Contacts of the helix formed by residues 24 - 50 (chain A) in PDB entry 2Q1V
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 THR 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.0 22.1 + - + +
23A ASP* 1.3 78.0 - - - +
25A THR* 1.3 65.6 + - - +
26A ASN* 3.6 15.0 + - - +
27A TYR* 3.1 23.4 + - - +
28A LEU* 2.9 21.8 + - - +
105A GLN* 4.2 2.5 - - - -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 1.3 73.5 - - - +
26A ASN* 1.3 71.0 + - - +
28A LEU* 3.3 2.0 + - - -
29A LEU* 2.9 44.3 + - + +
105A GLN* 2.6 25.2 + - - -
106A SER 3.3 22.2 - - - +
107A ALA* 3.6 17.5 - - + +
204A PHE* 5.8 0.2 - - + -
217A VAL* 5.9 1.1 - - + -
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.2 15.2 + - - +
25A THR* 1.3 83.6 + - - +
27A TYR* 1.3 56.0 + - - +
29A LEU* 4.2 0.7 - - - +
30A SER* 2.7 37.2 + - - -
215A LEU 2.8 28.5 + - - -
216A SER* 3.6 22.4 - - - +
217A VAL* 4.8 6.6 - - - +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 5.2 0.3 + - - -
17A TYR* 3.3 30.7 - + - -
18A ASP* 3.0 38.9 + - - +
21A GLN* 3.6 27.1 - - + +
22A PRO 3.5 22.2 - - - +
23A ASP* 4.2 4.3 - - - -
24A THR* 3.1 16.6 + - - +
26A ASN* 1.3 77.0 - - - +
28A LEU* 1.3 58.6 + - - +
30A SER* 4.5 2.2 - - - -
31A SER* 2.7 50.7 + - - -
34A ARG* 3.7 18.2 - - - -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 4.7 8.7 - - + -
23A ASP* 3.6 45.5 - - + +
24A THR 2.9 20.8 + - - +
25A THR* 3.9 3.4 - - - +
27A TYR* 1.3 76.7 - - - +
29A LEU* 1.3 57.7 + - - +
31A SER* 3.2 5.5 + - - -
32A LEU* 2.9 34.4 + - - +
96A LEU* 4.9 1.7 - - + +
98A PHE* 3.9 27.1 - - + -
102A ARG* 3.8 33.7 - - + +
105A GLN* 3.9 17.0 - - + -
106A SER* 3.9 7.2 - - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.9 40.1 + - + +
26A ASN 4.3 0.9 - - - +
28A LEU* 1.3 74.1 - - - +
30A SER* 1.3 61.8 + - - +
32A LEU* 3.2 8.5 + - + +
33A ASN* 2.9 34.9 + - - -
106A SER* 3.7 18.4 - - - +
108A MET* 4.3 12.8 - - + -
204A PHE* 3.9 27.6 - - + -
208A THR* 4.6 2.0 - - + -
217A VAL* 3.9 22.4 - - + -
248A PDN 3.7 34.0 - - - +
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN 2.7 24.0 + - - -
27A TYR* 3.9 3.1 - - - -
29A LEU* 1.3 76.0 - - - +
31A SER* 1.3 57.4 + - - +
33A ASN* 3.4 2.6 + - - +
34A ARG* 3.0 53.5 + - - +
216A SER 3.6 7.4 + - - -
217A VAL* 3.6 1.1 - - - +
218A GLU* 2.9 43.9 + - - +
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 4.8 4.1 - - - +
17A TYR* 3.8 22.3 - - - +
27A TYR* 2.7 50.8 + - - -
28A LEU* 3.4 6.5 - - - -
29A LEU 3.1 0.2 - - - -
30A SER* 1.3 75.1 - - - +
32A LEU* 1.3 64.2 + - - +
34A ARG* 3.3 14.1 + - - +
35A LEU* 3.1 21.5 + - - +
96A LEU* 4.2 12.2 - - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 2.9 19.5 + - - +
29A LEU* 3.7 9.9 - - + +
31A SER* 1.3 77.1 - - - +
33A ASN* 1.3 57.8 + - - +
35A LEU* 3.2 10.0 + - + +
36A ALA* 2.9 26.3 + - - +
92A PHE* 3.6 44.4 - - + -
96A LEU* 3.9 18.2 - - + -
98A PHE* 3.7 20.9 - - + -
108A MET* 3.6 30.5 - - + -
248A PDN 3.7 26.4 - - + +
