Contacts of the helix formed by residues 37 - 66 (chain i) 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 i).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367 T 3.9 22.4 - - - +
1377 A 3.9 4.5 - - - +
16h LYS* 4.7 11.4 - - + -
19h ALA* 3.7 19.1 - - + -
20h LYS* 3.6 30.3 - - + -
33i ILE 3.0 20.7 + - - +
34i LEU* 3.5 15.7 - - + +
36i ASN* 1.3 76.0 - - - +
38i SER* 1.3 69.4 + - - +
39i PRO* 3.5 1.6 - - - -
40i VAL* 3.3 8.5 + - + +
41i ALA* 2.9 20.5 + - + +
21j PHE* 4.5 8.5 - - + -
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Residues in contact with SER 38 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34i LEU 2.6 23.0 + - - -
35i SER* 3.3 15.9 - - - -
37i VAL* 1.3 80.8 - - - +
39i PRO* 1.4 71.8 - - - +
41i ALA* 2.9 10.7 + - - +
42i GLN* 2.9 26.7 + - - +
21j PHE* 3.5 21.5 - - - -
22j ASN* 5.5 2.0 + - - -
25j SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35i SER 4.0 3.6 - - - +
36i ASN 3.6 12.1 - - - +
37i VAL 3.5 1.8 - - - -
38i SER* 1.4 98.7 - - - +
40i VAL* 1.3 68.4 + - + +
42i GLN* 3.5 18.4 - - - +
43i GLN* 3.1 21.1 + - - +
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Residues in contact with VAL 40 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1367 T 4.8 1.6 - - - +
12h GLN* 5.0 2.0 - - - +
15h ALA* 4.1 30.1 - - + +
16h LYS* 3.9 33.0 - - + +
19h ALA* 4.5 4.0 - - + -
36i ASN 4.3 13.5 - - - +
37i VAL* 3.5 12.6 - - + +
38i SER 3.0 0.8 + - - -
39i PRO* 1.3 79.0 - - + +
41i ALA* 1.3 67.4 + - - +
43i GLN* 3.1 9.6 + - - +
44i ASN* 3.1 32.4 + - - +
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Residues in contact with ALA 41 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 A 3.9 4.6 - - - +
1367 T 3.5 39.5 - - - +
37i VAL 2.9 18.5 + - - +
38i SER 3.4 3.8 - - - +
40i VAL* 1.3 76.6 - - - +
42i GLN* 1.3 57.9 + - - +
44i ASN* 3.1 2.4 + - - +
45i PHE* 2.8 30.8 + - - +
17j TRP* 4.1 15.4 - - + -
21j PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 42 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38i SER* 2.9 20.9 + - - +
39i PRO* 3.5 29.5 - - + +
40i VAL 3.1 0.2 - - - -
41i ALA* 1.3 76.9 - - - +
43i GLN* 1.3 62.5 + - - +
45i PHE* 3.7 1.0 - - - +
46i GLN* 2.9 34.9 + - - +
14j TYR* 3.9 9.1 + - - +
17j TRP* 4.2 12.3 - - + -
18j GLN* 3.2 42.2 - - - +
21j PHE* 5.8 1.1 - - + -
22j ASN* 4.6 1.8 + - - -
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Residues in contact with GLN 43 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12h GLN* 5.3 7.9 - - + +
39i PRO 3.1 10.0 + - - +
40i VAL* 3.1 11.2 + - - +
42i GLN* 1.3 81.5 - - - +
44i ASN* 1.3 60.7 + - - +
46i GLN* 3.7 13.1 + - - +
47i THR* 2.6 61.0 + - - +
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Residues in contact with ASN 44 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 A 3.6 23.2 - - - +
1367 T 2.9 20.2 + - - -
8h ARG* 3.7 24.9 - - - +
12h GLN* 2.9 35.5 + - - +
16h LYS* 5.5 3.8 - - - +
40i VAL* 3.1 20.6 + - - +
41i ALA 3.1 8.1 + - - +
43i GLN* 1.3 76.4 - - - +
45i PHE* 1.3 65.1 + - - +
47i THR* 3.4 4.0 + - - -
48i ASN* 3.1 24.9 + - - +
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Residues in contact with PHE 45 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 T 4.5 10.3 - - - -
1357 A 3.5 27.5 - - - -
2168 T 5.3 6.1 - - - -
41i ALA 2.8 16.1 + - - +
42i GLN 3.7 4.3 - - - +
44i ASN* 1.3 77.4 - - - +
46i GLN* 1.3 58.3 + - - +
49i VAL* 2.9 68.6 + - + +
10j TYR* 5.1 1.3 - + - -
13j ARG* 4.4 6.1 - - + -
14j TYR* 3.5 44.0 - + + -
17j TRP* 3.5 56.3 - + + -
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Residues in contact with GLN 46 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42i GLN* 2.9 28.0 + - - +
43i GLN* 3.8 13.9 + - - +
45i PHE* 1.3 79.7 - - - +
