Contacts of the helix formed by residues 37 - 66 (chain o) 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 o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007 T 3.9 22.0 - - - +
1017 A 3.9 5.2 - - - +
16n LYS* 4.7 11.2 - - + -
19n ALA* 3.7 17.9 - - + -
20n LYS* 3.6 30.3 - - + -
33o ILE 3.0 19.8 + - - +
34o LEU* 3.5 15.3 - - + +
36o ASN* 1.3 76.3 - - - +
38o SER* 1.3 68.3 + - - +
39o PRO* 3.5 1.6 - - - -
40o VAL* 3.3 8.3 + - + +
41o ALA* 2.9 20.4 + - + +
21p PHE* 4.5 9.0 - - + -
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Residues in contact with SER 38 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34o LEU 2.6 23.3 + - - -
35o SER* 3.3 15.4 - - - -
37o VAL* 1.3 81.6 - - - +
39o PRO* 1.4 72.8 - - - +
41o ALA* 2.9 10.0 + - - +
42o GLN* 2.9 26.5 + - - +
21p PHE* 3.5 22.0 - - - -
22p ASN* 5.5 2.5 + - - -
25p SER* 4.7 4.5 + - - -
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Residues in contact with PRO 39 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35o SER 4.0 4.0 - - - +
36o ASN 3.6 12.1 - - - +
37o VAL 3.5 2.0 - - - -
38o SER* 1.4 96.7 - - - +
40o VAL* 1.3 68.1 + - + +
42o GLN* 3.5 19.0 + - - +
43o GLN* 3.1 21.5 + - - +
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Residues in contact with VAL 40 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007 T 4.8 1.6 - - - +
12n GLN* 5.0 2.0 - - - +
15n ALA* 4.1 30.5 - - + +
16n LYS* 3.9 31.4 - - + +
19n ALA* 4.5 3.6 - - + -
36o ASN 4.3 13.9 - - - +
37o VAL* 3.5 12.3 - - + +
38o SER 3.0 0.8 - - - -
39o PRO* 1.3 79.4 - - + +
41o ALA* 1.3 67.2 + - - +
43o GLN* 3.1 9.7 + - - +
44o ASN* 3.1 32.0 + - - +
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Residues in contact with ALA 41 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997 A 3.9 4.8 - - - +
1007 T 3.5 38.6 - - - +
37o VAL 2.9 17.1 + - - +
38o SER 3.4 4.0 - - - +
40o VAL* 1.3 76.5 - - - +
42o GLN* 1.3 58.1 + - - +
44o ASN* 3.1 2.3 + - - +
45o PHE* 2.8 31.0 + - - +
17p TRP* 4.2 14.8 - - + -
21p PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 42 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38o SER* 2.9 21.7 + - - +
39o PRO* 3.5 29.3 - - - +
41o ALA* 1.3 75.6 - - - +
43o GLN* 1.3 62.3 + - - +
45o PHE* 3.3 0.9 + - - +
46o GLN* 2.9 35.9 + - - +
14p TYR* 3.9 8.3 + - - +
17p TRP* 4.2 13.2 - - + -
18p GLN* 3.2 42.1 - - - +
21p PHE* 5.8 1.1 - - + -
22p ASN* 4.6 2.6 + - - -
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Residues in contact with GLN 43 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12n GLN* 5.3 7.0 - - + +
39o PRO 3.1 10.4 + - - +
40o VAL* 3.3 11.4 - - + +
42o GLN* 1.3 79.7 - - - +
44o ASN* 1.3 60.2 + - - +
46o GLN* 3.7 13.0 + - - +
47o THR* 2.6 61.4 + - - +
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Residues in contact with ASN 44 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997 A 3.6 24.6 - - - +
1007 T 2.9 20.0 + - - -
8n ARG* 3.7 25.2 - - - +
12n GLN* 2.9 34.4 + - - +
16n LYS* 5.5 3.8 - - - +
40o VAL* 3.1 20.3 + - - +
41o ALA 3.1 7.0 + - - +
43o GLN* 1.3 76.2 - - - +
45o PHE* 1.3 65.2 + - - +
47o THR* 3.7 4.0 - - - -
48o ASN* 3.1 25.2 + - - +
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Residues in contact with PHE 45 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987 T 4.5 11.0 - - - -
997 A 3.5 27.7 - - - -
2528 T 5.3 5.4 - - - -
41o ALA 2.8 16.8 + - - +
42o GLN 3.7 3.4 - - - +
44o ASN* 1.3 77.4 - - - +
46o GLN* 1.3 58.8 + - - +
49o VAL* 2.9 69.3 + - + +
10p TYR* 5.1 0.4 - + - -
13p ARG* 4.4 6.3 - - + -
14p TYR* 3.5 44.0 - + + -
17p TRP* 3.5 57.0 - + + -
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Residues in contact with GLN 46 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42o GLN* 2.9 27.6 + - - +
43o GLN* 3.8 13.7 + - - +
45o PHE* 1.3 79.2 - - - +
47o THR* 1.3 63.6 + - - +
50o PRO* 3.1 25.8 - - - +
10p TYR* 5.2 11.2 + - - +