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Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 2.9 17.2 + - - +
30A SER 3.7 0.7 - - - +
31A SER 3.3 0.2 - - - -
32A LEU* 1.3 74.0 - - - +
34A ARG* 1.3 66.1 + - - +
36A ALA* 3.2 7.1 + - - +
37A GLY 3.0 18.2 + - - -
217A VAL* 3.6 3.8 - - - +
218A GLU 3.1 28.5 + - - +
219A PHE* 3.4 26.6 - - + -
220A PRO* 3.3 18.3 - - + +
223A LEU* 4.1 2.9 - - + +
248A PDN 3.1 52.9 + - - +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 4.9 9.1 + - - +
16A GLY 5.9 1.6 + - - -
27A TYR* 3.7 19.4 - - - -
30A SER* 3.0 25.3 + - - +
31A SER* 3.6 35.2 + - - +
32A LEU 3.3 0.2 - - - -
33A ASN* 1.3 75.7 - - - +
35A LEU* 1.3 64.6 + - - +
37A GLY* 3.2 10.0 + - - -
38A LYS* 3.2 20.9 + - + +
218A GLU* 3.1 30.8 + - + +
220A PRO* 4.3 17.1 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 27.1 - - + +
14A TYR 3.8 11.9 - - - +
15A ALA* 3.9 21.7 + - + +
31A SER 3.1 13.4 + - - +
32A LEU* 3.4 13.2 - - + +
34A ARG* 1.3 77.6 - - - +
36A ALA* 1.3 57.0 + - - +
38A LYS* 3.1 6.5 + - - +
39A GLN* 2.9 46.1 + - - +
92A PHE* 3.5 42.2 - - + +
93A ALA* 4.1 4.5 - - + -
96A LEU* 5.0 0.2 - - + -
248A PDN 4.1 9.0 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 2.9 8.0 + - - +
33A ASN 3.3 10.1 - - - +
35A LEU* 1.3 77.4 - - - +
37A GLY* 1.3 57.4 + - - +
39A GLN* 3.2 2.0 + - - -
40A MET* 2.8 30.3 + - - +
69A TRP* 4.8 0.2 - - + -
73A MET* 3.6 15.3 - - - +
223A LEU* 3.9 17.9 - - + +
248A PDN 3.5 39.0 - - + +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN 3.0 11.1 + - - -
34A ARG 3.2 4.4 + - - -
36A ALA* 1.3 76.0 - - - +
38A LYS* 1.3 61.7 + - - +
40A MET* 3.3 15.2 + - - +
41A VAL* 3.5 8.9 + - - +
220A PRO* 3.8 20.2 - - - -
222A MET* 3.5 18.3 - - - +
223A LEU* 4.0 8.9 - - - +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.7 15.9 - - + +
14A TYR* 2.7 38.5 + - - +
15A ALA 4.4 12.9 + - - +
16A GLY* 4.6 3.6 - - - +
34A ARG* 3.2 15.0 + - + +
35A LEU* 3.1 8.4 + - - +
37A GLY* 1.3 73.2 - - - +
39A GLN* 1.3 66.1 + - - +
41A VAL* 3.3 22.7 + - - +
42A SER* 3.5 9.2 + - - -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.0 22.8 + - + +
35A LEU* 2.9 36.9 + - - +
36A ALA 3.7 4.0 - - - +
38A LYS* 1.3 74.2 - - - +
40A MET* 1.3 60.2 + - - +
42A SER* 3.0 10.6 + - - -
43A VAL* 2.8 32.9 + - + +
73A MET* 3.3 34.1 - - + +
76A SER* 5.7 0.9 - - - -
80A ARG* 3.5 21.4 + - - +
92A PHE 3.7 3.8 + - - -
248A PDN 3.1 29.3 + - - +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 2.8 13.6 + - - +
37A GLY* 3.4 12.1 - - - +
39A GLN* 1.3 76.3 - - - +
41A VAL* 1.3 62.7 + - - +
43A VAL* 3.1 6.3 + - - +
44A VAL* 2.9 36.0 + - + +
65A ILE* 4.5 11.7 - - - -
69A TRP* 3.6 44.9 - - + -
73A MET* 3.5 12.3 - - + +
222A MET* 3.8 19.1 - - + -
223A LEU* 3.8 18.2 - - + -
226A ILE* 3.3 36.8 - - + -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.7 13.5 - - - +
38A LYS* 3.3 12.3 + - - +
39A GLN 3.2 0.8 - - - -
40A MET* 1.3 77.8 - - - +
42A SER* 1.3 62.8 + - - +
