Contacts of the helix formed by residues 37 - 66 (chain k) 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 k).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247 T 3.9 22.7 - - - +
1257 A 3.9 4.7 - - - +
16j LYS* 4.7 10.8 - - + -
19j ALA* 3.7 17.7 - - + -
20j LYS* 3.6 30.1 - - + -
33k ILE 3.0 19.4 + - - +
34k LEU* 3.5 15.5 - - + +
36k ASN* 1.3 75.7 - - - +
38k SER* 1.3 68.7 + - - +
39k PRO* 3.5 1.3 - - - -
40k VAL* 3.9 7.4 - - + -
41k ALA* 2.9 21.2 + - + +
21l PHE* 4.5 9.0 - - + -
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Residues in contact with SER 38 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34k LEU 2.6 23.4 + - - -
35k SER* 3.3 15.5 - - - -
37k VAL* 1.3 80.4 - - - +
39k PRO* 1.4 72.8 - - - +
41k ALA* 2.9 10.4 + - - +
42k GLN* 2.9 26.4 + - - +
21l PHE* 3.5 22.8 - - - -
22l ASN* 5.5 2.3 + - - -
25l SER* 4.7 4.7 + - - -
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Residues in contact with PRO 39 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35k SER 4.0 3.8 - - - +
36k ASN 3.6 12.3 - - - +
37k VAL 3.5 1.8 - - - -
38k SER* 1.4 97.4 - - - +
40k VAL* 1.3 66.8 + - + +
42k GLN* 3.5 19.2 + - - +
43k GLN* 3.1 21.8 + - - +
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Residues in contact with VAL 40 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247 T 4.8 1.6 - - - +
12j GLN* 5.0 2.2 - - - +
15j ALA* 4.1 30.7 - - + +
16j LYS* 3.9 32.5 - - + +
19j ALA* 4.5 3.6 - - + -
36k ASN 4.3 13.5 - - - +
37k VAL* 3.5 12.1 - - + +
38k SER 3.0 0.4 + - - -
39k PRO* 1.3 78.5 - - + +
41k ALA* 1.3 67.2 + - - +
43k GLN* 3.1 9.3 + - - +
44k ASN* 3.1 32.2 + - - +
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Residues in contact with ALA 41 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237 A 3.9 4.4 - - - +
1247 T 3.5 38.4 - - - +
37k VAL 2.9 17.9 + - - +
38k SER 3.4 3.4 - - - +
40k VAL* 1.3 76.8 - - - +
42k GLN* 1.3 57.8 + - - +
44k ASN* 3.1 2.6 + - - +
45k PHE* 2.8 31.4 + - - +
17l TRP* 4.1 15.7 - - + -
21l PHE* 4.5 8.7 - - + -
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Residues in contact with GLN 42 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38k SER* 2.9 21.3 + - - +
39k PRO* 3.5 29.4 - - - +
41k ALA* 1.3 77.5 - - - +
43k GLN* 1.3 62.8 + - - +
45k PHE* 3.3 1.0 + - - +
46k GLN* 2.9 35.6 + - - +
14l TYR* 3.9 8.6 + - - +
17l TRP* 4.2 12.3 - - + -
18l GLN* 3.2 43.9 - - - +
21l PHE* 5.6 1.3 - - + -
22l ASN* 4.6 2.2 + - - -
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Residues in contact with GLN 43 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j GLN* 5.3 7.4 - - + +
39k PRO 3.1 9.9 + - - +
40k VAL* 3.3 11.4 - - - +
42k GLN* 1.3 79.2 - - - +
44k ASN* 1.3 61.4 + - - +
46k GLN* 3.7 12.0 + - - +
47k THR* 2.6 60.4 + - - +
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Residues in contact with ASN 44 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237 A 3.6 23.5 - - - +
1247 T 2.9 19.6 + - - -
8j ARG* 3.7 24.8 - - - +
12j GLN* 2.9 34.7 + - - +
16j LYS* 5.5 4.2 - - - +
40k VAL* 3.1 20.5 + - - +
41k ALA 3.1 7.2 + - - +
43k GLN* 1.3 76.5 - - - +
45k PHE* 1.3 66.0 + - - +
47k THR* 3.7 5.0 - - - -
48k ASN* 3.1 24.1 + - - +
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Residues in contact with PHE 45 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227 T 4.5 10.5 - - - -
1237 A 3.5 28.0 - - - -
2288 T 5.3 6.7 - - - -
41k ALA 2.8 16.1 + - - +
42k GLN 3.7 3.8 - - - +
44k ASN* 1.3 78.0 - - - +
46k GLN* 1.3 58.5 + - - +
49k VAL* 2.9 68.9 + - + +
10l TYR* 5.1 0.7 - + - -
13l ARG* 4.4 5.6 - - + -
14l TYR* 3.5 44.2 - + + -
17l TRP* 3.5 57.0 - + + -
