Contacts of the helix formed by residues 37 - 66 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287 T 3.9 22.2 - - - +
3297 A 3.9 5.2 - - - +
16B LYS* 4.7 10.5 - - + -
19B ALA* 3.7 18.6 - - + -
20B LYS* 3.6 30.3 - - + -
33C ILE 3.0 20.3 + - - +
34C LEU* 3.5 15.3 - - + +
36C ASN* 1.3 76.2 - - - +
38C SER* 1.3 69.3 + - - +
39C PRO* 3.5 1.6 - - - -
40C VAL* 3.3 9.2 + - + +
41C ALA* 2.9 20.0 + - + +
21D PHE* 4.5 9.2 - - + -
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU 2.6 23.1 + - - -
35C SER* 3.3 15.5 - - - -
37C VAL* 1.3 81.7 - - - +
39C PRO* 1.4 71.6 - - - +
41C ALA* 2.9 10.4 + - - +
42C GLN* 2.9 27.2 + - - +
21D PHE* 3.5 21.7 - - - -
22D ASN* 5.5 2.0 + - - -
25D SER* 4.7 4.7 + - - -
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Residues in contact with PRO 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C SER 4.0 4.0 - - - +
36C ASN 3.6 12.3 - - - +
37C VAL 3.5 1.8 - - - -
38C SER* 1.4 98.4 - - - +
40C VAL* 1.3 68.0 + - + +
42C GLN* 3.5 19.4 - - + +
43C GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287 T 4.8 1.6 - - - +
12B GLN* 5.0 2.2 - - - +
15B ALA* 4.1 30.3 - - + +
16B LYS* 3.9 32.8 - - + +
19B ALA* 4.5 3.6 - - + -
36C ASN 4.3 13.5 - - - +
37C VAL* 3.5 13.5 - - + +
38C SER 3.0 0.8 + - - -
39C PRO* 1.3 78.8 - - + +
41C ALA* 1.3 67.2 + - - +
43C GLN* 3.1 9.8 + - - +
44C ASN* 3.1 31.6 + - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3277 A 3.9 4.6 - - - +
3287 T 3.5 38.6 + - - +
37C VAL 2.9 18.2 + - - +
38C SER 3.4 3.6 - - - +
40C VAL* 1.3 77.0 - - - +
42C GLN* 1.3 58.8 + - - +
44C ASN* 3.1 2.9 + - - +
45C PHE* 2.8 30.7 + - - +
17D TRP* 4.1 15.7 - - + -
21D PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER* 2.9 20.6 + - - +
39C PRO* 3.5 30.1 - - - +
40C VAL 3.1 0.2 - - - -
41C ALA* 1.3 76.6 - - - +
43C GLN* 1.3 62.8 + - - +
45C PHE* 3.7 0.9 - - - +
46C GLN* 2.9 35.5 + - - +
14D TYR* 3.9 9.4 + - - +
17D TRP* 4.2 12.3 - - + -
18D GLN* 3.2 41.8 - - - +
21D PHE* 5.6 0.9 - - + -
22D ASN* 4.6 2.2 + - - -
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Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 5.3 7.9 - - + +
39C PRO 3.1 10.6 + - - +
40C VAL* 3.3 12.1 - - - +
42C GLN* 1.3 79.8 - - - +
44C ASN* 1.3 60.7 + - - +
46C GLN* 3.7 11.6 + - - +
47C THR* 2.6 60.5 + - - +
43f GLN* 3.1 40.1 - - - +
11g SER* 5.1 10.3 - - - -
12g GLN* 6.1 2.6 - - - +
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Residues in contact with ASN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3277 A 3.6 23.5 - - - +
3287 T 2.9 20.2 + - - -
8B ARG* 3.7 25.3 - - - +
12B GLN* 2.9 34.5 + - - +
16B LYS* 5.5 3.4 - - - +
40C VAL* 3.1 20.7 + - - +
