Contacts of the helix formed by residues 4 - 28 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 4.6 5.1 - - - +
2B GLU* 3.8 14.5 + - + +
3B ILE* 1.3 72.1 - - - +
5B LYS* 1.3 64.6 + - - +
6B GLY* 2.9 10.4 + - - -
7B LEU* 2.8 42.9 + - + +
8B ALA* 3.0 21.1 + - - +
67B ALA* 4.5 4.7 - - - +
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Residues in contact with LYS 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 3.4 7.6 + - - +
4B ASP* 1.3 73.0 + - - +
6B GLY* 1.3 58.1 + - - +
8B ALA* 3.2 8.3 + - + +
9B LYS* 2.9 66.8 + - + +
63B ASP* 3.0 38.4 + - + +
66B GLU* 5.5 0.4 + - - -
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Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO 3.3 23.1 - - - +
31A THR* 3.3 14.3 - - - -
4B ASP* 2.9 10.7 + - - -
5B LYS* 1.3 77.5 - - - +
7B LEU* 1.3 62.7 + - - +
9B LYS* 3.4 7.5 + - - +
10B PHE 3.1 17.5 + - - -
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Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 3.8 21.4 + - + +
4B ASP* 2.8 29.2 + - + +
6B GLY* 1.3 71.3 - - - +
8B ALA* 1.3 59.7 + - - +
10B PHE* 3.4 1.4 + - + +
11B GLY* 2.9 22.9 + - - -
67B ALA* 3.4 32.4 - - + +
70B ALA* 3.5 26.0 - - + +
71B LYS* 4.1 19.5 - - + +
74B LEU* 3.7 24.0 - - + -
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 5.5 0.9 - - + -
4B ASP 3.0 13.6 + - - +
5B LYS* 3.2 16.1 + - + +
7B LEU* 1.3 77.4 - - - +
9B LYS* 1.3 56.8 + - - +
11B GLY* 3.1 2.4 + - - -
12B ASP* 2.8 24.9 + - - +
63B ASP* 3.5 42.4 - - + +
66B GLU* 3.3 11.9 - - - +
67B ALA* 4.0 13.8 - - + +
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Residues in contact with LYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 5.0 2.7 - - - +
32A GLY* 3.0 45.3 - - - +
33A ASP* 4.8 8.7 + - - +
34A ARG 5.8 0.6 - - - +
5B LYS* 2.9 50.8 + - + +
6B GLY* 3.6 9.0 - - - +
8B ALA* 1.3 72.5 - - - +
10B PHE* 1.3 65.8 + - - +
12B ASP* 3.3 9.1 + - - +
13B SER* 3.3 17.7 + - - -
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 4.3 11.9 - + - -
20A SER 4.0 3.6 - - - -
21A LEU* 4.0 32.8 - - + -
24A THR* 3.6 10.8 - - + -
30A PRO* 4.6 4.3 - - + -
31A THR 3.4 28.8 - - - +
32A GLY* 4.3 0.7 - - - -
6B GLY 3.1 11.8 + - - +
7B LEU* 3.7 7.2 - - - +
8B ALA 3.3 0.2 - - - -
9B LYS* 1.3 77.1 - - - +
11B GLY* 1.3 62.9 + - - +
13B SER* 2.9 31.3 + - - -
14B LEU* 3.0 13.5 + - + -
70B ALA* 3.7 19.3 - - + -
73B TRP* 3.5 39.7 - + - -
74B LEU* 4.0 19.7 - - + -
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU 2.9 11.9 + - - -
8B ALA 3.1 4.7 + - - -
10B PHE* 1.3 78.2 - - - +
12B ASP* 1.3 55.5 + - - +
14B LEU* 3.7 5.7 - - - +
15B ILE* 2.8 34.3 + - - +
66B GLU* 3.7 25.7 - - - -
69B ILE* 5.4 1.5 - - - +
70B ALA* 3.7 11.9 - - - -
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 4.4 15.8 + - - -
