Contacts of the helix formed by residues 5 - 32 (chain A) in PDB entry 4HYJ
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 ASN 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU 4.4 4.4 + - - +
4A VAL* 1.3 78.0 - - - +
6A LEU* 1.3 65.8 + - - +
7A LEU* 3.0 37.8 + - - +
8A VAL* 3.1 28.2 + - + +
9A LEU* 3.2 15.1 + - - +
69A GLY 2.7 17.4 + - - +
71A LEU* 4.5 23.4 - - + +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.1 2.0 + - - +
5A ASN* 1.3 72.9 + - - +
7A LEU* 1.3 57.5 + - - +
9A LEU* 3.1 20.5 + - + +
10A ALA* 2.9 32.2 + - + +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 12.9 + - - +
6A LEU* 1.3 76.4 - - - +
8A VAL* 1.3 58.8 + - - +
10A ALA* 3.4 9.7 + - + +
11A THR* 2.9 48.8 + - + +
71A LEU* 6.4 0.2 - - + -
208A GLU* 4.0 37.7 - - + +
211A LEU* 4.2 10.8 - - + -
212A VAL* 4.5 13.2 - - + -
215A LEU* 4.4 15.5 - - + -
308A LFA 5.3 5.2 - - + -
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.1 32.1 + - + +
7A LEU* 1.3 76.1 - - - +
9A LEU* 1.3 61.9 + - - +
11A THR* 3.3 7.7 + - - -
12A GLN* 3.0 39.0 + - + +
65A VAL* 4.7 8.1 - - + +
69A GLY* 3.6 27.8 - - - +
70A LEU 4.4 3.6 - - - +
71A LEU* 4.1 26.9 - - + +
74A ILE* 4.2 13.5 - - + -
211A LEU* 4.1 10.1 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.1 18.6 - - + -
5A ASN 3.2 11.9 + - - +
6A LEU* 3.1 21.6 + - + +
8A VAL* 1.3 74.0 - - - +
10A ALA* 1.3 63.6 + - - +
12A GLN* 3.2 26.0 + - - +
13A TYR* 3.0 21.3 + - - +
67A THR 5.2 3.4 - - - +
68A SER 5.2 1.1 - - - -
69A GLY* 3.8 22.0 - - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 18.1 + - + +
7A LEU* 3.4 17.3 - - + +
9A LEU* 1.3 77.9 - - - +
11A THR* 1.3 59.6 + - + +
13A TYR* 3.0 13.2 + - + +
14A MET* 2.9 32.1 + - + +
215A LEU* 5.0 4.3 - - + -
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 2.9 26.7 + - + +
8A VAL* 3.3 8.1 + - - -
10A ALA* 1.3 72.2 - - - +
12A GLN* 1.3 68.0 + - - +
14A MET* 3.7 1.1 - - - +
15A PHE* 2.9 39.3 + - - -
65A VAL* 3.7 18.5 - - - +
211A LEU* 3.8 34.3 - - + +
215A LEU* 3.9 28.3 - - + -
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.0 28.3 + - - +
9A LEU* 3.3 26.3 - - - +
11A THR* 1.3 80.9 + - - +
13A TYR* 1.3 62.5 + - - +
15A PHE* 3.3 10.0 + - - +
16A TRP* 3.2 23.2 + - + +
65A VAL* 3.8 23.1 - - + +
66A GLY 2.9 30.8 + - - +
67A THR* 3.9 7.5 - - - +
69A GLY* 3.7 25.5 - - - +
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.0 11.5 + - - +
10A ALA* 3.0 13.9 + - + +
12A GLN* 1.3 76.5 - - - +
14A MET* 1.3 73.1 + - + +
16A TRP* 2.8 34.5 + + + +
17A VAL* 3.0 35.2 + - + +
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 2.9 16.9 + - + +
11A THR 3.3 2.4 + - - +
13A TYR* 1.3 92.7 - - + +
15A PHE* 1.3 68.0 + - + +
17A VAL* 3.1 18.2 + - + +
18A GLY 2.9 10.0 + - - -
215A LEU* 3.5 35.7 - - + -
218A ASN* 2.9 47.5 + - + +