41C ALA 3.1 7.9 + - - +
43C GLN* 1.3 76.4 - - - +
45C PHE* 1.3 64.4 + - - +
47C THR* 3.7 4.9 - - - -
48C ASN* 3.1 24.4 + - - +
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Residues in contact with PHE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3267 T 4.5 10.5 - - - -
3277 A 3.5 27.5 - - - -
248 T 5.3 6.1 - - - -
41C ALA 2.8 16.1 + - - +
42C GLN 3.7 4.0 - - - +
44C ASN* 1.3 77.1 - - - +
46C GLN* 1.3 57.9 + - - +
49C VAL* 2.9 69.2 + - + +
10D TYR* 5.1 0.9 - + - -
13D ARG* 4.4 6.1 - - + -
14D TYR* 3.5 44.4 - + + -
17D TRP* 3.5 57.0 - + + -
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Residues in contact with GLN 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 2.9 27.3 + - - +
43C GLN* 3.8 12.1 + - - +
45C PHE* 1.3 78.9 - - - +
47C THR* 1.3 63.8 + - - +
50C PRO* 3.1 22.5 - - - +
10D TYR* 5.2 9.4 + - - +
14D TYR* 3.4 48.3 + - + -
11g SER* 2.8 30.3 + - - +
14g TYR* 6.2 1.6 - - - -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 4.9 12.4 + - - +
43C GLN* 2.6 47.0 + - - +
44C ASN* 3.7 6.9 - - - -
45C PHE 3.2 0.2 - - - -
46C GLN* 1.3 79.8 - - - +
48C ASN* 1.3 71.1 + - - +
50C PRO* 4.3 2.6 - - - +
51C LYS* 3.4 24.5 - - - +
9g SER* 5.5 11.7 - - - +
11g SER* 4.1 6.4 - - - -
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3267 T 3.8 17.7 + - - +
3277 A 3.0 21.0 + - - -
7B SER* 4.5 8.1 + - - -
8B ARG* 3.8 12.9 - - - +
12B GLN* 5.5 4.0 - - - +
44C ASN* 3.1 10.3 + - - +
47C THR* 1.3 86.6 - - - +
49C VAL* 1.3 67.6 + - - +
50C PRO* 3.4 1.6 - - - -
51C LYS* 2.9 49.0 + - + +
52C PHE* 3.4 12.3 - - + -
88C ASN* 4.9 6.0 + - - -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3267 T 3.6 33.7 - - + +
45C PHE* 2.9 57.7 + - + +
48C ASN* 1.3 74.4 - - - +
50C PRO* 1.3 64.8 - - + +
52C PHE* 2.9 26.0 + - + +
53C THR* 3.0 12.3 + - - +
10D TYR* 4.6 6.7 - - + -
13D ARG* 3.8 30.7 + - + +
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Residues in contact with PRO 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE 3.8 0.7 - - - +
46C GLN 3.1 26.2 - - - +
47C THR 4.2 2.0 - - - +
48C ASN 3.4 3.1 - - - +
49C VAL* 1.3 97.4 - - + +
51C LYS* 1.3 61.4 + - + +
53C THR* 3.7 1.3 - - - +
54C SER* 3.2 24.1 + - - -
10D TYR* 3.7 47.3 - - + -
10g TYR* 4.9 13.2 - - + -
11g SER* 4.8 2.2 - - - +
50h PRO* 5.8 1.8 - - + -
54h SER* 5.3 1.2 - - - -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.4 24.2 + - - +
48C ASN* 2.9 36.4 + - - +
49C VAL 3.0 0.4 - - - -
50C PRO* 1.3 78.4 - - + +
52C PHE* 1.3 64.1 + - + +
54C SER* 2.9 19.2 + - - -
55C VAL* 3.3 12.5 - - - +
84C ALA* 5.5 1.0 - - - +
88C ASN* 3.9 27.0 + - - +
9g SER* 6.0 5.4 - - - -
57h GLU* 4.2 27.4 - - - +