8B ALA 2.8 9.3 + - - +
9B LYS* 3.5 13.2 - - - +
11B GLY* 1.3 76.8 - - - +
13B SER* 1.3 61.9 + - - +
15B ILE* 3.4 3.0 - - - +
16B ASN* 3.1 44.6 + - - +
35B VAL 4.7 5.6 - - - +
66B GLU* 3.0 30.5 - - - +
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 4.5 2.1 - - - +
16A ASN* 3.7 20.6 - - - -
17A PHE* 3.8 16.6 - - - +
20A SER* 3.3 34.3 - - - -
9B LYS 3.3 5.3 + - - -
10B PHE* 2.9 17.9 + - - -
12B ASP* 1.3 81.6 - - - +
14B LEU* 1.3 60.5 + - - +
16B ASN* 3.5 6.4 + - - +
17B PHE* 3.3 22.0 + - - +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.7 34.1 - - + -
10B PHE* 3.0 16.8 + - + +
11B GLY* 3.7 3.4 - - - +
13B SER* 1.3 80.9 + - - +
15B ILE* 1.3 63.9 + - - +
17B PHE* 3.2 7.7 + - + +
18B LEU* 3.0 51.2 + - + +
69B ILE* 3.9 22.7 - - + +
70B ALA* 4.2 9.6 - - - -
73B TRP* 3.6 47.8 - - + +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 2.8 20.4 + - - +
12B ASP* 3.4 16.4 - - - +
14B LEU* 1.3 74.8 - - - +
16B ASN* 1.3 68.1 + - - +
18B LEU* 4.4 13.0 - - + -
19B TYR* 2.8 29.3 + - + +
35B VAL* 4.4 12.1 - - + -
40B LEU* 4.8 2.7 - - + -
66B GLU* 4.3 13.5 - - + +
69B ILE* 3.6 34.1 - - + -
87B ILE* 4.5 5.4 - - + -
109B LEU* 4.1 26.9 - - + -
112B LEU* 4.0 18.6 - - + -
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.0 11.4 - - - +
16A ASN* 6.4 2.0 - - + +
34A ARG* 4.6 6.7 - - - +
12B ASP* 3.1 38.3 + - - +
13B SER* 3.9 6.1 - - - +
14B LEU 3.2 0.2 - - - -
15B ILE* 1.3 77.4 - - - +
17B PHE* 1.3 58.7 + - - +
19B TYR* 3.9 3.9 - - - +
20B SER* 2.9 34.5 + - - -
33B ASP 3.9 6.9 - - - +
34B ARG* 3.8 27.6 - - + +
35B VAL* 2.8 34.2 + - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.1 11.9 - + - -
13A SER* 3.9 25.5 - - - +
14A LEU* 3.6 31.9 - - + -
17A PHE* 3.8 36.6 - + + -
73A TRP* 3.9 21.5 - + - -
80A GLU* 5.5 1.6 - - - -
13B SER 3.3 9.7 + - - +
14B LEU* 3.2 10.4 + - + +
16B ASN* 1.3 76.4 - - - +
18B LEU* 1.3 71.6 + - + +
20B SER* 3.1 2.3 + - - -
21B LEU* 3.0 55.6 + - + +
80B GLU* 3.7 13.9 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.0 49.7 + - + +
15B ILE* 3.9 15.3 - - + +
17B PHE* 1.3 78.9 - - + +
19B TYR* 1.3 63.0 + - - +
21B LEU* 3.3 9.1 + - + +
22B ALA* 3.1 22.9 + - - +
69B ILE* 4.7 5.8 - - + -
73B TRP* 5.6 2.9 - - + +
80B GLU* 3.6 47.3 - - + +
83B ALA* 4.0 17.7 - - + -
84B VAL* 4.0 8.4 - - + +
87B ILE* 4.1 14.1 - - + +
112B LEU* 5.5 0.4 - - + -
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 2.8 21.7 + - + +
16B ASN 3.9 3.1 - - - +
18B LEU* 1.3 77.5 - - - +
20B SER* 1.3 60.9 + - - +
22B ALA* 3.4 2.6 + - - +
23B LEU* 2.9 36.2 + - + +
33B ASP* 4.0 32.9 + - + -
35B VAL* 3.9 23.3 - - + -
87B ILE* 4.0 23.0 - - + +
91B LEU* 3.7 21.9 - - + +
95B VAL* 2.9 39.8 - - + +
105B ILE* 3.6 31.5 - - + +
108B ALA* 5.1 1.8 - - + -