14p TYR* 3.4 47.8 + - + -
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Residues in contact with THR 47 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12n GLN* 4.9 12.6 + - - +
43o GLN* 2.6 46.2 + - - +
44o ASN* 3.7 6.7 - - - -
45o PHE 3.2 0.2 - - - -
46o GLN* 1.3 80.0 - - - +
48o ASN* 1.3 72.1 + - - +
50o PRO* 4.3 2.1 - - - +
51o LYS* 3.4 24.0 - - - +
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Residues in contact with ASN 48 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987 T 3.8 18.6 + - - +
997 A 3.0 20.6 + - - -
7n SER* 4.5 8.3 + - - -
8n ARG* 3.8 13.3 - - - +
12n GLN* 5.5 3.6 - - - +
44o ASN* 3.1 10.3 + - - +
47o THR* 1.3 87.5 - - - +
49o VAL* 1.3 67.4 + - - +
50o PRO* 3.4 1.6 - - - -
51o LYS* 2.9 48.9 + - + +
52o PHE* 3.4 12.4 - - + -
88o ASN* 4.9 5.4 + - - -
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Residues in contact with VAL 49 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987 T 3.6 32.8 - - + +
45o PHE* 2.9 57.9 + - + +
48o ASN* 1.3 74.6 - - - +
50o PRO* 1.3 64.4 - - + +
51o LYS 3.0 0.2 - - - -
52o PHE* 2.9 26.3 + - + +
53o THR* 3.0 12.9 + - - +
10p TYR* 4.6 6.3 - - + -
13p ARG* 3.8 28.9 - - + +
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Residues in contact with PRO 50 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45o PHE 3.8 0.9 - - - +
46o GLN 3.1 26.0 - - - +
47o THR 4.2 2.5 - - - +
48o ASN 3.4 3.4 - - - +
49o VAL* 1.3 95.9 - - + +
51o LYS* 1.3 61.1 + - + +
53o THR* 3.7 1.9 - - - +
54o SER* 3.2 24.4 + - - -
10p TYR* 3.7 48.2 - - + -
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Residues in contact with LYS 51 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47o THR* 3.4 24.3 + - - +
48o ASN* 2.9 37.4 + - - +
49o VAL 3.0 0.6 - - - -
50o PRO* 1.3 78.4 - - + +
52o PHE* 1.3 63.4 + - + +
54o SER* 2.9 19.5 + - - -
55o VAL* 3.3 12.6 - - - +
84o ALA* 5.5 1.0 - - - +
88o ASN* 3.9 26.6 + - - +
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Residues in contact with PHE 52 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977 A 3.7 16.4 - - + -
987 T 3.4 40.4 - - - +
48o ASN* 3.4 20.6 - - + -
49o VAL* 2.9 7.2 + - + +
51o LYS* 1.3 76.9 - - + +
53o THR* 1.3 66.8 + - - +
54o SER 3.2 1.3 - - - -
55o VAL* 3.1 7.2 + - - +
56o ASN* 2.9 27.8 + - - +
81o LEU* 3.7 29.6 - - + +
84o ALA* 3.6 27.1 - - + -
85o ARG* 3.6 14.1 - - - -
88o ASN* 3.3 31.4 - - - -
13p ARG* 5.0 5.6 - - - +
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Residues in contact with THR 53 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49o VAL* 3.0 7.8 + - - +
50o PRO 3.4 6.0 + - - -
52o PHE* 1.3 77.4 - - - +
54o SER* 1.3 63.5 + - - +
56o ASN* 3.1 8.0 + - + +
57o GLU* 3.0 23.4 + - + +
8p ARG 4.7 4.5 - - - +
9p SER* 4.2 6.1 - - - -
10p TYR* 3.1 45.9 - - + +
13p ARG* 2.7 29.3 + - - +
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Residues in contact with SER 54 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50o PRO 3.2 11.7 + - - -
51o LYS* 2.9 21.8 + - - -
53o THR* 1.3 78.7 - - - +
55o VAL* 1.3 58.4 + - - +
57o GLU* 3.4 6.1 + - - +
58o ASN* 3.0 41.1 + - - -
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Residues in contact with VAL 55 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51o LYS 3.3 17.5 - - - +
52o PHE* 3.1 11.6 + - - +
53o THR 3.1 0.6 - - - -
54o SER* 1.3 77.6 + - - +
56o ASN* 1.3 61.3 + - - +
58o ASN* 4.9 3.1 - - - +
59o VAL* 2.8 52.1 + - + +
77o GLN* 5.2 1.1 - - - +
80o GLY 4.1 13.7 - - - +
81o LEU* 4.3 9.6 - - + -
84o ALA* 4.0 20.9 - - + -
125o ILE* 3.9 27.1 - - + -
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Residues in contact with ASN 56 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2538 A 4.8 4.4 + - - +
2548 T 4.1 35.9 + - - +
52o PHE* 2.9 17.6 + - - +
53o THR* 3.4 9.3 - - + +
55o VAL* 1.3 74.7 - - - +
57o GLU* 1.3 57.1 + - - +
60o SER* 2.9 31.2 + - - -