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Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3257 A 3.7 16.2 - - + +
3267 T 3.4 40.4 - - - +
48C ASN* 3.4 20.2 - - + -
49C VAL* 2.9 7.6 + - - +
51C LYS* 1.3 76.3 - - + +
53C THR* 1.3 65.7 + - - +
54C SER 3.2 1.1 - - - -
55C VAL* 3.1 7.0 + - + +
56C ASN* 2.9 27.5 + - - +
81C LEU* 3.7 29.9 - - + +
84C ALA* 3.6 25.8 - - + -
85C ARG* 3.6 14.6 - - - -
88C ASN* 3.3 30.3 - - - -
13D ARG* 4.5 6.3 - - - +
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 3.0 7.1 + - - +
50C PRO 3.4 6.0 + - - -
52C PHE* 1.3 77.6 - - - +
54C SER* 1.3 63.4 + - - +
56C ASN* 3.1 8.0 + - + +
57C GLU* 3.0 23.0 + - + +
8D ARG 4.7 5.2 - - - +
9D SER* 4.2 6.3 - - - -
10D TYR* 3.1 47.0 - - + +
13D ARG* 2.7 29.9 + - - +
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C PRO 3.2 10.5 + - - -
51C LYS* 2.9 22.0 + - - -
53C THR* 1.3 78.6 - - - +
55C VAL* 1.3 57.3 + - - +
57C GLU* 3.4 6.9 + - - +
58C ASN* 3.0 39.2 + - - -
54h SER* 3.3 35.5 - - - -
57h GLU* 5.7 0.7 + - - -
58h ASN* 5.5 4.2 + - - -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LYS 3.3 17.9 - - - +
52C PHE* 3.1 9.8 + - - +
53C THR 3.1 0.4 - - - -
54C SER* 1.3 77.3 + - - +
56C ASN* 1.3 61.2 + - - +
58C ASN* 3.3 3.5 + - - +
59C VAL* 2.8 52.4 + - + +
77C GLN* 5.2 0.7 - - - +
80C GLY 4.1 13.7 - - - +
81C LEU* 4.3 10.1 - - + -
84C ALA* 4.0 20.0 - - + -
125C ILE* 3.9 26.5 - - + -
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Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 A 4.8 4.4 + - - +
268 T 4.1 36.5 + - - +
52C PHE* 2.9 18.0 + - - +
53C THR* 3.4 9.7 - - + +
55C VAL* 1.3 75.7 - - - +
57C GLU* 1.3 57.3 + - - +
60C SER* 2.9 30.8 + - - -
77C GLN* 3.1 21.2 + - - +
81C LEU* 3.3 30.6 - - - +
13D ARG* 4.0 21.8 - - - +
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C THR* 3.0 14.0 + - + +
54C SER* 3.5 11.7 - - - +
56C ASN* 1.3 76.0 - - - +
58C ASN* 1.3 74.6 + - - +
60C SER* 3.2 8.6 + - - -
61C ALA* 3.0 23.4 + - + +
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Residues in contact with ASN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.0 22.8 + - - +
55C VAL* 4.1 3.5 - - - +
57C GLU* 1.3 89.1 - - - +
59C VAL* 1.3 64.0 + - + +
61C ALA* 3.2 9.9 + - - +
62C VAL* 3.2 24.5 + - - +
124C ILE* 3.7 25.6 - - + +
54h SER* 5.3 4.6 + - - -
58h ASN* 4.2 19.6 - - - +
124h ILE* 4.7 9.6 + - - +
125h ILE* 4.8 9.7 - - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 2.8 37.5 + - + +
58C ASN* 1.3 74.1 - - + +
60C SER* 1.3 66.4 + - - +
62C VAL* 3.1 9.6 + - - +
63C LEU* 2.9 32.8 + - + +
76C TYR 4.3 1.3 - - - +
77C GLN* 3.3 32.8 - - - +
80C GLY* 4.7 1.6 - - - -
121C VAL* 4.0 37.7 - - + +
124C ILE* 5.5 2.9 - - + -
