Contacts of the helix formed by residues 37 - 66 (chain E) in PDB entry 3J9X
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 VAL 37 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3167 T 3.9 22.7 - - - +
3177 A 3.9 5.2 - - - +
16D LYS* 4.7 10.8 - - + -
19D ALA* 3.7 17.9 - - + -
20D LYS* 3.6 30.5 - - + -
33E ILE 3.0 20.4 + - - +
34E LEU* 3.5 15.0 - - + +
36E ASN* 1.3 75.8 - - - +
38E SER* 1.3 68.5 + - - +
39E PRO* 3.5 1.6 - - - -
40E VAL* 3.9 7.6 - - + -
41E ALA* 2.9 20.9 + - + +
21F PHE* 4.5 9.4 - - + -
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Residues in contact with SER 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU 2.6 23.2 + - - -
35E SER* 3.3 15.3 - - - -
36E ASN 3.3 0.2 - - - -
37E VAL* 1.3 80.9 - - - +
39E PRO* 1.4 73.0 - - - +
41E ALA* 2.9 10.4 + - - +
42E GLN* 2.9 27.0 + - - +
21F PHE* 3.5 23.3 - - - -
22F ASN* 5.5 2.3 + - - -
25F SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E SER 4.0 3.8 - - - +
36E ASN 3.6 12.1 - - - +
37E VAL 3.5 1.8 - - - -
38E SER* 1.4 96.6 - - - +
40E VAL* 1.3 67.4 + - + +
42E GLN* 3.5 19.0 - - - +
43E GLN* 3.1 21.7 + - - +
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3167 T 4.8 1.6 - - - +
12D GLN* 5.0 2.2 - - - +
15D ALA* 4.1 31.0 - - + +
16D LYS* 3.9 31.6 - - + +
19D ALA* 4.5 3.4 - - + -
36E ASN 4.3 13.2 - - - +
37E VAL* 3.5 12.3 - - + +
38E SER 3.0 0.4 + - - -
39E PRO* 1.3 79.7 - - + +
41E ALA* 1.3 66.6 + - - +
43E GLN* 3.1 9.3 + - - +
44E ASN* 3.1 32.2 + - - +
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 A 3.9 4.2 - - - +
3167 T 3.5 38.8 - - - +
37E VAL 2.9 17.3 + - - +
38E SER 3.4 3.8 - - - +
40E VAL* 1.3 77.0 - - - +
42E GLN* 1.3 58.4 + - - +
44E ASN* 3.1 2.3 + - - +
45E PHE* 2.8 31.7 + - - +
17F TRP* 4.1 15.4 - - + -
21F PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E SER* 2.9 21.9 + - - +
39E PRO* 3.5 29.2 - - - +
41E ALA* 1.3 76.2 - - - +
43E GLN* 1.3 62.6 + - - +
45E PHE* 3.3 1.0 + - - +
46E GLN* 2.9 35.9 + - - +
14F TYR* 3.9 8.9 + - - +
17F TRP* 4.2 13.7 - - + -
18F GLN* 3.2 42.9 - - - +
21F PHE* 5.8 0.9 - - + -
22F ASN* 4.6 2.4 + - - -
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Residues in contact with GLN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 5.3 7.2 - - + +
39E PRO 3.1 9.8 + - - +
40E VAL* 3.3 11.0 - - + +
42E GLN* 1.3 79.6 - - - +
44E ASN* 1.3 60.7 + - - +
46E GLN* 3.7 10.5 + - - +
47E THR* 2.6 61.6 + - - +
43h GLN* 3.1 41.6 - - - +
11i SER* 5.1 9.7 - - - -
12i GLN* 6.1 2.4 - - - +
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Residues in contact with ASN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 A 3.6 23.6 - - - +
3167 T 2.9 20.0 + - - -
8D ARG* 3.7 25.3 - - - +
12D GLN* 2.9 34.7 + - - +
16D LYS* 5.5 3.8 - - - +
40E VAL* 3.1 20.5 + - - +
