Contacts of the helix formed by residues 37 - 66 (chain u) 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 u).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647 T 3.9 22.4 - - - +
657 A 3.9 4.5 - - - +
16t LYS* 4.7 10.8 - - + -
19t ALA* 3.7 18.2 - - + -
20t LYS* 3.6 31.4 - - + -
33u ILE 3.0 19.6 + - - +
34u LEU* 3.5 15.5 - - + +
36u ASN* 1.3 76.1 - - - +
38u SER* 1.3 67.6 - - - +
39u PRO* 3.5 1.3 - - - -
40u VAL* 3.3 7.9 + - + +
41u ALA* 2.9 20.6 + - + +
21v PHE* 4.5 9.4 - - + -
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Residues in contact with SER 38 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34u LEU 2.6 22.8 + - - -
35u SER* 3.3 15.4 - - - -
36u ASN 3.3 0.2 - - - -
37u VAL* 1.3 82.0 - - - +
39u PRO* 1.4 73.0 - - - +
41u ALA* 2.9 10.6 + - - +
42u GLN* 2.9 26.8 + - - +
21v PHE* 3.5 21.7 - - - -
22v ASN* 5.5 2.5 + - - -
25v SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35u SER 4.0 3.8 - - - +
36u ASN 3.6 12.8 - - - +
37u VAL 3.5 2.5 - - - -
38u SER* 1.4 96.5 - - - +
40u VAL* 1.3 67.5 + - + +
42u GLN* 3.5 19.2 - - - +
43u GLN* 3.1 21.7 + - - +
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Residues in contact with VAL 40 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647 T 4.8 1.3 - - - +
12t GLN* 5.0 2.0 - - - +
15t ALA* 4.1 30.3 - - + +
16t LYS* 3.9 31.6 - - + +
19t ALA* 4.5 3.6 - - + -
36u ASN 4.3 13.2 - - - +
37u VAL* 3.5 13.9 - - + +
38u SER 3.0 0.4 + - - -
39u PRO* 1.3 79.1 - - + +
41u ALA* 1.3 66.4 + - - +
43u GLN* 3.1 9.2 + - - +
44u ASN* 3.1 32.7 + - - +
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Residues in contact with ALA 41 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637 A 3.9 4.8 - - - +
647 T 3.5 39.3 - - - +
37u VAL* 2.9 17.9 + - - +
38u SER 3.4 3.8 - - - +
40u VAL* 1.3 76.2 - - - +
42u GLN* 1.3 58.1 + - - +
44u ASN* 3.1 2.3 + - - +
45u PHE* 2.8 30.7 + - - +
17v TRP* 4.1 15.4 - - + -
21v PHE* 4.5 9.2 - - + -
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Residues in contact with GLN 42 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38u SER* 2.9 21.3 + - - +
39u PRO* 3.5 30.1 - - + +
41u ALA* 1.3 76.5 - - - +
43u GLN* 1.3 62.1 + - - +
45u PHE* 3.3 1.2 + - - +
46u GLN* 2.9 35.2 + - - +
14v TYR* 3.9 8.9 + - - +
17v TRP* 4.2 13.0 - - + -
18v GLN* 3.2 42.0 - - - +
21v PHE* 5.8 1.1 - - + -
22v ASN* 4.6 2.6 + - - -
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Residues in contact with GLN 43 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12t GLN* 5.3 7.2 - - + +
39u PRO 3.1 10.2 + - - +
40u VAL* 3.1 11.4 + - - +
42u GLN* 1.3 79.4 - - - +
44u ASN* 1.3 60.3 + - - +
46u GLN* 3.7 12.8 + - - +
47u THR* 2.6 60.1 + - - +
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Residues in contact with ASN 44 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637 A 3.6 23.8 - - - +
647 T 2.9 19.8 + - - -
8t ARG* 3.7 25.0 - - - +
12t GLN* 2.9 35.7 + - - +
16t LYS* 5.5 3.8 - - - +
40u VAL* 3.1 21.0 + - - +
41u ALA 3.1 7.4 + - - +
43u GLN* 1.3 78.1 - - - +
45u PHE* 1.3 65.7 + - - +
47u THR* 3.7 4.1 - - - -
48u ASN* 3.1 24.8 + - - +
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Residues in contact with PHE 45 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 T 4.5 11.0 - - - -
637 A 3.5 27.1 - - - -
2888 T 5.3 6.5 - - - -
41u ALA 2.8 15.7 + - - +
42u GLN 3.7 3.8 - - - +
44u ASN* 1.3 77.4 - - - +
46u GLN* 1.3 59.1 + - - +
49u VAL* 2.9 69.0 + - + +
10v TYR* 5.1 1.1 - + - -
13v ARG* 4.4 6.1 - - + -
14v TYR* 3.5 44.4 - + + -
17v TRP* 3.5 58.1 - + + -
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Residues in contact with GLN 46 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42u GLN* 2.9 28.1 + - - +
43u GLN* 3.8 13.7 + - - +
45u PHE* 1.3 80.2 - - - +
47u THR* 1.3 62.5 + - - +
