Contacts of the helix formed by residues 2 - 27 (chain A) in PDB entry 1NLW
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 SER 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 1.3 97.2 + - - +
4A SER* 3.0 14.7 + - - -
5A THR* 2.7 47.4 + - - -
6A HIS* 3.6 2.4 + - - +
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Residues in contact with ARG 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 1.3 112.9 + - - +
4A SER* 1.3 51.9 + - - +
5A THR 2.9 1.4 + - - -
6A HIS* 3.1 7.3 + - - +
7A ASN* 2.8 52.2 + - - +
112F T 4.1 21.1 - - - +
113F G 5.2 9.9 - - - +
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Residues in contact with SER 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 4.0 15.0 + - - -
3A ARG* 1.3 76.9 - - - +
5A THR* 1.3 58.3 + - - +
7A ASN* 4.3 8.3 + - - -
8A GLU* 3.0 29.6 + - - +
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Residues in contact with THR 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 2.7 27.9 + - - -
4A SER* 1.3 79.7 + - - +
6A HIS* 1.3 58.0 + - - +
7A ASN 3.3 0.2 - - - -
8A GLU* 3.5 3.1 + - - +
9A MET* 2.9 54.7 + - + +
305G T 4.7 8.7 - - - +
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Residues in contact with HIS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 3.6 2.1 + - - +
3A ARG* 3.1 10.9 + - - +
5A THR* 1.3 79.9 - - - +
7A ASN* 1.3 61.9 + - - +
9A MET* 3.2 19.3 + - + +
10A GLU* 3.0 31.8 + - + +
112F T 3.8 25.9 - + + +
113F G 2.9 36.7 + + - -
114F C 3.9 6.4 + - - -
305G T 6.3 0.8 - - - +
306G A 4.9 7.4 + - - -
307G G 3.4 25.6 - + - -
308G C 4.5 4.9 - - - -
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Residues in contact with ASN 7 (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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3A ARG* 2.8 27.0 + - - +
4A SER* 4.3 5.8 + - - -
6A HIS* 1.3 82.3 - - - +
8A GLU* 1.3 63.6 + - - +
10A GLU* 3.8 2.1 + - - +
11A LYS* 3.3 22.3 + - - +
14A ARG* 5.6 0.3 + - - -
111F G 3.3 33.4 + - + +
112F T 2.4 62.2 + - + +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 3.0 21.8 + - - +
5A THR* 3.9 3.8 - - - +
6A HIS 3.2 0.4 - - - -
7A ASN* 1.3 80.4 - - - +
9A MET* 1.3 66.5 + - + +
11A LYS* 3.6 16.7 + - - +
12A ASN* 3.2 22.5 + - - +
111F G 5.7 0.5 + - - -
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Residues in contact with MET 9 (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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5A THR* 2.9 45.9 + - + +
6A HIS* 3.2 23.1 + - + +
8A GLU* 1.3 76.0 - - + +
10A GLU* 1.3 59.4 + - - +
12A ASN* 3.2 8.7 + - - +
13A ARG* 2.8 27.7 + - - +
305G T 4.3 40.4 - - + +
306G A 4.0 25.4 - - + +
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Residues in contact with GLU 10 (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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6A HIS* 3.0 20.6 + - + +
7A ASN 3.9 4.0 - - - +
9A MET* 1.3 76.9 - - - +
11A LYS* 1.3 57.3 + - - +
13A ARG* 2.9 44.7 + - - +
14A ARG* 2.8 50.7 + - - +
111F G 4.6 5.5 - - + +
112F T 3.4 27.8 - - + +
307G G 4.4 1.2 - - - +
308G C 2.7 29.2 + - - +
309G A 3.6 9.5 + - - +
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Residues in contact with LYS 11 (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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7A ASN 3.3 16.4 + - - +
8A GLU* 3.8 20.2 - - - +
9A MET 3.3 0.2 - - - -
10A GLU* 1.3 78.7 - - - +
12A ASN* 1.3 57.2 + - - +
14A ARG* 3.5 23.5 + - - +
15A ALA* 3.1 26.1 + - + +
