 82.9 + - - +
11J ASP* 1.3 64.6 + - - +
13J GLU* 3.4 19.0 + - - +
14J ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J HIS* 2.8 21.5 + - - +
10J SER* 1.3 74.1 - - - +
12J CYS* 1.3 62.5 + - - +
14J ALA* 3.4 7.1 + - - +
15J ALA* 2.9 28.6 + - - +
18J ARG* 4.6 1.9 + - - -
116J LEU* 3.6 22.0 - - + +
120J LYS* 3.1 21.9 + - - +
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Residues in contact with CYS 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J TYR* 4.1 9.6 - - + -
9J HIS* 3.1 25.7 + - + +
11J ASP* 1.3 80.1 - - - +
13J GLU* 1.3 58.0 - - - +
15J ALA* 3.1 3.7 + - - +
16J VAL* 2.9 35.5 + - - +
113J LEU* 4.3 1.0 - - - +
116J LEU* 4.0 24.7 - - - -
117J ALA* 4.3 7.6 - - - -
120J LYS* 4.1 15.5 - - - -
122J ASP* 5.0 4.9 - - - -
125J LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ARG* 2.7 34.2 + - - -
8J TYR* 3.7 21.4 + - + -
9J HIS 3.1 8.3 + - - +
10J SER* 3.5 18.4 + - - +
12J CYS* 1.3 79.9 - - - +
14J ALA* 1.3 61.6 + - - +
16J VAL 3.3 0.7 + - - -
17J ASN* 3.1 22.6 + - - +
69J GLN* 3.2 27.8 + - - +
74J GLY* 3.8 2.2 - - - -
75J ARG* 2.9 32.7 + - - +
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J SER 3.1 16.7 + - - +
11J ASP* 3.7 7.2 - - - +
12J CYS 3.3 0.2 - - - -
13J GLU* 1.3 77.4 - - - +
15J ALA* 1.3 62.2 + - - +
17J ASN* 3.5 10.6 + - - +
18J ARG* 3.1 38.3 + - - +
79J GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ASP 2.9 16.9 + - - +
12J CYS 3.5 1.6 - - - +
14J ALA* 1.3 76.1 - - - +
16J VAL* 1.3 60.6 + - - +
18J ARG* 3.3 24.6 + - - +
19J MET* 2.9 29.1 + - - +
113J LEU* 3.5 27.0 - - + +
116J LEU* 3.7 11.9 - - + -
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Residues in contact with VAL 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J TYR* 3.6 15.3 - - - +
12J CYS 2.9 18.5 + - - +
13J GLU 3.6 5.2 - - - +
14J ALA 3.3 0.2 - - - -
15J ALA* 1.3 77.6 - - - +
17J ASN* 1.3 57.9 + - - +
19J MET* 3.2 7.5 + - - +
20J LEU* 2.9 29.7 + - + +
65J PHE* 3.9 33.2 - - + +
68J TYR* 4.6 5.2 - - + -
69J GLN* 3.5 22.2 - - + +
113J LEU* 4.3 13.0 - - + -
125J LEU* 4.3 22.7 - - + -
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Residues in contact with ASN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLU* 3.1 14.6 + - - +
14J ALA* 3.6 12.2 - - - +
15J ALA 3.3 0.2 - - - -
16J VAL* 1.3 76.7 - - - +
18J ARG* 1.3 60.9 + - - +
20J LEU* 3.5 17.4 - - - +
21J ASN* 3.4 19.8 + - - +
69J GLN* 3.4 13.1 + - - +
75J ARG 3.2 19.0 + - - -
76J VAL* 3.3 10.2 - - - -
77J VAL* 3.1 47.3 + - - +
79J GLN* 4.6 9.5 + - - +
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Residues in contact with ARG 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ASP 4.6 2.8 + - - -
14J ALA* 3.1 21.9 + - - +
15J ALA* 3.4 33.6 - - - +
17J ASN* 1.3 79.7 - - - +
19J MET* 1.3 63.9 + - - +
21J ASN* 3.4 7.0 + - - +
22J LEU* 3.1 20.8 + - - +
79J GLN* 4.8 16.4 - - - +
116J LEU* 5.4 1.8 - - - +