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Residues in contact with GLN 46 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42k GLN* 2.9 28.3 + - - +
43k GLN* 3.8 13.9 + - - +
45k PHE* 1.3 79.3 - - - +
47k THR* 1.3 61.4 - - - +
50k PRO* 3.1 24.8 - - - +
10l TYR* 5.2 11.4 + - - +
14l TYR* 3.4 47.6 + - + -
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Residues in contact with THR 47 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12j GLN* 4.9 12.4 + - - +
43k GLN* 2.6 47.1 + - - +
44k ASN* 3.7 7.0 - - - -
45k PHE 3.2 0.4 - - - -
46k GLN* 1.3 79.0 - - - +
48k ASN* 1.3 72.1 + - - +
50k PRO* 4.3 2.3 - - - +
51k LYS* 3.4 23.6 - - - +
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Residues in contact with ASN 48 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227 T 3.8 18.1 + - - +
1237 A 3.0 21.2 + - - -
7j SER* 4.5 8.3 + - - -
8j ARG* 3.8 12.5 - - - +
12j GLN* 5.5 3.6 - - - +
44k ASN* 3.1 10.1 + - - +
47k THR* 1.3 87.2 - - - +
49k VAL* 1.3 67.5 + - - +
50k PRO* 3.4 1.6 - - - -
51k LYS* 2.9 49.1 + - + +
52k PHE* 3.4 12.4 - - + -
88k ASN* 4.9 5.6 + - - +
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Residues in contact with VAL 49 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227 T 3.6 32.8 - - + +
45k PHE* 2.9 58.8 + - + +
48k ASN* 1.3 74.7 - - - +
50k PRO* 1.3 63.2 - - + +
52k PHE* 2.9 27.1 + - + +
53k THR* 3.0 12.8 + - - +
10l TYR* 4.6 6.3 - - + -
13l ARG* 3.8 28.9 - - + +
----------------------------------------------------------
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Residues in contact with PRO 50 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45k PHE 3.8 1.1 - - - +
46k GLN 3.1 25.6 - - - +
47k THR 4.2 3.4 - - - +
48k ASN 3.4 2.9 - - - -
49k VAL* 1.3 97.2 - - + +
51k LYS* 1.3 59.2 + - + +
53k THR* 3.7 1.1 - - - -
54k SER* 3.2 24.3 + - - -
10l TYR* 3.7 47.8 - - + -
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Residues in contact with LYS 51 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47k THR* 3.4 23.8 + - - +
48k ASN* 2.9 37.2 + - - +
49k VAL 3.0 0.6 - - - -
50k PRO* 1.3 78.6 - - + +
52k PHE* 1.3 64.6 + - + +
54k SER* 2.9 18.3 + - - -
55k VAL* 3.3 13.0 - - - +
84k ALA* 5.5 0.7 - - - +
88k ASN* 3.9 26.8 + - - +
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Residues in contact with PHE 52 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1217 A 3.7 17.3 - - + -
1227 T 3.4 40.2 - - - +
48k ASN* 3.4 20.9 - - + -
49k VAL* 2.9 7.1 + - - +
51k LYS* 1.3 76.7 - - + +
53k THR* 1.3 67.2 + - - +
54k SER 3.2 1.6 - - - -
55k VAL* 3.1 7.2 + - - +
56k ASN* 2.9 27.9 + - - +
81k LEU* 3.7 29.8 - - + +
84k ALA* 3.6 26.5 - - + -
85k ARG* 3.6 15.0 - - - -
88k ASN* 3.3 31.4 - - - -
13l ARG* 5.0 5.8 - - - +
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Residues in contact with THR 53 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49k VAL* 3.0 7.7 + - - +
50k PRO 3.4 6.3 + - - -
52k PHE* 1.3 78.0 - - - +
54k SER* 1.3 62.6 + - - +
56k ASN* 3.1 9.0 + - + +
57k GLU* 3.0 23.4 + - + +
8l ARG 4.7 4.5 - - - +
9l SER* 4.2 6.7 - - - -
10l TYR* 3.1 46.2 - - + +
13l ARG* 2.7 29.2 + - - +
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Residues in contact with SER 54 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50k PRO 3.2 10.2 + - - -
51k LYS* 2.9 22.2 + - - -
53k THR* 1.3 80.1 - - - +
55k VAL* 1.3 59.2 + - - +
57k GLU* 3.4 6.3 + - - +
58k ASN* 3.0 40.6 + - - -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51k LYS 3.3 17.7 - - - +
52k PHE* 3.1 10.5 + - - +
53k THR 3.1 0.8 - - - -
54k SER* 1.3 77.6 + - - +
56k ASN* 1.3 61.6 + - - +
58k ASN* 4.9 2.9 - - - +
59k VAL* 2.8 52.7 + - + +
77k GLN* 5.2 1.3 - - - +
80k GLY 4.1 13.5 - - - -
81k LEU* 4.3 9.6 - - + +