219A PHE* 3.4 35.4 - - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 2.9 31.7 + - - +
12A GLN* 3.7 5.2 - - - +
13A TYR 3.2 0.4 - - - -
14A MET* 1.3 78.7 - - + +
16A TRP* 1.3 60.1 + - + +
18A GLY* 3.2 2.8 + - - -
19A PHE* 2.9 27.4 + - - +
58A TYR* 3.7 39.8 - + - +
61A MET* 3.4 50.0 - - + -
62A LYS* 5.1 5.2 - - + +
65A VAL* 4.2 33.4 - - + -
211A LEU* 5.7 3.4 - - + -
214A GLU* 3.9 34.3 - - + -
215A LEU* 6.1 1.3 - - + -
218A ASN* 5.3 2.0 - - + -
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Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLN* 3.2 27.7 + - + +
13A TYR* 2.8 19.1 + + + +
15A PHE* 1.3 76.3 - - + +
17A VAL* 1.3 56.7 + - - +
19A PHE* 3.2 33.5 + + + +
20A VAL* 2.8 40.7 + - + +
58A TYR 5.8 0.9 - - - -
59A TYR* 4.4 18.8 - + - -
62A LYS* 3.9 42.4 - - + +
310A LFA 4.4 26.7 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.0 51.7 + - + +
14A MET* 3.1 30.0 + - + +
16A TRP* 1.3 74.2 - - - +
18A GLY* 1.3 58.3 + - - +
20A VAL* 4.1 3.9 - - - +
21A GLY* 2.8 29.1 + - - -
218A ASN* 4.2 2.7 - - - +
219A PHE* 5.3 2.7 - - + -
222A LEU* 4.3 15.3 - - + +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MET 2.9 11.9 + - - -
15A PHE 3.2 3.8 + - - -
17A VAL* 1.3 75.9 - - - +
19A PHE* 1.3 58.3 + - - +
21A GLY 3.8 0.2 - - - -
22A MET* 2.9 35.8 + - - +
58A TYR* 4.0 12.6 - - - -
218A ASN* 3.2 23.5 + - - -
222A LEU* 4.3 8.7 - - - +
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE 2.9 14.2 + - - +
16A TRP* 3.5 33.4 - + + +
18A GLY* 1.3 75.3 - - - +
20A VAL* 1.3 65.0 + - + +
22A MET* 3.7 3.3 - - - +
23A ALA* 2.8 43.4 + - + +
55A ALA* 3.2 27.9 - - + +
58A TYR* 3.6 12.6 - - + +
59A TYR* 3.8 29.6 - + + +
309A LFA 4.1 32.1 - - + -
310A LFA 4.6 21.5 - - + -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 2.8 28.2 + - + +
17A VAL* 4.1 4.0 - - - +
19A PHE* 1.3 83.5 - - + +
21A GLY* 1.3 60.2 + - - +
23A ALA* 3.7 4.5 - - + +
24A ALA* 2.9 33.8 + - + +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL 2.8 21.6 + - - -
18A GLY 3.8 0.4 - - - -
20A VAL* 1.3 74.9 - - - +
22A MET* 1.3 56.8 + - - +
24A ALA* 3.3 5.5 + - - +
25A GLY* 2.9 26.7 + - - -
222A LEU* 4.2 15.9 - - - -
226A VAL* 4.2 5.8 - - - +
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Residues in contact with MET 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 2.9 22.4 + - - +
19A PHE 3.8 2.5 - - - +
21A GLY* 1.3 73.9 - - - +
23A ALA* 1.3 55.0 + - - +
25A GLY 3.4 0.2 + - - -
26A THR* 2.7 38.9 + - - -
51A THR* 3.4 37.5 - - - +
54A ALA* 3.7 24.5 - - + +
55A ALA* 3.8 9.6 - - - +
58A TYR* 4.5 5.8 - - + -
221A ASP* 3.4 46.4 - - + +
222A LEU* 3.6 15.0 - - + +
225A LYS* 3.9 11.0 - - + -
226A VAL* 4.2 7.9 - - - -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.8 35.5 + - + +
20A VAL* 3.7 8.1 - - + +
22A MET* 1.3 73.1 - - - +