109B LEU* 4.7 5.6 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.5 5.4 - - - -
13A SER* 3.3 23.5 - - - -
16B ASN 2.9 23.5 + - - -
17B PHE 3.1 2.0 + - - -
19B TYR* 1.3 75.6 - - - +
21B LEU* 1.3 60.4 + - - +
23B LEU* 3.9 3.0 - - - +
24B THR* 2.9 33.5 + - - -
31B THR 3.5 4.0 - - - +
32B GLY* 3.2 15.8 - - - -
33B ASP 3.0 27.5 + - - -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.7 28.7 - - + -
73A TRP* 4.6 7.2 - - + +
74A LEU* 5.8 1.8 - - + -
17B PHE* 3.0 52.1 + - + +
18B LEU* 3.6 6.7 - - - +
20B SER* 1.3 75.5 - - - +
22B ALA* 1.3 65.0 + - - +
24B THR* 3.3 5.6 + - + -
25B GLU* 3.2 33.1 + - - +
80B GLU* 3.8 23.3 - - + +
84B VAL* 3.8 22.0 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU 3.1 16.3 + - - +
19B TYR 3.7 3.8 - - - +
21B LEU* 1.3 77.8 - - - +
23B LEU* 1.3 57.3 + - - +
25B GLU 3.2 2.1 + - - -
26B PHE* 2.9 29.1 + - - +
84B VAL* 3.8 11.4 - - + +
87B ILE* 3.8 25.1 - - + -
88B LYS* 3.4 31.1 - - + +
91B LEU* 4.0 4.7 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 2.9 29.1 + - + +
20B SER* 3.9 4.7 - - - +
21B LEU 3.4 0.2 - - - -
22B ALA* 1.3 75.8 - - - +
24B THR* 1.3 58.6 + - - +
26B PHE* 3.7 11.2 - - + +
27B LEU* 2.9 50.5 + - + +
31B THR* 3.8 22.0 - - + +
32B GLY* 4.1 24.0 - - - +
33B ASP* 4.1 12.1 - - + +
91B LEU* 4.1 5.5 - - + +
95B VAL* 3.7 29.6 - - + -
96B LEU* 4.3 7.4 - - + -
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.6 12.0 - - + -
74A LEU* 5.4 7.4 - - + -
20B SER 2.9 23.9 + - - -
21B LEU* 3.4 8.7 - - + +
22B ALA 3.1 0.2 - - - -
23B LEU* 1.3 78.0 - - - +
25B GLU* 1.3 61.5 + - + +
28B GLY* 2.9 23.2 + - - -
29B LYS* 3.1 33.2 + - - +
30B PRO* 3.8 7.6 - - + -
31B THR* 3.0 24.9 + - - -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.2 20.8 + - - +
22B ALA 3.9 0.2 - - - +
24B THR* 1.3 79.9 - - + +
26B PHE* 1.3 64.0 + - - +
28B GLY* 3.4 11.0 + - - -
84B VAL* 4.4 11.8 - - - +
85B GLU* 4.7 2.4 - - - +
88B LYS* 2.7 49.8 + - + +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 2.9 18.2 + - - +
23B LEU* 3.7 9.6 - - + +
25B GLU* 1.3 79.6 - - - +
27B LEU* 1.3 79.0 + - + +
88B LYS* 4.3 10.3 - - + +
91B LEU* 3.6 43.3 - - + -
92B TYR* 3.8 31.0 - - - -
93B PRO* 4.0 12.1 - - + -
95B VAL* 5.6 0.9 - - + -
96B LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 2.9 25.4 + - + +
24B THR 4.3 1.8 - - - +
26B PHE* 1.3 93.5 - - + +
28B GLY* 1.3 62.8 + - - +
29B LYS* 3.2 33.7 + - + +
31B THR* 3.6 27.1 - - + +
96B LEU* 3.7 38.1 - - + -
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 2.9 9.2 + - - -
25B GLU* 3.4 11.8 + - - -
26B PHE 3.4 0.4 + - - -
27B LEU* 1.3 76.9 - - - +
29B LYS* 1.3 61.4 + - - +
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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