84k ALA* 4.0 20.9 - - + -
125k ILE* 3.9 26.5 - - + -
----------------------------------------------------------
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Residues in contact with ASN 56 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2298 A 4.8 3.6 + - - +
2308 T 4.1 35.9 + - - +
52k PHE* 2.9 17.4 + - - +
53k THR* 3.1 8.8 + - + +
55k VAL* 1.3 75.1 - - - +
57k GLU* 1.3 57.6 + - - +
60k SER* 2.9 31.2 + - - -
77k GLN* 3.1 20.6 + - - +
81k LEU* 3.3 30.1 - - - +
13l ARG* 4.0 22.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53k THR* 3.0 14.6 + - + +
54k SER* 3.5 11.2 - - - +
55k VAL 3.1 0.2 - - - -
56k ASN* 1.3 76.2 - - - +
58k ASN* 1.3 74.4 + - - +
60k SER* 3.2 8.1 + - - -
61k ALA* 3.0 21.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 58 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54k SER* 3.0 24.4 + - - +
55k VAL* 4.1 3.1 - - - +
57k GLU* 1.3 89.1 - - - +
59k VAL* 1.3 62.0 + - + +
61k ALA* 3.2 9.1 + - - +
62k VAL* 3.2 25.2 + - - +
124k ILE* 3.7 26.8 - - + +
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Residues in contact with VAL 59 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55k VAL* 2.8 37.7 + - + +
58k ASN* 1.3 74.9 - - + +
60k SER* 1.3 66.2 + - - +
62k VAL* 3.1 9.3 + - - +
63k LEU* 2.9 33.5 + - + +
76k TYR 4.3 1.3 - - - +
77k GLN* 3.3 32.8 - - - +
80k GLY* 4.7 1.8 - - - -
121k VAL* 4.0 39.0 - - + +
124k ILE* 5.5 2.7 - - + -
125k ILE* 4.4 7.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 60 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2308 T 4.9 0.4 - - - -
2318 A 3.4 10.2 + - - -
56k ASN 2.9 21.3 + - - -
57k GLU* 3.4 9.4 - - - -
59k VAL* 1.3 76.7 - - - +
61k ALA* 1.3 63.1 + - - +
63k LEU* 3.1 2.8 + - - -
64k THR* 3.0 12.9 + - - -
73k ARG* 2.7 41.6 + - - +
77k GLN* 3.4 12.3 - - - +
89m ARG 4.7 2.6 + - - -
90m ILE 4.7 3.5 + - - -
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Residues in contact with ALA 61 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57k GLU* 3.0 16.0 + - + +
58k ASN* 3.4 13.7 - - - +
59k VAL 3.2 0.2 - - - -
60k SER* 1.3 76.3 - - - +
62k VAL* 1.3 63.4 + - + +
64k THR* 3.2 7.4 + - - -
65k GLN* 3.1 31.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58k ASN 3.4 12.6 - - - +
59k VAL* 3.1 11.8 + - + +
61k ALA* 1.3 77.6 - - + +
63k LEU* 1.3 69.3 + - + +
65k GLN* 2.9 24.3 + - - +
66k TYR* 3.0 39.9 + - + -
117k VAL* 5.3 0.9 - - + +
120k ALA* 4.0 17.7 - - + +
121k VAL* 4.8 6.1 - - + +
124k ILE* 3.6 32.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59k VAL* 2.9 35.7 + - + +
60k SER* 3.1 7.6 + - - +
62k VAL* 1.3 77.7 - - + +
64k THR* 1.3 61.7 + - - +
66k TYR* 3.2 3.0 + - - +
67k GLY 3.0 4.5 + - - -
68k ILE* 2.9 42.5 + - + +
73k ARG* 3.5 48.5 - - + +
76k TYR* 3.6 34.5 - - + -
77k GLN* 4.0 9.4 - - + +
117k VAL* 4.1 11.0 - - + -
121k VAL* 5.1 0.9 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60k SER 3.0 5.8 + - - -
61k ALA* 3.6 10.5 - - - -
63k LEU* 1.3 77.7 - - - +
65k GLN* 1.3 62.0 + - + +
67k GLY 3.1 9.9 + - - -
73k ARG* 3.0 22.4 + - - +
90m ILE* 2.6 33.5 + - + +
91m GLY* 3.8 7.9 - - - +
92m SER 3.3 28.5 - - - +
93m GLY* 4.6 1.1 - - - -
94m PRO* 3.3 4.7 - - + +
95m ALA* 3.3 19.2 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61k ALA* 3.1 18.9 + - - +
62k VAL* 2.9 16.6 + - - +
64k THR* 1.3 77.7 - - + +
66k TYR* 1.3 66.1 + - + +
67k GLY 3.3 0.4 - - - -
94m PRO* 3.4 24.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62k VAL* 3.0 37.0 + - + +
63k LEU* 3.2 6.9 + - - +
65k GLN* 1.3 84.1 - - + +
67k GLY* 1.3 62.0 + - - +
68k ILE* 3.2 21.9 + - + +
116k GLN* 2.9 43.3 + - - -
117k VAL* 4.1 15.3 - - + -
120k ALA* 3.5 27.6 - - + +
94m 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