Contacts of the helix formed by residues 4 - 28 (chain A) in PDB entry 1ZTD
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 ASP 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLU 3.9 3.2 + - - -
3A ILE* 1.3 73.1 - - - +
5A LYS* 1.3 66.9 + - - +
6A GLY* 3.6 6.3 + - - -
7A LEU* 2.7 47.8 + - + +
8A ALA* 3.0 22.2 + - - +
67A ALA* 4.3 3.5 - - - +
30B PRO* 4.6 2.8 - - - +
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Residues in contact with LYS 5 (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 ILE* 3.4 13.3 + - + +
4A ASP* 1.3 74.4 + - - +
6A GLY* 1.3 61.7 + - - +
8A ALA* 3.4 8.0 + - - +
9A LYS* 3.1 35.8 + - + +
63A ASP* 5.5 5.2 + - - +
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Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 3.2 8.8 + - - -
5A LYS* 1.3 75.5 - - - +
7A LEU* 1.3 64.7 + - - +
9A LYS* 3.2 6.7 + - - +
10A PHE* 3.0 18.9 + - - +
29B LYS* 5.7 2.7 - - - -
30B PRO 3.1 28.4 - - - +
31B THR* 3.4 11.8 - - - -
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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
----------------------------------------------------------
4A ASP* 2.7 45.2 + - + +
6A GLY* 1.3 74.1 - - - +
8A ALA* 1.3 58.3 + - - +
10A PHE* 3.3 3.2 + - - -
11A GLY* 2.8 24.9 + - - -
67A ALA* 3.8 25.0 - - + +
70A ALA* 3.1 18.1 - - + +
71A LYS* 3.8 35.2 - - + +
74A LEU* 5.1 4.3 - - + -
30B PRO* 3.3 29.2 - - + -
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.4 5.6 - - + -
4A ASP 3.0 12.1 + - - +
5A LYS* 3.7 10.1 - - - +
7A LEU* 1.3 77.6 - - - +
9A LYS* 1.3 56.5 + - + +
11A GLY 3.3 0.3 + - - -
12A ASP* 2.9 24.8 + - - +
63A ASP* 3.7 34.3 - - + +
66A GLU* 3.3 18.8 - - - +
67A ALA* 3.9 11.4 - - - +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 3.1 28.3 + - + +
6A GLY* 3.2 5.1 + - - +
8A ALA* 1.3 73.8 - - + +
10A PHE* 1.3 64.8 + - - +
12A ASP* 3.4 9.7 + - - +
13A SER* 3.4 17.0 + - - -
31B THR* 3.6 14.8 - - - +
32B GLY* 3.2 44.3 + - - +
33B ASP* 5.0 7.1 + - - +
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 3.0 15.0 + - - +
7A LEU* 3.7 5.4 - - - +
9A LYS* 1.3 73.4 - - - +
11A GLY* 1.3 66.1 + - - +
13A SER* 2.8 22.4 + - - -
14A LEU* 3.0 16.8 + - + +
70A ALA* 3.7 19.5 - - + -
73A TRP* 3.6 30.3 - + - -
74A LEU* 3.9 23.8 - - + -
17B PHE* 4.1 9.0 - + - -
20B SER* 4.2 6.7 - - - -
21B LEU* 3.7 40.6 - - + -
24B THR* 3.6 15.9 - - + -
30B PRO* 4.7 3.1 - - + -
31B THR 3.4 26.4 - - - +
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 2.8 11.6 + - - -
8A ALA 3.6 1.3 - - - -
10A PHE* 1.3 77.6 - - - +
12A ASP* 1.3 56.2 + - - +
14A LEU* 3.3 5.7 + - - +
15A ILE* 2.9 34.0 + - - +
66A GLU* 3.3 30.5 - - - -
69A ILE* 5.1 2.8 - - - +
70A ALA* 3.7 9.3 - - - +
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 2.9 14.9 + - - +
9A LYS* 3.6 10.1 - - - +
10A PHE 3.2 0.2 - - - -
11A GLY* 1.3 77.2 - - - +
13A SER* 1.3 64.1 + - - +
15A ILE* 3.4 3.2 - - - +