41E ALA 3.1 7.6 + - - +
43E GLN* 1.3 76.8 - - - +
45E PHE* 1.3 66.2 + - - +
47E THR* 3.7 3.7 - - - -
48E ASN* 3.1 25.2 + - - +
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Residues in contact with PHE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3147 T 4.5 10.8 - - - -
3157 A 3.5 29.1 - - - -
368 T 5.3 5.8 - - - -
41E ALA 2.8 15.9 + - - +
42E GLN 3.7 3.6 - - - +
44E ASN* 1.3 77.6 - - - +
46E GLN* 1.3 58.1 + - - +
49E VAL* 2.9 67.8 + - + +
10F TYR* 5.1 0.7 - + - -
13F ARG* 4.4 6.1 - - + -
14F TYR* 3.5 44.4 - + + -
17F TRP* 3.5 57.2 - + + -
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Residues in contact with GLN 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E GLN* 2.9 28.5 + - - +
43E GLN* 3.8 12.3 + - - +
45E PHE* 1.3 79.4 - - - +
47E THR* 1.3 62.3 - - - +
50E PRO* 3.1 22.2 - - - +
10F TYR* 5.2 10.8 + - - +
14F TYR* 3.4 47.6 + - + -
11i SER* 2.8 30.0 + - - +
14i TYR* 6.2 2.0 - - - -
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 4.9 12.0 + - - +
43E GLN* 2.6 47.7 + - - +
44E ASN* 3.7 6.7 - - - -
45E PHE 3.2 0.2 - - - -
46E GLN* 1.3 79.0 - - - +
48E ASN* 1.3 72.1 + - - +
50E PRO* 4.3 2.4 - - - +
51E LYS* 3.4 24.2 - - - +
9i SER* 5.5 12.1 - - - +
11i SER* 4.1 6.8 - - - -
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Residues in contact with ASN 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3147 T 3.8 18.4 + - - +
3157 A 3.0 20.4 + - - -
7D SER* 4.5 8.3 + - - -
8D ARG* 3.8 13.1 - - - +
12D GLN* 5.5 3.4 - - - +
44E ASN* 3.1 10.3 + - - +
47E THR* 1.3 87.9 - - - +
49E VAL* 1.3 68.7 + - - +
50E PRO* 3.4 1.8 - - - -
51E LYS* 2.9 49.6 + - + +
52E PHE* 3.4 12.0 - - + -
88E ASN* 4.9 5.2 + - - -
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3147 T 3.6 34.1 - - + +
45E PHE* 2.9 57.9 + - + +
48E ASN* 1.3 74.0 - - - +
50E PRO* 1.3 63.8 - - + +
52E PHE* 2.9 26.5 + - + +
53E THR* 3.0 12.4 + - - +
10F TYR* 4.6 6.5 - - + -
13F ARG* 3.8 28.9 - - + +
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Residues in contact with PRO 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E PHE 3.8 0.9 - - - +
46E GLN 3.1 26.0 - - - +
47E THR 4.2 3.1 - - - +
48E ASN 3.4 2.9 - - - -
49E VAL* 1.3 97.0 - - + +
51E LYS* 1.3 60.2 + - + +
53E THR* 3.7 1.5 - - - -
54E SER* 3.2 24.3 + - - -
10F TYR* 3.7 48.0 - - + -
10i TYR* 4.9 13.9 - - + -
11i SER* 4.8 2.2 - - - +
50j PRO* 5.8 2.0 - - + -
54j SER* 5.3 1.0 - - - -
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Residues in contact with LYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E THR* 3.4 23.8 + - - +
48E ASN* 2.9 36.8 + - - +
49E VAL 3.0 0.6 - - - -
50E PRO* 1.3 78.2 - - + +
52E PHE* 1.3 63.3 + - + +
54E SER* 2.9 18.5 + - - -
55E VAL* 3.3 13.3 - - - +
84E ALA* 5.5 0.7 - - - +
88E ASN* 3.9 27.1 + - - +