18A ARG* 5.0 1.5 + - - +
110F C 3.0 44.3 + - - +
111F G 4.7 12.1 + - - +
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Residues in contact with ASN 12 (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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8A GLU 3.2 14.6 + - - +
9A MET* 3.5 10.3 + - - +
10A GLU 3.1 0.6 - - - -
11A LYS* 1.3 74.7 - - - +
13A ARG* 1.3 65.8 + - - +
15A ALA* 3.4 7.3 + - - +
16A HIS* 3.2 47.1 + - - -
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Residues in contact with ARG 13 (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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9A MET 2.8 13.6 + - - +
10A GLU* 2.9 44.1 + - - +
12A ASN* 1.3 81.2 - - - +
14A ARG* 1.3 70.1 + - - +
16A HIS* 3.4 6.7 + - - +
17A LEU* 3.1 42.3 + - - +
306G A 5.0 2.7 - - - -
307G G 3.8 50.7 + - - +
308G C 3.5 30.6 + - - -
309G A 5.1 1.8 + - - +
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Residues in contact with ARG 14 (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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7A ASN 5.6 0.2 + - - -
10A GLU* 2.8 39.0 + - - +
11A LYS* 3.8 23.9 + - - +
13A ARG* 1.3 85.6 - - - +
15A ALA* 1.3 56.9 + - - +
17A LEU* 3.3 10.9 + - + +
18A ARG* 2.9 42.1 + - - +
109F A 3.3 25.7 + - - +
110F C 3.0 68.2 + - - +
111F G 5.0 3.0 + - - -
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Residues in contact with ALA 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 LYS* 3.1 18.1 + - + +
12A ASN* 3.7 11.4 - - - +
13A ARG 3.3 0.2 - - - -
14A ARG* 1.3 76.5 - - - +
16A HIS* 1.3 57.4 + - + +
18A ARG* 3.0 20.9 + - - +
19A LEU* 2.9 32.9 + - + +
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Residues in contact with HIS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN* 3.2 47.5 + - - -
13A ARG* 3.8 8.3 - - - +
15A ALA* 1.3 79.9 - - + +
17A LEU* 1.3 61.8 + - - +
19A LEU* 3.2 24.0 + - + +
20A SER* 3.1 24.3 + - - -
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Residues in contact with LEU 17 (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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13A ARG* 3.1 35.4 + - - +
14A ARG* 3.5 14.1 - - + +
16A HIS* 1.3 77.0 - - - +
18A ARG* 1.3 62.3 + - - +
20A SER* 3.2 6.5 + - - +
21A LEU* 3.0 22.4 + - + +
222B PHE* 5.3 4.3 - - + -
239B ARG* 4.1 24.7 - - + +
240B ALA* 4.0 31.4 - - + +
243B LEU* 3.7 22.2 - - + -
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Residues in contact with ARG 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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11A LYS* 5.0 2.0 + - - +
14A ARG* 2.9 49.2 + - - +
15A ALA* 3.0 20.1 + - - +
17A LEU* 1.3 78.3 - - - +
19A LEU* 1.3 55.2 + - + +
21A LEU* 3.2 10.6 + - + +
22A GLU* 3.0 44.6 + - + +
37A HIS* 5.6 7.4 - - + +
562D HIS* 3.1 44.7 + - - -
566D GLN* 4.6 2.0 - - - -
109F A 3.4 32.5 + - - +
110F C 3.6 12.3 + - - -
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Residues in contact with LEU 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 ALA* 2.9 17.7 + - + +
16A HIS* 3.2 29.6 + - + +
18A ARG* 1.3 79.1 - - + +
20A SER* 1.3 62.0 + - - +
22A GLU* 3.5 8.2 + - + +
23A LYS* 3.2 22.5 + - - +
559D LYS* 4.4 19.3 - - - +
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Residues in contact with SER 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 HIS 3.1 13.4 + - - -
17A LEU* 3.2 12.1 + - - -
19A LEU* 1.3 76.0 - - - +
21A LEU* 1.3 62.8 + - - +
23A LYS* 3.5 9.4 + - - +
24A LEU* 3.2 21.7 + - - +