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Residues in contact with MET 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ALA 2.9 15.3 + - - +
16J VAL* 3.5 6.5 - - - +
18J ARG* 1.3 75.6 - - - +
20J LEU* 1.3 63.9 + - - +
22J LEU* 3.2 13.6 + - - +
23J GLU* 2.9 28.4 + - + +
65J PHE* 3.4 29.6 - - + -
106J VAL* 4.6 3.4 - - - +
109J ALA* 3.1 50.0 - - + +
110J LEU* 3.5 21.1 - - + +
113J LEU* 3.7 20.9 - - + -
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Residues in contact with LEU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J VAL* 2.9 16.2 + - + +
17J ASN* 3.5 20.6 - - - +
19J MET* 1.3 77.3 - - - +
21J ASN* 1.3 62.2 + - - +
23J GLU* 3.4 8.7 + - - +
24J LEU* 3.1 43.0 + - + +
62J ALA* 3.7 16.4 - - - +
65J PHE* 4.2 14.1 - - + +
66J MET* 3.8 35.4 - - + +
69J GLN* 5.8 0.4 - - + +
76J VAL* 4.0 19.1 - - + -
77J VAL 5.6 0.4 - - - +
78J LEU* 3.7 16.8 - - + -
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Residues in contact with ASN 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ASN 3.4 8.5 + - - +
18J ARG* 3.6 8.3 - - - +
19J MET 3.2 0.4 - - - -
20J LEU* 1.3 83.3 - - + +
22J LEU* 1.3 61.1 + - - +
24J LEU* 3.1 8.6 + - - +
25J TYR* 2.8 29.8 + - - +
79J GLN* 3.5 44.4 + - - +
80J ASP 3.2 27.6 + - - +
81J ILE* 4.3 9.5 - - - +
82J LYS 5.6 0.5 + - - -
28X TYR* 4.4 2.8 + - - +
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Residues in contact with LEU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG 3.1 13.7 + - - +
19J MET* 3.2 16.1 + - - +
21J ASN* 1.3 78.9 + - - +
23J GLU* 1.3 58.0 + - - +
25J TYR* 3.2 23.9 + - + -
26J ALA* 2.9 26.9 + - - +
102J LEU* 5.4 0.9 - - + -
105J THR* 4.4 16.6 - - + +
106J VAL* 3.9 31.0 - - + +
109J ALA* 3.7 29.8 - - + -
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Residues in contact with GLU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J MET* 2.9 19.6 + - + +
20J LEU 3.4 9.6 - - - +
21J ASN 3.2 0.2 - - - -
22J LEU* 1.3 77.7 - - - +
24J LEU* 1.3 57.8 + - - +
26J ALA* 3.3 5.2 + - - +
27J SER* 2.9 28.6 + - - -
58J GLU* 2.7 27.7 - - - +
61J HIS* 3.4 18.2 - - + +
62J ALA* 3.8 7.0 - - + -
65J PHE* 4.1 18.8 - - + -
106J VAL* 4.0 15.1 - - + +
110J LEU* 4.9 2.4 - - - +
133J TYR* 3.7 15.2 - - - -
176J MG 2.4 31.8 - - - -
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Residues in contact with LEU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.1 31.0 + - + +
21J ASN* 3.5 9.9 - - - +
23J GLU* 1.3 75.0 - - - +
25J TYR* 1.3 57.2 + - - +
27J SER* 3.5 6.5 - - - -
28J TYR* 3.0 27.2 + - - +
59J ARG* 4.9 17.3 - - + -
62J ALA* 3.7 18.4 - - + -
63J GLU* 6.4 0.4 - - + -
66J MET* 5.1 6.3 - - + -
81J ILE* 3.7 25.6 - - + +
28X TYR* 3.5 39.7 - - + +
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Residues in contact with TYR 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ASN* 2.8 17.9 + - - +
22J LEU* 3.4 26.7 - - + +
24J LEU* 1.3 72.8 - - - +
26J ALA* 1.3 62.7 + - - +
28J TYR* 3.2 4.1 + - + +
29J THR* 2.9 48.6 + - - -
81J ILE* 4.0 9.8 - - + +