24A ALA* 1.3 58.0 + - - +
26A THR* 3.3 7.6 + - - -
27A LEU* 3.0 36.4 + - + +
55A ALA* 4.1 2.1 - - + +
309A LFA 4.1 24.4 - - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 2.9 22.5 + - + +
21A GLY* 3.7 5.2 - - - +
23A ALA* 1.3 75.0 - - - +
25A GLY* 1.3 60.8 + - - +
27A LEU* 3.3 8.6 + - - +
28A TYR* 2.9 29.0 + - - +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 2.9 15.7 + - - -
22A MET 3.9 1.3 - - - -
24A ALA* 1.3 74.6 - - - +
26A THR* 1.3 63.7 + - - +
28A TYR* 3.2 7.2 + - - +
29A PHE* 3.0 38.2 + - - -
51A THR* 3.9 1.3 - - - -
226A VAL* 4.4 23.3 - - - -
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET 2.7 18.7 + - - -
23A ALA* 3.3 12.4 - - - -
24A ALA 3.2 0.2 - - - -
25A GLY* 1.3 77.3 - - - +
27A LEU* 1.3 61.5 + - - +
29A PHE* 3.4 3.9 + - - +
30A LEU* 3.1 41.3 + - + +
48A ALA* 3.7 16.9 - - + +
51A THR* 2.6 23.5 + - - -
52A PHE* 3.1 25.7 + - + -
309A LFA 4.2 17.9 - - + +
314B LFA 4.8 1.8 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.0 24.2 + - + +
24A ALA* 3.8 7.0 - - - +
26A THR* 1.3 74.8 - - + +
28A TYR* 1.3 66.2 + - - +
30A LEU* 3.9 9.8 - - + +
31A VAL* 3.0 39.9 + - + +
309A LFA 4.6 22.2 - - + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 2.9 17.9 + - - +
25A GLY* 3.2 8.3 + - - +
27A LEU* 1.3 77.5 - - - +
29A PHE* 1.3 71.6 + + - +
31A VAL* 3.2 4.0 + - + +
32A GLU* 3.0 48.6 + - + +
230A LEU* 3.6 31.6 - - + -
233A PHE* 3.7 28.4 - + - -
234A PHE* 3.8 13.5 - + - -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 3.0 32.4 + - - +
28A TYR* 1.3 82.3 - + - +
30A LEU* 1.3 63.7 + - - +
32A GLU* 3.8 2.6 - - - -
33A ARG* 3.2 22.3 + - - +
44A ALA* 3.6 19.1 - - - +
47A ALA* 3.9 17.3 - - + -
48A ALA* 3.6 31.2 - - + -
51A THR* 4.0 20.9 - - + -
225A LYS 4.6 2.7 - - - -
226A VAL* 3.9 10.1 - - + -
229A GLY* 3.7 34.8 - - - -
230A LEU* 3.8 27.1 - - + -
233A PHE* 4.3 17.2 - + + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.1 35.5 + - + +
27A LEU* 4.0 13.5 - - + +
29A PHE* 1.3 78.0 - - - +
31A VAL* 1.3 63.1 + - + +
33A ARG* 3.3 53.3 + - - +
34A ASN* 5.1 0.5 + - - -
44A ALA 5.9 0.2 - - - -
45A THR* 5.2 2.2 - - - -
48A ALA* 3.9 17.7 - - + -
309A LFA 5.7 4.3 - - + -
314B LFA 4.3 22.4 - - + -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.0 31.5 + - + +
28A TYR* 4.0 3.8 - - - +
30A LEU* 1.3 77.8 - - + +
32A GLU* 1.3 74.7 + - + +
33A ARG 3.3 1.7 + - - -
34A ASN* 4.3 6.9 + - - +
35A SER* 5.0 1.0 + - - -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.0 51.6 + - + +
29A PHE 3.8 2.0 - - - +
31A VAL* 1.3 90.2 - - + +
33A ARG* 1.3 63.4 - - - +
34A ASN 3.4 0.9 - - - -
35A SER* 3.1 36.0 + - - -
36A LEU* 3.9 1.4 - - - +
233A PHE* 3.3 33.5 - - + -
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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