77o GLN* 3.1 21.0 + - - +
81o LEU* 3.3 30.2 - - - +
13p ARG* 4.0 22.0 - - - +
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Residues in contact with GLU 57 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53o THR* 3.0 14.4 + - + +
54o SER* 3.5 11.9 - - - +
56o ASN* 1.3 74.9 - - - +
58o ASN* 1.3 74.3 + - - +
60o SER* 3.2 8.4 + - - -
61o ALA* 3.0 23.8 + - + +
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Residues in contact with ASN 58 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54o SER* 3.0 22.5 + - - +
55o VAL* 4.1 4.0 - - - +
57o GLU* 1.3 89.0 - - - +
59o VAL* 1.3 62.9 + - + +
61o ALA* 3.2 9.5 + - - +
62o VAL* 3.2 25.3 + - - +
124o ILE* 3.7 26.1 - - + +
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Residues in contact with VAL 59 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55o VAL* 2.8 36.2 + - + +
58o ASN* 1.3 74.7 - - + +
60o SER* 1.3 66.2 + - - +
62o VAL* 3.1 9.2 + - - +
63o LEU* 2.9 33.7 + - + +
76o TYR 4.3 1.1 - - - +
77o GLN* 3.3 32.3 - - - +
80o GLY* 4.7 1.8 - - - -
121o VAL* 4.0 38.6 - - + +
124o ILE* 5.5 2.7 - - + -
125o ILE* 4.4 7.6 - - + -
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Residues in contact with SER 60 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2548 T 4.9 0.2 - - - -
2558 A 3.4 10.1 + - - -
56o ASN 2.9 21.6 + - - -
57o GLU* 3.4 10.1 - - - -
59o VAL* 1.3 76.5 - - - +
61o ALA* 1.3 61.3 + - - +
63o LEU* 3.1 2.8 + - - -
64o THR* 3.0 13.4 + - - -
73o ARG* 2.7 41.1 + - - +
77o GLN* 3.4 13.6 - - - +
89q ARG 4.7 2.4 + - - -
90q ILE 4.7 3.9 + - - -
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Residues in contact with ALA 61 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57o GLU* 3.0 16.0 + - + +
58o ASN* 3.4 13.2 - - - +
59o VAL 3.2 0.4 - - - -
60o SER* 1.3 76.0 - - - +
62o VAL* 1.3 62.9 + - + +
64o THR* 3.2 7.3 + - - -
65o GLN* 3.1 31.5 + - - +
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Residues in contact with VAL 62 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58o ASN 3.2 13.2 + - - +
59o VAL* 3.1 11.8 + - + +
61o ALA* 1.3 77.3 - - + +
63o LEU* 1.3 68.7 + - + +
65o GLN* 2.9 23.7 + - - +
66o TYR* 3.0 38.9 + - + -
117o VAL* 5.3 1.1 - - + +
120o ALA* 4.0 16.8 - - + +
121o VAL* 4.8 6.5 - - + +
124o ILE* 3.6 32.3 - - + -
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Residues in contact with LEU 63 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59o VAL* 2.9 34.3 + - + +
60o SER* 3.5 7.2 - - - +
62o VAL* 1.3 78.8 - - + +
64o THR* 1.3 63.1 + - - +
66o TYR* 3.2 3.3 + - - +
67o GLY 3.0 4.5 + - - -
68o ILE* 2.9 41.8 + - + +
73o ARG* 3.5 48.7 - - + +
76o TYR* 3.6 34.8 - - + -
77o GLN* 4.0 9.4 - - + +
117o VAL* 4.1 10.5 - - + -
121o VAL* 5.1 0.9 - - + -
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Residues in contact with THR 64 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60o SER 3.0 6.5 + - - -
61o ALA* 3.6 10.2 - - - -
63o LEU* 1.3 77.4 - - - +
65o GLN* 1.3 62.3 + - + +
67o GLY 3.1 9.7 + - - -
73o ARG* 3.0 21.2 + - - +
90q ILE* 2.6 34.0 + - + +
91q GLY 3.7 7.2 - - - +
92q SER 3.3 28.0 - - - +
93q GLY* 4.6 1.6 - - - -
94q PRO* 3.3 4.8 - - + +
95q ALA* 3.3 19.1 + - + +
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Residues in contact with GLN 65 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61o ALA* 3.1 19.7 + - - +
62o VAL* 2.9 18.4 + - - +
64o THR* 1.3 77.1 - - + +
66o TYR* 1.3 66.7 + - + +
67o GLY 3.3 0.2 - - - -
94q PRO* 3.4 24.9 - - + +
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Residues in contact with TYR 66 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62o VAL* 3.0 35.8 + - + -
63o LEU* 3.2 6.9 + - - +
65o GLN* 1.3 84.6 - - + +
67o GLY* 1.3 62.2 + - - +
68o ILE* 3.2 21.6 + - + +
116o GLN* 2.9 42.8 + - - -
117o VAL* 4.1 15.5 - - + -
120o ALA* 3.5 27.6 - - + +
94q 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