82J LYS* 3.4 37.7 - - + +
83J LYS 3.8 11.6 + - - -
84J PRO* 4.1 1.6 - - + -
85J GLU* 3.8 25.5 + - - +
102J LEU* 4.1 17.5 - - + -
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Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU 2.9 14.0 + - - +
23J GLU* 3.5 9.9 - - - +
25J TYR* 1.3 78.0 - - - +
27J SER* 1.3 62.0 + - - +
29J THR* 3.3 3.5 + - - -
30J TYR* 3.1 30.9 + - + -
58J GLU* 4.2 15.9 - - + -
102J LEU* 3.9 26.6 - - + +
103J GLU* 6.2 0.7 - - - +
106J VAL* 4.2 18.8 - - + -
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Residues in contact with SER 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU 2.9 16.0 + - - -
24J LEU* 3.5 11.3 - - - +
25J TYR 3.2 0.2 - - - -
26J ALA* 1.3 76.7 - - - +
28J TYR* 1.3 62.7 + - - +
30J TYR 3.1 2.8 + - - -
31J SER* 3.0 19.0 + - - -
55J SER* 2.9 39.6 + - - +
58J GLU* 3.8 13.4 - - - +
59J ARG* 3.6 16.4 - - - +
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Residues in contact with TYR 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J LEU 3.0 18.4 + - - +
25J TYR* 3.2 5.8 + - - +
27J SER* 1.3 77.2 + - - +
29J THR* 1.3 60.6 + - - +
31J SER* 3.2 16.0 - - - -
32J SER* 3.2 19.1 + - - -
81J ILE* 4.0 13.9 - - + -
82J LYS 3.6 17.9 - - - +
83J LYS* 4.0 3.6 - - - -
84J PRO* 3.7 17.6 - - + +
21X ASN* 4.4 3.3 + - - +
24X LEU* 3.7 27.0 - - + +
66X MET* 5.6 0.4 - - + -
78X LEU* 3.4 38.3 - - + +
79X GLN 2.9 31.3 + - - -
81X ILE* 3.8 23.3 - - + +
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Residues in contact with THR 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J TYR* 2.9 31.4 + - + +
26J ALA* 3.6 8.7 - - - -
27J SER 3.2 0.2 - - - -
28J TYR* 1.3 76.5 - - - +
30J TYR* 1.3 62.9 + - - +
32J SER* 3.2 6.9 + - - -
33J MET* 3.2 39.0 + - + +
84J PRO* 3.4 21.3 - - - +
85J GLU* 5.8 0.4 - - - +
89J TRP* 4.0 15.5 - - + -
102J LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ALA* 3.1 23.4 + - + -
27J SER 3.1 6.7 + - - +
29J THR* 1.3 75.1 - - - +
31J SER* 1.3 60.7 + - - +
33J MET* 3.2 12.4 + - + +
34J TYR* 2.8 28.9 + - - +
50J PHE* 5.9 0.2 - + - -
51J PHE* 3.6 46.3 - + - +
54J HIS* 3.9 29.8 + + + -
55J SER* 3.7 7.4 - - - -
58J GLU* 4.0 13.2 - - + -
99J ALA* 3.9 24.9 + - + +
102J LEU* 3.9 17.0 - - + +
103J GLU* 2.8 40.5 + - - +
144J ILE* 4.3 4.1 - - + +
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J SER 3.0 12.5 + - - -
28J TYR* 3.2 24.3 - - - -
30J TYR* 1.3 75.1 - - - +
32J SER* 1.3 61.1 + - - +
34J TYR* 3.4 12.3 + - - +
35J ALA* 3.1 23.2 + - - +
55J SER* 3.8 12.9 + - - -
24X LEU* 6.1 0.3 - - - +
63X GLU* 5.0 5.5 + - - +
66X MET* 3.4 29.6 - - - +
78X LEU* 4.8 2.9 - - - -
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Residues in contact with SER 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J TYR 3.2 5.3 + - - -
29J THR 3.2 11.5 + - - -
30J TYR 3.2 0.2 - - - -
31J SER* 1.3 73.3 - - - +
33J MET* 1.3 60.7 + - - +
35J ALA* 3.2 6.7 + - - +
36J PHE* 2.9 28.1 + - - +