50u PRO* 3.1 25.7 - - - +
10v TYR* 5.2 11.6 + - - +
14v TYR* 3.4 47.8 + - + -
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Residues in contact with THR 47 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12t GLN* 4.9 12.9 + - - +
43u GLN* 2.6 47.9 + - - +
44u ASN* 3.7 7.0 - - - -
45u PHE 3.2 0.4 - - - -
46u GLN* 1.3 80.3 - - - +
48u ASN* 1.3 73.1 + - - +
50u PRO* 4.3 2.6 - - - +
51u LYS* 3.4 23.6 - - - +
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Residues in contact with ASN 48 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 T 3.8 17.9 - - - +
637 A 3.0 21.6 + - - -
7t SER* 4.5 8.3 + - - -
8t ARG* 3.8 12.5 - - - +
12t GLN* 5.5 4.0 - - - +
44u ASN* 3.1 10.3 + - - +
47u THR* 1.3 87.5 - - - +
49u VAL* 1.3 68.5 + - - +
50u PRO* 3.4 1.3 - - - -
51u LYS* 2.9 50.0 + - + +
52u PHE* 3.4 12.1 - - + -
88u ASN* 4.9 5.0 + - - -
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Residues in contact with VAL 49 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 T 3.6 32.5 - - + +
45u PHE* 2.9 59.0 + - + +
48u ASN* 1.3 73.8 - - - +
50u PRO* 1.3 63.0 - - + +
51u LYS 3.0 0.2 - - - -
52u PHE* 2.9 26.8 + - + +
53u THR* 3.0 12.7 + - - +
10v TYR* 4.6 7.2 - - + -
13v ARG* 3.8 28.7 + - + +
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Residues in contact with PRO 50 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45u PHE 3.8 1.1 - - - +
46u GLN 3.1 25.6 - - - +
47u THR 4.2 2.7 - - - +
48u ASN 3.4 2.9 - - - +
49u VAL* 1.3 96.5 - - + +
51u LYS* 1.3 61.3 + - + +
53u THR* 3.7 1.9 - - - +
54u SER* 3.2 23.9 + - - -
10v TYR* 3.7 48.2 - - + -
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Residues in contact with LYS 51 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47u THR* 3.4 23.8 + - - +
48u ASN* 2.9 35.9 + - - +
49u VAL 3.0 0.4 - - - -
50u PRO* 1.3 79.7 - - + +
52u PHE* 1.3 63.9 + - + +
54u SER* 2.9 18.7 + - - -
55u VAL* 3.3 13.2 - - - +
84u ALA* 5.5 0.7 - - - +
88u ASN* 3.9 26.6 + - - +
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Residues in contact with PHE 52 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617 A 3.7 17.0 - - + -
627 T 3.4 41.5 - - - +
48u ASN* 3.4 20.2 - - + -
49u VAL* 2.9 7.8 + - + +
51u LYS* 1.3 75.9 - - + +
53u THR* 1.3 66.3 + - - +
54u SER 3.2 1.3 - - - -
55u VAL* 3.1 7.4 + - - +
56u ASN* 2.9 28.1 + - - +
81u LEU* 3.7 30.0 - - + +
84u ALA* 3.6 26.5 - - + -
85u ARG* 3.6 14.8 - - - -
88u ASN* 3.3 31.0 - - - -
13v ARG* 5.0 5.6 - - - +
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Residues in contact with THR 53 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49u VAL* 3.0 7.7 + - - +
50u PRO 3.8 5.6 - - - -
52u PHE* 1.3 78.3 - - - +
54u SER* 1.3 63.6 + - - +
56u ASN* 3.1 8.6 + - + +
57u GLU* 3.0 23.8 + - + +
8v ARG 4.7 4.5 - - - +
9v SER* 4.2 6.5 - - - -
10v TYR* 3.1 46.5 - - + +
13v ARG* 2.7 28.2 + - - +
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Residues in contact with SER 54 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50u PRO 3.2 10.7 + - - -
51u LYS* 2.9 22.3 + - - -
53u THR* 1.3 79.7 - - - +
55u VAL* 1.3 58.5 + - - +
57u GLU* 3.4 6.6 + - - +
58u ASN* 3.0 40.7 + - - -
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Residues in contact with VAL 55 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51u LYS 3.3 17.7 - - - +
52u PHE* 3.1 11.2 + - - +
53u THR 3.1 0.4 - - - -
54u SER* 1.3 77.7 + - - +
56u ASN* 1.3 59.9 + - - +
57u GLU 3.2 0.2 + - - -
58u ASN* 3.3 3.5 + - - +
59u VAL* 2.8 52.0 + - + +
77u GLN* 5.2 0.4 - - - +
80u GLY 4.1 14.1 - - - -
81u LEU* 4.3 10.1 - - + +
84u ALA* 4.0 19.5 - - + -
125u ILE* 3.9 26.7 - - + -
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Residues in contact with ASN 56 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2898 A 4.8 4.8 + - - +