9i SER* 6.0 5.2 - - - -
57j GLU* 4.2 26.7 - - - +
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Residues in contact with PHE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137 A 3.7 16.8 - - + +
3147 T 3.4 40.4 - - - +
48E ASN* 3.4 20.6 - - + -
49E VAL* 2.9 6.9 + - - +
51E LYS* 1.3 76.3 - - + +
53E THR* 1.3 67.0 + - - +
54E SER 3.2 1.3 - - - -
55E VAL* 3.1 7.2 + - - +
56E ASN* 2.9 28.2 + - - +
81E LEU* 3.7 29.6 - - + +
84E ALA* 3.6 26.2 - - + -
85E ARG* 3.6 15.0 - - - -
88E ASN* 3.3 31.4 - - - -
13F ARG* 5.0 6.1 - - - +
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Residues in contact with THR 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E VAL* 3.0 7.2 + - - +
50E PRO 3.8 6.1 - - - -
52E PHE* 1.3 78.4 - - - +
54E SER* 1.3 61.3 + - - +
56E ASN* 3.1 8.3 + - + +
57E GLU* 3.0 23.4 + - + +
8F ARG 4.7 4.7 - - - +
9F SER* 4.2 5.8 - - - -
10F TYR* 3.1 47.0 - - + +
13F ARG* 2.7 29.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO 3.2 9.6 + - - -
51E LYS* 2.9 22.0 + - - -
53E THR* 1.3 80.5 - - - +
55E VAL* 1.3 58.7 + - - +
57E GLU* 3.4 6.1 + - - +
58E ASN* 3.0 39.8 + - - -
54j SER* 3.3 36.4 - - - -
57j GLU* 5.7 0.7 + - - -
58j ASN* 5.5 4.3 + - - -
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Residues in contact with VAL 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LYS 3.3 17.5 - - - +
52E PHE* 3.1 11.0 + - - +
53E THR 3.1 0.6 - - - -
54E SER* 1.3 77.8 + - - +
56E ASN* 1.3 60.8 + - - +
58E ASN* 4.1 3.3 - - - +
59E VAL* 2.8 52.4 + - + +
77E GLN* 5.2 0.9 - - - +
80E GLY 4.1 13.0 - - - -
81E LEU* 4.3 10.1 - - + -
84E ALA* 4.0 20.6 - - + -
125E ILE* 3.9 26.2 - - + -
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Residues in contact with ASN 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378 A 4.8 4.2 + - - +
388 T 4.1 35.0 + - - +
52E PHE* 2.9 17.1 + - - +
53E THR* 3.4 9.1 - - + +
55E VAL* 1.3 75.5 - - - +
57E GLU* 1.3 57.4 + - - +
60E SER* 2.9 30.8 + - - -
77E GLN* 3.1 20.8 + - - +
81E LEU* 3.3 30.5 - - - +
13F ARG* 4.0 23.0 - - - +
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E THR* 3.0 14.4 + - + +
54E SER* 3.5 11.7 - - - +
55E VAL 3.1 0.2 - - - -
56E ASN* 1.3 75.4 - - - +
58E ASN* 1.3 74.3 + - - +
60E SER* 3.2 8.2 + - - -
61E ALA* 3.0 23.3 + - + +
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Residues in contact with ASN 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 3.0 22.5 + - - +
55E VAL* 4.1 3.3 - - - +
57E GLU* 1.3 88.6 - - - +
59E VAL* 1.3 62.5 + - + +
61E ALA* 3.2 9.5 + - - +
62E VAL* 3.2 25.6 + - - +
124E ILE* 3.7 23.5 - - + +
54j SER* 5.3 4.9 + - - -
58j ASN* 4.2 20.2 - - - +
124j ILE* 4.7 9.6 + - - +
125j ILE* 4.8 9.1 - - - +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E VAL* 2.8 37.1 + - + +
58E ASN* 1.3 73.6 - - + +