84J PRO* 3.2 29.3 - - - +
86J ARG 4.0 6.4 + - - -
87J ASP* 5.1 7.3 + - - +
89J TRP* 3.4 17.7 + - - -
78X LEU* 3.4 17.2 - - - +
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Residues in contact with MET 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J THR* 3.2 33.5 + - + +
30J TYR* 3.2 16.1 + - + +
32J SER* 1.3 77.7 - - - +
34J TYR* 1.3 65.9 + - - +
36J PHE* 3.3 1.1 + - - +
37J PHE* 3.0 32.7 + - + -
51J PHE* 3.8 42.0 - - + -
89J TRP* 3.7 43.3 - - + +
95J ALA* 3.8 23.6 - - + +
98J ALA* 4.0 8.1 - - + +
99J ALA* 4.2 9.0 - - - +
102J LEU* 5.2 0.4 - - + -
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Residues in contact with TYR 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR 2.8 13.8 + - - +
31J SER* 3.4 14.8 - - - +
33J MET* 1.3 77.1 - - - +
35J ALA* 1.3 71.3 + - - +
36J PHE 3.3 0.2 + - - -
37J PHE 3.4 0.7 + - - -
38J ASP* 3.2 30.0 + - + +
48J ALA* 3.2 37.7 - - + +
49J GLU* 3.6 19.7 + - - -
51J PHE* 4.0 2.8 - - - +
52J LYS* 3.7 42.5 + - + +
63X GLU* 5.2 12.1 + - + -
66X MET* 4.5 23.3 - - + -
67X LYS* 3.4 36.1 - - + +
70X ASN* 6.2 0.2 - - - -
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Residues in contact with ALA 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J SER 3.1 10.8 + - - +
32J SER* 3.6 9.2 - - - +
34J TYR* 1.3 85.0 - - - +
36J PHE* 1.3 62.1 + - - +
38J ASP* 3.9 1.1 - - - -
39J ARG* 3.5 10.4 + - - +
66X MET* 4.4 14.4 - - + -
70X ASN* 3.2 27.4 + - - +
76X VAL* 4.2 32.1 - - + -
78X LEU* 6.3 0.2 - - + -
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Residues in contact with PHE 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J SER 2.9 16.6 + - - +
33J MET 3.5 4.5 - - - +
34J TYR 3.1 0.2 - - - -
35J ALA* 1.3 78.4 - - - +
37J PHE* 1.3 84.3 + + - +
39J ARG* 3.3 51.6 - - - +
42J VAL* 3.3 37.2 - - + +
87J ASP 4.5 3.6 - - - +
88J GLU* 3.8 12.1 - - + -
89J TRP* 3.6 33.9 - - + -
90J GLY* 3.5 40.8 - - - -
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Residues in contact with PHE 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J MET* 3.0 26.8 + - + +
34J TYR 3.4 0.6 + - - -
36J PHE* 1.3 90.8 - + - +
38J ASP* 1.3 60.6 + - - +
39J ARG 3.2 0.4 - - - -
42J VAL* 3.5 22.9 - - + -
43J ALA* 3.5 7.3 + - - -
44J LEU* 3.2 50.2 + - + +
45J HIS* 4.3 0.5 + - - -
47J VAL* 3.9 12.1 - - + -
48J ALA* 3.7 14.8 - - + -
51J PHE* 3.7 19.7 - + - -
89J TRP* 4.8 0.2 - - + -
91J ASN* 3.5 24.9 - - - -
92J THR* 3.6 27.4 - - - -
95J ALA* 3.7 21.8 - - + -
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Residues in contact with ASP 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 3.0 31.7 + - - -
34J TYR* 3.2 29.7 + - + +
35J ALA* 4.3 1.6 - - - -
36J PHE 3.2 0.4 - - - -
37J PHE* 1.3 74.8 - - - +
39J ARG* 1.3 61.5 + - - +
45J HIS* 3.4 23.6 + - - -
48J ALA* 4.1 2.3 - - + +
67X LYS* 3.3 42.1 + - - +
70X ASN* 3.0 32.3 + - - +
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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