2908 T 4.1 35.8 + - - +
52u PHE* 2.9 18.0 + - - +
53u THR* 3.4 9.7 - - + +
55u VAL* 1.3 75.3 - - - +
57u GLU* 1.3 57.8 + - - +
60u SER* 2.9 30.5 + - - -
77u GLN* 3.1 20.9 + - - +
81u LEU* 3.3 30.7 - - - +
13v ARG* 4.0 21.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53u THR* 3.0 15.4 + - + +
54u SER* 3.5 11.2 - - - +
56u ASN* 1.3 74.6 - - - +
58u ASN* 1.3 74.3 + - - +
60u SER* 3.2 8.2 + - - -
61u ALA* 3.0 23.7 + - + +
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Residues in contact with ASN 58 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54u SER* 3.0 23.0 + - - +
55u VAL* 4.1 3.8 - - - +
57u GLU* 1.3 88.7 - - - +
59u VAL* 1.3 61.1 + - - +
61u ALA* 3.2 10.8 + - - +
62u VAL* 3.2 25.7 + - - +
124u ILE* 3.7 26.2 - - + +
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Residues in contact with VAL 59 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55u VAL* 2.8 36.8 + - + +
58u ASN* 1.3 73.4 - - + +
60u SER* 1.3 67.3 + - - +
62u VAL* 3.1 9.4 + - - +
63u LEU* 2.9 32.6 + - + +
76u TYR 4.3 1.1 - - - +
77u GLN* 3.3 31.9 - - - +
80u GLY* 4.7 2.0 - - - -
121u VAL* 4.0 39.3 - - + +
124u ILE* 5.5 3.4 - - + -
125u ILE* 4.4 7.4 - - + -
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Residues in contact with SER 60 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2908 T 4.9 0.2 - - - -
2918 A 3.4 11.0 + - - -
56u ASN 2.9 22.3 + - - -
57u GLU* 3.4 10.1 - - - -
58u ASN 3.2 0.2 - - - -
59u VAL* 1.3 77.2 - - - +
61u ALA* 1.3 63.2 + - - +
63u LEU* 3.1 3.2 + - - -
64u THR* 3.0 12.7 + - - -
73u ARG* 2.7 41.2 + - - +
77u GLN* 3.4 12.9 - - - +
89w ARG 4.7 2.6 + - - -
90w ILE 4.7 3.5 + - - -
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Residues in contact with ALA 61 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57u GLU* 3.0 15.8 + - + +
58u ASN* 3.4 13.2 - - - +
59u VAL 3.2 0.2 - - - -
60u SER* 1.3 77.3 - - - +
62u VAL* 1.3 62.8 + - + +
64u THR* 3.2 7.8 + - - -
65u GLN* 3.1 31.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58u ASN 3.4 13.7 - - - +
59u VAL* 3.1 11.8 + - + +
61u ALA* 1.3 77.7 - - + +
63u LEU* 1.3 69.1 + - + +
65u GLN* 2.9 24.7 + - - +
66u TYR* 3.0 38.6 + - + -
117u VAL* 5.3 0.4 - - + +
120u ALA* 4.0 18.4 - - + +
121u VAL* 4.8 7.9 - - + +
124u ILE* 3.6 31.9 - - + -
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Residues in contact with LEU 63 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59u VAL* 2.9 34.6 + - + +
60u SER* 3.1 7.4 + - - +
62u VAL* 1.3 77.6 - - + +
64u THR* 1.3 62.6 + - - +
66u TYR* 3.2 3.0 + - - +
67u GLY 3.0 4.3 + - - -
68u ILE* 2.9 43.2 + - + +
73u ARG* 3.5 48.5 - - + +
76u TYR* 3.6 34.3 - - + -
77u GLN* 4.0 9.9 - - + +
117u VAL* 4.1 11.4 - - + -
121u VAL* 5.1 1.1 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60u SER 3.0 5.7 + - - -
61u ALA* 3.6 10.5 - - - -
62u VAL 3.2 0.2 - - - -
63u LEU* 1.3 75.9 - - - +
65u GLN* 1.3 62.7 + - + +
67u GLY 3.1 9.4 + - - -
73u ARG* 3.0 22.2 + - - +
90w ILE* 2.6 34.6 + - + +
91w GLY 3.8 6.7 - - - +
92w SER 3.3 27.6 - - - +
93w GLY* 4.6 1.3 - - - -
94w PRO* 3.3 5.0 - - + +
95w ALA* 3.3 18.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61u ALA* 3.1 19.5 + - - +
62u VAL* 2.9 18.2 + - - +
64u THR* 1.3 76.7 - - + +
66u TYR* 1.3 65.8 + - + +
67u GLY 3.3 0.2 - - - -
94w PRO* 3.4 23.8 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62u VAL* 3.0 35.5 + - + +
63u LEU 3.2 6.0 + - - +
65u GLN* 1.3 85.0 - - + +
67u GLY* 1.3 61.4 + - - +
68u ILE* 3.2 21.5 + - + +
116u GLN* 2.9 42.4 + - - -
117u VAL* 4.1 15.7 - - + -
120u ALA* 3.5 28.0 - - + +
94w PRO* 4.6 0.9 - - - -
----------------------------------------------------------
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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