60E SER* 1.3 66.1 + - - +
62E VAL* 3.1 9.6 + - - +
63E LEU* 2.9 33.8 + - + +
76E TYR 4.3 1.1 - - - +
77E GLN* 3.3 31.9 - - - +
80E GLY* 4.7 2.0 - - - -
121E VAL* 4.0 39.7 - - + +
124E ILE* 5.5 3.1 - - + -
125E ILE* 4.4 6.7 - - + -
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388 T 4.9 0.4 - - - -
398 A 3.4 9.9 + - - -
56E ASN 2.9 21.2 + - - -
57E GLU* 3.4 9.9 - - - -
59E VAL* 1.3 77.2 - - - +
61E ALA* 1.3 62.9 + - - +
63E LEU* 3.1 2.8 + - - -
64E THR* 3.0 13.1 + - - -
73E ARG* 2.7 41.5 + - - +
77E GLN* 3.4 12.9 - - - +
89G ARG 4.7 2.3 + - - -
90G ILE 4.7 3.6 + - - -
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLU* 3.0 15.8 + - - +
58E ASN* 3.4 13.0 - - - +
59E VAL 3.2 0.2 - - - -
60E SER* 1.3 77.2 - - - +
62E VAL* 1.3 62.5 + - + +
64E THR* 3.2 7.4 + - - -
65E GLN* 3.1 31.1 + - - +
125j ILE 6.1 0.7 - - - +
126j THR 5.7 4.0 - - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ASN 3.4 13.0 - - - +
59E VAL* 3.1 12.3 + - + +
61E ALA* 1.3 77.3 - - + +
63E LEU* 1.3 68.5 + - + +
65E GLN* 2.9 24.1 + - - +
66E TYR* 3.0 39.5 + - + -
117E VAL* 5.3 1.1 - - + +
120E ALA* 4.0 17.7 - - + +
121E VAL* 4.8 6.7 - - + +
124E ILE* 3.6 32.1 - - + -
126j THR 5.4 5.6 - - - +
127j GLY* 5.7 0.4 - - - -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E VAL* 2.9 35.2 + - + +
60E SER* 3.5 7.6 - - - +
62E VAL* 1.3 77.3 - - + +
64E THR* 1.3 62.5 + - - +
66E TYR* 3.2 3.6 + - - +
67E GLY 3.0 4.3 + - - -
68E ILE* 2.9 42.0 + - + +
73E ARG* 3.5 48.2 - - + +
76E TYR* 3.6 34.8 - - + -
77E GLN* 4.0 9.9 - - + +
117E VAL* 4.1 11.2 - - + -
121E VAL* 5.1 0.9 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E SER 3.0 6.3 + - - -
61E ALA* 3.6 10.3 - - - -
63E LEU* 1.3 77.6 - - - +
65E GLN* 1.3 63.7 + - + +
67E GLY 3.1 9.9 + - - -
73E ARG* 3.0 21.5 + - - +
90G ILE* 2.6 33.9 + - + +
91G GLY* 3.8 7.9 - - - +
92G SER 3.3 27.6 - - - +
93G GLY* 4.6 1.6 - - - -
94G PRO* 3.3 4.4 - - + +
95G ALA* 3.3 18.8 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ALA* 3.1 18.9 + - - +
62E VAL* 2.9 15.9 + - - +
64E THR* 1.3 76.8 - - + +
66E TYR* 1.3 66.5 + - + +
67E GLY 3.3 0.4 - - - -
94G PRO* 3.4 24.4 - - + +
92j SER* 5.8 5.5 - - - -
126j THR* 3.9 20.9 + - - +
127j GLY 5.8 0.7 - - - -
128j SER* 4.9 5.0 + - - -
134j SER* 3.7 30.6 + - - +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 3.0 36.5 + - + -
63E LEU* 3.2 6.9 + - - +
65E GLN* 1.3 85.5 - - + +
67E GLY* 1.3 62.5 + - - +
68E ILE* 3.2 21.6 + - + +
116E GLN* 2.9 43.8 + - - -
117E VAL* 4.1 16.8 - - + -
120E ALA* 3.5 28.3 - - + +
94G PRO* 4.6 1.1 - - - -
----------------------------------------------------------
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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).
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