44A VAL* 3.5 5.2 + - - +
45A LYS* 3.2 25.3 + - + +
222A MET* 4.2 19.7 - - + -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 3.9 27.6 - - - +
11A GLU 4.8 0.9 + - - -
13A VAL* 3.5 24.6 - - - +
38A LYS 3.5 4.9 + - - -
39A GLN* 3.0 10.8 + - - -
41A VAL* 1.3 81.1 - - - +
43A VAL* 1.3 57.7 + - - +
45A LYS* 3.5 8.4 + - - +
46A TRP* 2.9 29.3 + - - +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PRO* 5.3 0.7 - - - -
39A GLN* 2.8 21.7 + - + +
40A MET* 3.1 13.7 + - - +
42A SER* 1.3 77.3 - - - +
44A VAL* 1.3 58.7 + - - +
46A TRP* 3.1 15.5 + - + +
47A ALA* 2.8 29.8 + - + +
65A ILE* 5.0 14.8 - - + -
69A TRP* 5.5 2.5 - - + -
72A LEU* 3.9 31.9 - - + -
73A MET* 4.1 21.1 - - + -
140A LEU* 6.2 0.4 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 2.9 28.9 + - + +
41A VAL* 4.0 5.2 - - - +
43A VAL* 1.3 72.5 - - - +
45A LYS* 1.3 67.0 + - - +
47A ALA* 3.1 7.0 + - - +
48A LYS* 3.0 52.3 + - + +
65A ILE* 4.3 30.1 - - + -
222A MET* 6.0 4.0 - - + -
226A ILE* 5.9 1.3 - - + -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.2 18.8 + - + +
42A SER* 3.7 7.4 - - - +
44A VAL* 1.3 78.8 - - - +
46A TRP* 1.3 62.7 + - - +
48A LYS* 3.6 11.0 + - - +
49A ALA* 3.4 21.7 + - + +
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Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 5.3 2.8 + - - +
8A ILE* 3.6 39.8 - - + +
9A GLU* 3.9 4.0 + - - -
10A PRO* 3.7 21.3 - - + -
42A SER 2.9 14.6 + - - +
43A VAL* 3.2 23.1 - - + +
45A LYS* 1.3 74.9 - - - +
47A ALA* 1.3 78.8 + - + +
49A ALA* 2.9 17.6 + - - +
50A LEU* 3.2 32.6 + - + +
72A LEU* 4.0 23.6 - - + -
133A LEU 5.3 0.2 - - - -
136A LYS* 3.4 48.4 - - + +
137A VAL* 4.0 18.6 - - + -
140A LEU* 3.9 19.3 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 2.8 17.2 + - + +
44A VAL 3.1 8.3 + - - +
46A TRP* 1.3 81.9 - - + +
48A LYS* 1.3 60.3 + - - +
50A LEU* 3.1 14.3 + - - +
53A PHE* 3.0 52.7 - - + +
65A ILE* 4.3 13.9 - - + -
140A LEU* 4.3 10.5 - - + -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.0 42.8 + - + +
45A LYS* 3.8 9.2 - - - +
47A ALA* 1.3 74.6 - - - +
49A ALA* 1.3 59.3 + - - +
50A LEU 3.3 1.5 + - - +
53A PHE* 4.1 9.6 - - + -
54A ARG* 3.5 59.1 + - - +
61A GLN* 4.9 9.9 - - - +
65A ILE* 6.2 0.2 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.6 2.6 - - - +
8A ILE* 3.6 34.6 - - + +
45A LYS* 3.4 10.9 + - + +
46A TRP 2.9 10.7 + - - +
48A LYS* 1.3 78.1 - - - +
50A LEU* 1.3 62.9 + - - +
51A PRO* 3.4 9.7 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.5 31.4 - - + -
8A ILE* 3.7 9.6 - - + -
46A TRP* 3.2 36.1 + - + +
47A ALA* 3.1 12.4 + - - +
48A LYS 4.5 1.9 - - - +
49A ALA* 1.3 78.0 - - - +
51A PRO* 1.3 70.4 - - - +
52A GLY 2.9 4.0 + - - -
53A PHE* 3.0 21.1 + - + +
54A ARG* 4.3 3.1 + - - +
137A VAL* 3.8 22.0 - - + -
140A LEU* 3.5 32.3 - - + -
158A MET* 6.0 2.7 - - - -
162A TYR* 4.0 9.9 - - + +
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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