16A ASN* 2.9 56.6 + - - -
35A VAL 5.7 0.2 - - - +
66A GLU* 3.3 27.1 - - - +
33B ASP 5.9 0.5 - - - -
34B ARG* 3.1 38.8 + - - +
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS 3.4 6.0 + - - -
10A PHE* 2.8 17.3 + - - -
12A ASP* 1.3 82.7 + - - +
14A LEU* 1.3 61.3 + - - +
16A ASN* 3.6 4.5 + - - +
17A PHE* 3.3 21.8 + - - +
13B SER 4.5 2.3 - - - +
16B ASN* 3.7 21.1 - - - -
17B PHE* 3.9 16.2 - - - +
20B SER* 3.3 34.6 - - - -
33B ASP 4.8 3.1 - - - -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.0 19.1 + - + +
11A GLY* 3.3 4.2 + - - +
13A SER* 1.3 79.7 + - - +
15A ILE* 1.3 60.7 + - - +
17A PHE* 3.2 4.4 + - + +
18A LEU* 3.0 56.5 + - + +
69A ILE* 3.8 22.7 - - + +
70A ALA* 4.6 0.9 - - - -
73A TRP* 3.5 48.5 - - + -
17B PHE* 3.6 36.6 - - + -
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 2.9 23.2 + - - +
12A ASP* 3.4 11.7 - - - +
14A LEU* 1.3 72.1 - - - +
16A ASN* 1.3 69.2 + - - +
18A LEU* 4.4 12.1 - - + -
19A TYR* 2.9 28.1 + - - +
35A VAL* 4.4 15.3 - - + -
40A LEU* 4.6 11.4 - - + -
66A GLU* 4.8 11.2 - - + +
69A ILE* 3.8 28.9 - - + -
87A ILE* 4.5 4.9 - - + -
109A LEU* 3.6 32.3 - - + -
112A LEU* 4.0 13.7 - - + -
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 2.9 41.5 + - - +
13A SER* 4.0 4.9 - - - +
14A LEU 3.2 0.6 - - - -
15A ILE* 1.3 83.6 - - - +
17A PHE* 1.3 61.9 + - - +
19A TYR* 4.0 0.9 - - - +
20A SER* 3.0 35.6 + - - +
33A ASP 4.0 2.1 - - - +
34A ARG* 3.2 16.5 - - - -
35A VAL* 2.7 39.7 + - - +
13B SER* 4.0 12.3 - - - -
16B ASN* 6.4 2.0 - - + +
34B ARG* 4.1 9.5 - - - +
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.3 11.1 + - - +
14A LEU* 3.2 9.5 + - + +
16A ASN* 1.3 76.5 - - - +
18A LEU* 1.3 76.9 + - + +
20A SER* 3.3 1.4 + - - -
21A LEU* 2.9 33.5 + - + +
80A GLU* 3.4 39.7 - - + -
10B PHE* 4.3 18.4 - + - -
13B SER* 3.8 20.6 - - - +
14B LEU* 3.7 39.7 - - + -
17B PHE* 3.8 31.4 - + + -
73B TRP* 4.0 13.0 - + - -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.0 51.9 + - + +
15A ILE* 4.0 15.7 - - + +
17A PHE* 1.3 81.6 - - + +
19A TYR* 1.3 62.4 + - - +
21A LEU* 3.3 5.0 + - - +
22A ALA* 3.0 23.9 + - - +
69A ILE* 4.9 6.3 - - + -
73A TRP* 5.3 2.5 - - + -
80A GLU* 3.8 44.6 - - + +
83A ALA* 3.9 19.1 - - + -
84A VAL* 4.2 9.1 - - + +
87A ILE* 4.1 14.0 - - + +
112A LEU* 5.0 1.8 - - + -
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Residues in contact with TYR 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 ILE* 2.9 21.0 + - + +
16A ASN 4.0 1.3 - - - +
18A LEU* 1.3 75.8 - - - +
20A SER* 1.3 60.6 + - - +
22A ALA* 3.2 2.3 + - - +
23A LEU* 2.9 46.9 + - + +
33A ASP* 3.4 31.3 + - + -
35A VAL* 3.7 16.6 - - + -
87A ILE* 4.1 23.6 - - + +
91A LEU* 3.7 24.4 - - + +
95A VAL* 2.7 35.0 - - + +
105A ILE* 3.4 41.5 - - + +
108A ALA* 5.5 0.9 - - + -
109A LEU* 5.4 4.5 - - + -
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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
----------------------------------------------------------