240B ALA* 4.8 5.1 + - - +
243B LEU* 3.8 23.4 - - - +
244B ASP* 3.1 29.4 + - - -
247B THR* 4.7 2.4 + - - -
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Residues in contact with LEU 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 LEU* 3.0 13.2 + - + +
18A ARG* 3.2 13.4 + - + +
20A SER* 1.3 74.7 - - - +
22A GLU* 1.3 60.2 + - - +
24A LEU* 3.3 3.0 + - - +
25A LYS* 2.9 24.6 + - - +
37A HIS* 3.2 38.4 - - + +
39A THR* 3.9 24.9 - - + +
42A LEU* 3.4 34.6 - - + +
43A LEU* 4.7 6.3 - - + -
222B PHE* 5.3 2.9 - - + -
243B LEU* 3.7 29.3 - - + +
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Residues in contact with GLU 22 (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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18A ARG* 3.0 30.2 + - + +
19A LEU* 4.0 9.2 - - + +
20A SER 3.4 0.2 - - - -
21A LEU* 1.3 75.7 - - + +
23A LYS* 1.3 57.7 + - - +
25A LYS* 3.0 14.6 + - - +
26A GLY 2.9 16.1 + - - -
37A HIS* 4.1 19.8 + - - -
555D ASP* 4.8 6.1 - - - +
558D ARG* 2.8 64.4 + - - +
559D LYS* 6.3 0.7 - - - -
562D HIS* 5.9 3.3 - - - +
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Residues in contact with LYS 23 (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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19A LEU 3.2 15.7 + - - +
20A SER* 3.6 6.7 - - - +
21A LEU 3.2 0.2 - - - -
22A GLU* 1.3 77.5 - - - +
24A LEU* 1.3 58.5 + - - +
26A GLY* 2.8 19.3 + - - -
27A LEU* 3.3 13.4 + - + +
244B ASP* 4.1 21.6 + - - +
247B THR* 3.6 35.8 - - + +
251B GLN* 5.4 2.7 - - - +
555D ASP* 5.3 4.5 + - - -
558D ARG* 5.1 0.2 - - - +
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Residues in contact with LEU 24 (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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20A SER 3.2 10.6 + - - +
21A LEU* 3.6 7.4 - - - +
23A LYS* 1.3 78.3 - - - +
25A LYS* 1.3 57.6 + - - +
27A LEU* 2.8 29.8 + - + +
28A VAL* 3.8 5.7 - - + +
42A LEU* 4.2 15.1 - - + +
43A LEU* 5.3 1.8 - - + -
46A ALA* 4.1 24.5 - - + -
225B LEU* 4.3 9.6 - - + -
243B LEU* 3.9 32.3 - - + +
246B ALA* 4.8 2.2 - - + -
247B THR* 3.8 25.9 + - - +
250B ILE* 3.8 28.7 - - + -
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Residues in contact with LYS 25 (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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21A LEU 2.9 11.6 + - - +
22A GLU* 3.1 30.4 + - - +
24A LEU* 1.3 76.8 - - - +
26A GLY* 1.3 57.6 + - - +
27A LEU 2.8 11.8 - - - +
28A VAL 3.9 4.7 - - - +
35A SER* 5.6 10.5 - - - -
36A ARG 4.3 8.3 - - - -
37A HIS* 3.2 46.0 + - - +
42A LEU* 3.3 37.7 - - + +
558D ARG* 3.8 18.8 + - + +
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 2.9 8.8 + - - -
23A LYS* 2.8 11.6 + - - -
25A LYS* 1.3 76.0 - - - +
27A LEU* 1.3 64.4 + - - +
28A VAL 4.1 2.6 - - - +
551D LYS* 4.8 17.3 + - - +
558D ARG* 4.2 15.9 - - - -
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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
----------------------------------------------------------
23A LYS* 3.3 8.8 + - + +
24A LEU* 2.8 13.2 + - + +
25A LYS 2.8 12.3 - - - +
26A GLY* 1.3 74.6 - - - +
28A VAL* 1.3 84.4 + - + +
247B THR* 3.8 27.4 - - + +
250B ILE* 4.1 10.3 - - + -
251B GLN* 3.6 36.1 - - + +
254B ARG* 3.5 24.0 - - - +
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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) + - + + + + + -
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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