47i THR* 1.3 63.4 + - - +
50i PRO* 3.1 25.2 - - - +
10j TYR* 5.2 12.2 + - - +
14j TYR* 3.4 47.0 + - + -
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Residues in contact with THR 47 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12h GLN* 4.9 12.6 + - - +
43i GLN* 2.6 46.5 + - - +
44i ASN* 3.7 6.9 - - - -
45i PHE 3.2 0.2 - - - -
46i GLN* 1.3 80.2 - - - +
48i ASN* 1.3 71.2 + - - +
50i PRO* 4.3 2.3 - - - +
51i LYS* 3.4 24.1 - - - +
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Residues in contact with ASN 48 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 T 3.8 18.3 + - - +
1357 A 3.0 21.0 + - - -
7h SER* 4.5 7.7 + - - -
8h ARG* 3.8 13.3 - - - +
12h GLN* 5.5 4.0 - - - +
44i ASN* 3.1 10.4 + - - +
47i THR* 1.3 86.6 - - - +
49i VAL* 1.3 67.9 + - - +
50i PRO* 3.4 1.8 - - - -
51i LYS* 2.9 48.2 + - + +
52i PHE* 3.4 12.4 - - + -
88i ASN* 4.9 5.9 + - - -
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Residues in contact with VAL 49 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 T 3.6 34.1 - - + +
45i PHE* 2.9 56.8 + - + +
48i ASN* 1.3 74.9 - - - +
50i PRO* 1.3 65.3 - - + +
52i PHE* 2.9 26.8 + - + +
53i THR* 3.0 12.8 + - - +
10j TYR* 4.6 6.1 - - + -
13j ARG* 3.8 30.1 - - + +
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Residues in contact with PRO 50 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45i PHE 3.8 0.7 - - - +
46i GLN* 3.1 26.2 - - - +
47i THR 4.2 2.7 - - - +
48i ASN 3.4 3.1 - - - +
49i VAL* 1.3 97.4 - - + +
51i LYS* 1.3 60.2 + - + +
53i THR* 3.8 0.9 - - - +
54i SER* 3.2 23.9 + - - -
10j TYR* 3.7 48.2 - - + -
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Residues in contact with LYS 51 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47i THR* 3.4 23.2 + - - +
48i ASN* 2.9 36.3 + - - +
49i VAL 3.0 0.6 - - - -
50i PRO* 1.3 78.0 - - + +
52i PHE* 1.3 64.6 + - + +
54i SER* 2.9 19.4 + - - -
55i VAL* 3.3 13.0 - - - +
84i ALA* 5.5 0.7 - - - +
88i ASN* 3.9 26.8 + - - +
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Residues in contact with PHE 52 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337 A 3.7 16.8 - - + +
1347 T 3.4 39.9 - - - +
48i ASN* 3.4 19.5 - - + -
49i VAL* 2.9 8.0 + - - +
51i LYS* 1.3 77.2 - - + +
53i THR* 1.3 65.2 + - - +
54i SER 3.2 1.8 - - - -
55i VAL* 3.1 6.3 + - - +
56i ASN* 2.9 27.9 + - - +
81i LEU* 3.7 29.1 - - + +
84i ALA* 3.6 25.6 - - + -
85i ARG* 3.6 14.4 - - - -
88i ASN* 3.3 30.7 - - - -
13j ARG* 4.5 6.3 - - - +
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Residues in contact with THR 53 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49i VAL* 3.0 7.4 + - - +
50i PRO 3.4 5.8 + - - -
52i PHE* 1.3 77.0 - - - +
54i SER* 1.3 63.0 + - - +
56i ASN* 3.1 8.1 + - + +
57i GLU* 3.0 23.4 + - + +
8j ARG 4.7 4.7 - - - +
9j SER* 4.2 6.7 - - - -
10j TYR* 3.1 46.7 - - + +
13j ARG* 2.7 29.3 + - - +
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Residues in contact with SER 54 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50i PRO 3.2 10.7 + - - -
51i LYS* 2.9 22.0 + - - -
53i THR* 1.3 79.0 - - - +
55i VAL* 1.3 57.5 + - - +
57i GLU* 3.4 6.4 + - - +
58i ASN* 3.0 41.2 + - - -
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Residues in contact with VAL 55 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51i LYS 3.3 17.9 - - - +
52i PHE* 3.3 10.8 - - - +
54i SER* 1.3 76.7 + - - +
56i ASN* 1.3 62.0 + - - +
58i ASN* 4.9 3.4 - - - +
59i VAL* 2.8 52.6 + - + +
77i GLN* 5.2 0.7 - - - +
80i GLY 4.1 13.0 - - - +
81i LEU* 4.3 10.5 - - + +
84i ALA* 4.0 20.0 - - + -
125i ILE* 3.9 26.5 - - + -
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Residues in contact with ASN 56 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2178 A 4.8 4.6 + - - +