16A ASN* 3.0 20.5 + - - +
17A PHE 3.9 0.4 - - - -
19A TYR* 1.3 79.3 - - - +
21A LEU* 1.3 57.0 + - - +
23A LEU* 3.8 5.1 - - - +
24A THR* 2.9 32.4 + - - -
31A THR 3.4 5.0 - - - +
32A GLY* 3.3 28.8 - - - -
33A ASP 3.3 12.1 + - - -
10B PHE* 4.2 3.8 - - - -
13B SER* 3.3 24.7 - - - -
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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
----------------------------------------------------------
17A PHE* 2.9 31.4 + - + +
18A LEU 3.8 4.0 - - - +
20A SER* 1.3 73.9 - - - +
22A ALA* 1.3 64.9 + - - +
24A THR* 3.4 6.9 + - + -
25A GLU* 3.1 47.5 + - + +
80A GLU* 3.1 30.3 - - + +
84A VAL* 4.1 20.2 - - + -
10B PHE* 4.0 26.0 - - + -
73B TRP* 4.0 12.8 - - + -
74B LEU* 5.4 3.1 - - + -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 3.0 17.9 + - - +
19A TYR 3.6 4.3 - - - +
21A LEU* 1.3 77.6 - - - +
23A LEU* 1.3 57.3 + - - +
25A GLU* 3.4 3.2 + - - +
26A PHE* 2.9 30.7 + - - +
84A VAL* 3.7 26.6 - - + +
87A ILE* 3.7 27.8 - - + -
88A LYS* 4.0 8.4 - - + +
91A LEU* 3.8 5.8 - - + +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 2.9 39.9 + - + +
20A SER 3.8 4.7 - - - +
22A ALA* 1.3 74.7 - - - +
24A THR* 1.3 59.1 + - - +
26A PHE* 3.6 8.9 - - + +
27A LEU* 2.9 53.4 + - + +
31A THR* 3.6 24.9 - - + +
32A GLY* 4.5 4.3 - - - -
33A ASP* 4.0 17.9 - - + -
91A LEU* 4.1 5.1 - - + +
95A VAL* 3.3 35.0 - - + -
96A LEU* 5.9 0.2 - - + -
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 2.9 23.4 + - - -
21A LEU* 3.6 13.2 - - + +
22A ALA 3.3 0.2 - - - -
23A LEU* 1.3 77.2 - - - +
25A GLU* 1.3 62.2 + - + +
28A GLY* 2.9 24.0 + - - -
29A LYS* 3.1 18.8 + - - +
30A PRO* 3.6 25.1 - - + +
31A THR* 2.9 24.9 + - - +
10B PHE* 3.6 10.3 - - + -
74B LEU* 5.3 9.4 - - + -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.1 32.9 + - + +
22A ALA 3.9 0.2 - - - +
24A THR* 1.3 77.6 - - + +
26A PHE* 1.3 62.7 + - - +
28A GLY* 3.2 12.4 + - - +
84A VAL* 3.6 14.6 - - - +
85A GLU* 4.1 2.6 - - - +
88A LYS* 2.7 46.5 + - - +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.9 18.4 + - - +
23A LEU* 3.6 5.4 - - + +
25A GLU* 1.3 78.0 - - - +
27A LEU* 1.3 74.4 + - + +
28A GLY 3.8 0.2 + - - -
88A LYS* 4.2 21.4 - - + +
91A LEU* 3.6 51.1 - - + -
92A TYR* 3.9 22.9 - - - -
93A PRO* 4.7 5.8 - - + -
95A VAL* 4.3 9.9 - - + -
96A LEU* 5.4 0.4 - - + -
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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 LEU* 2.9 31.8 + - + +
24A THR 4.3 0.7 - - - +
26A PHE* 1.3 94.1 - - + +
28A GLY* 1.3 63.7 + - - +
29A LYS* 3.4 39.2 + - + +
31A THR* 3.9 23.6 - - + +
96A LEU* 4.2 35.7 - - + -
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.9 9.0 + - - -
25A GLU* 3.2 12.2 + - - -
26A PHE 3.4 0.4 + - - -
27A LEU* 1.3 79.3 - - - +
29A LYS* 1.3 60.3 + - - +
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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