125C ILE* 4.4 7.6 - - + -
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Residues in contact with SER 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 T 4.9 0.7 - - - -
278 A 3.4 9.2 + - - -
56C ASN 2.9 22.9 + - - -
57C GLU* 3.4 10.1 - - - -
59C VAL* 1.3 75.9 - - - +
61C ALA* 1.3 63.3 + - - +
63C LEU* 3.1 3.0 + - - -
64C THR* 3.0 13.2 + - - -
73C ARG* 2.7 40.5 + - - +
77C GLN* 3.4 12.9 - - - +
89E ARG 4.7 2.6 + - - -
90E ILE 4.7 3.9 + - - -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 3.0 15.2 + - - +
58C ASN* 3.4 13.0 - - - +
59C VAL 3.2 0.2 - - - -
60C SER* 1.3 76.6 - - - +
62C VAL* 1.3 63.5 + - + +
64C THR* 3.2 7.8 + - - -
65C GLN* 3.1 31.1 + - - +
125h ILE 6.1 0.7 - - - +
126h THR 5.7 3.6 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN 3.2 13.4 + - - +
59C VAL* 3.1 12.1 + - + +
61C ALA* 1.3 78.4 - - + +
63C LEU* 1.3 69.3 + - + +
65C GLN* 2.9 24.0 + - - +
66C TYR* 3.0 39.5 + - + -
117C VAL* 5.3 0.9 - - + +
120C ALA* 4.0 16.8 - - + +
121C VAL* 4.8 6.3 - - + +
124C ILE* 3.6 32.1 - - + -
126h THR 5.4 4.9 - - - +
127h GLY* 5.7 0.7 - - - -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 2.9 34.8 + - + +
60C SER* 3.1 7.2 + - - +
62C VAL* 1.3 78.5 - - + +
64C THR* 1.3 62.0 + - - +
66C TYR* 3.2 2.6 + - - +
67C GLY 3.0 4.2 + - - -
68C ILE* 2.9 43.2 + - + -
73C ARG* 3.5 49.4 - - + +
76C TYR* 3.6 34.8 - - + -
77C GLN* 4.0 9.4 - - + +
117C VAL* 4.1 11.0 - - + -
121C VAL* 5.1 0.7 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C SER 3.0 5.1 + - - -
61C ALA* 3.6 11.6 - - - -
63C LEU* 1.3 77.6 - - - +
65C GLN* 1.3 61.2 + - + +
67C GLY 3.1 10.2 + - - -
73C ARG* 3.0 21.4 + - - +
90E ILE* 2.6 33.8 + - + +
91E GLY 3.7 7.2 - - - +
92E SER 3.3 27.8 - - - +
93E GLY* 4.6 1.3 - - - -
94E PRO* 3.3 4.8 - - + +
95E ALA* 3.3 19.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 3.1 19.1 + - - +
62C VAL* 2.9 17.1 + - - +
64C THR* 1.3 78.6 - - + +
66C TYR* 1.3 66.3 + - + +
67C GLY 3.3 0.2 - - - -
94E PRO* 3.4 24.1 - - + +
92h SER* 5.8 5.7 - - - -
126h THR* 3.9 22.1 + - - +
127h GLY 5.8 0.7 - - - -
128h SER* 4.9 4.9 + - - -
134h SER* 3.7 31.3 + - - +
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Residues in contact with TYR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.0 36.8 + - + +
63C LEU* 3.2 6.2 + - - +
65C GLN* 1.3 83.9 - - + +
67C GLY* 1.3 62.4 + - - +
68C ILE* 3.2 22.7 + - + +
116C GLN* 2.9 42.5 + - - -
117C VAL* 4.1 17.5 - - + -
120C ALA* 3.5 27.9 - - + +
94E PRO* 4.6 0.7 - - - -
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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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