2188 T 4.1 35.8 + - - +
52i PHE* 2.9 17.5 + - - +
53i THR* 3.4 9.3 - - + +
55i VAL* 1.3 75.7 - - - +
57i GLU* 1.3 58.2 + - - +
60i SER* 2.9 31.4 + - - -
77i GLN* 3.1 21.0 + - - +
81i LEU* 3.3 30.0 - - - +
13j ARG* 4.0 22.2 - - - +
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Residues in contact with GLU 57 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53i THR* 3.0 14.2 + - + +
54i SER* 3.5 11.4 - - - +
56i ASN* 1.3 75.5 - - - +
58i ASN* 1.3 74.4 + - - +
60i SER* 3.2 8.4 + - - -
61i ALA* 3.0 23.3 + - + +
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Residues in contact with ASN 58 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54i SER* 3.0 23.6 + - - +
55i VAL* 4.1 3.5 - - - +
57i GLU* 1.3 90.0 - - - +
59i VAL* 1.3 62.6 + - - +
61i ALA* 3.2 10.3 + - - +
62i VAL* 3.2 25.6 + - - +
124i ILE* 3.7 27.9 - - + +
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Residues in contact with VAL 59 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55i VAL* 2.8 37.3 + - + +
58i ASN* 1.3 74.3 - - + +
60i SER* 1.3 66.3 + - - +
62i VAL* 3.1 8.6 + - - +
63i LEU* 2.9 33.6 + - + +
76i TYR 4.3 0.9 - - - +
77i GLN* 3.3 32.5 - - - +
80i GLY* 4.7 2.0 - - - -
121i VAL* 4.0 39.0 - - + +
124i ILE* 5.5 3.4 - - + -
125i ILE* 4.4 7.2 - - + -
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Residues in contact with SER 60 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2188 T 4.9 0.2 - - - -
2198 A 3.4 9.8 + - - -
56i ASN 2.9 22.0 + - - -
57i GLU* 3.4 9.9 - - - -
59i VAL* 1.3 76.5 - - - +
61i ALA* 1.3 63.1 + - - +
63i LEU* 3.1 3.0 + - - -
64i THR* 3.0 13.4 + - - -
73i ARG* 2.7 41.5 + - - +
77i GLN* 3.4 12.7 - - - +
89k ARG 4.7 2.6 + - - -
90k ILE 4.7 3.6 + - - -
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Residues in contact with ALA 61 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57i GLU* 3.0 15.8 + - + +
58i ASN* 3.4 13.0 - - - +
59i VAL 3.2 0.2 - - - -
60i SER* 1.3 74.6 - - - +
62i VAL* 1.3 64.5 + - + +
64i THR* 3.2 7.6 + - - -
65i GLN* 3.1 31.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58i ASN 3.2 13.2 + - - +
59i VAL* 3.1 11.8 + - + +
61i ALA* 1.3 78.4 - - + +
63i LEU* 1.3 69.4 + - + +
65i GLN* 2.9 23.3 + - - +
66i TYR* 3.0 39.1 + - + -
117i VAL* 5.3 0.7 - - + +
120i ALA* 4.0 16.8 - - + +
121i VAL* 4.8 6.1 - - + +
124i ILE* 3.6 32.5 - - + -
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Residues in contact with LEU 63 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59i VAL* 2.9 34.6 + - + +
60i SER* 3.1 6.9 + - - +
62i VAL* 1.3 79.4 - - + +
64i THR* 1.3 61.5 + - - +
66i TYR* 3.2 3.1 + - + +
67i GLY 3.0 4.2 + - - -
68i ILE* 2.9 43.9 + - + -
73i ARG* 3.5 49.6 - - + +
76i TYR* 3.6 34.1 - - + -
77i GLN* 4.0 9.2 - - + +
117i VAL* 4.1 11.0 - - + -
121i VAL* 5.1 1.1 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60i SER 3.0 5.4 + - - -
61i ALA* 3.6 10.9 - - - -
63i LEU* 1.3 77.0 - - - +
65i GLN* 1.3 63.9 + - + +
67i GLY 3.1 9.9 + - - -
73i ARG* 3.0 21.7 + - - +
90k ILE* 2.6 33.5 + - + +
91k GLY* 3.8 7.0 - - - +
92k SER 3.3 28.3 - - - +
93k GLY* 4.6 1.3 - - - -
94k PRO* 3.3 4.7 - - + +
95k ALA* 3.3 19.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61i ALA* 3.1 19.2 + - - +
62i VAL* 2.9 18.0 + - - +
64i THR* 1.3 78.4 - - + +
66i TYR* 1.3 66.0 + - + +
67i GLY 3.3 0.4 - - - -
94k PRO* 3.4 24.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62i VAL* 3.0 35.9 + - + +
63i LEU* 3.2 6.7 + - - +
65i GLN* 1.3 83.5 - - + +
67i GLY* 1.3 62.4 + - - +
68i ILE* 3.2 22.3 + - + +
116i GLN* 2.9 42.5 + - - -
117i VAL* 4.1 16.4 - - + -
120i ALA* 3.5 28.0 - - + +
94k 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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il