Contacts of the helix formed by residues 16 - 41 (chain B) in PDB entry 4ZPK
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 LYS 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 3.7 10.6 + - - +
14B LEU 3.5 0.2 - - - -
15B ARG* 1.3 107.4 - - + +
17B GLU* 1.3 62.5 + - - +
18B LYS 3.3 1.8 - - - -
19B SER* 3.3 12.2 - - - +
20B ARG* 2.6 38.1 + - - +
14D T 3.5 43.8 + - + +
15D A 3.3 32.5 + - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 5.7 2.3 + - - -
12B SER 3.8 6.2 - - - +
13B GLU* 3.2 43.0 + - + +
16B LYS* 1.3 76.3 + - - +
18B LYS* 1.3 68.4 + - + +
20B ARG* 3.1 33.5 + - - +
21B ASP* 3.0 32.9 + - - +
14D T 6.1 0.2 - - - -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.7 36.3 + - - +
15B ARG 4.7 2.5 - - - +
17B GLU* 1.3 78.1 - - + +
19B SER* 1.3 57.4 + - - +
21B ASP* 2.8 21.5 - - - +
22B ALA* 2.9 25.1 + - + +
4C T 3.9 24.1 + - - -
5C G 3.3 33.6 + - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG 3.8 9.2 + - - -
16B LYS* 3.1 22.8 + - - +
18B LYS* 1.3 80.2 - - - +
20B ARG* 1.3 63.3 + - - +
22B ALA* 4.9 1.1 - - - -
23B ALA* 2.9 30.7 + - - +
13D G 6.3 0.2 - - - -
14D T 3.8 23.1 - - - +
15D A 5.6 5.0 + - - -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS 2.6 20.0 + - - +
17B GLU* 3.1 40.5 + - - +
19B SER* 1.3 72.5 - - - +
21B ASP* 1.3 63.7 + - - +
23B ALA* 3.9 1.2 - - - +
24B ARG* 2.9 56.7 + - - +
13D G 3.5 47.7 + - + +
14D T 3.3 26.4 - - - +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.0 18.2 + - - +
18B LYS* 2.8 17.7 - - - +
20B ARG* 1.3 81.0 + - - +
22B ALA* 1.3 76.2 + - - +
24B ARG* 3.4 29.6 + - - +
25B CYS* 2.9 25.1 + - - +
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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 LYS* 2.9 18.9 + - + +
19B SER* 4.5 1.3 - - - +
21B ASP* 1.3 79.9 + - - +
23B ALA* 1.3 61.3 + - - +
24B ARG 3.1 1.1 - - - -
25B CYS* 3.0 10.0 + - - +
26B ARG* 2.9 27.2 + - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 2.9 20.9 + - - +
20B ARG 4.0 1.6 - - - +
22B ALA* 1.3 77.1 - - - +
24B ARG* 1.3 57.0 + - - +
26B ARG* 3.4 11.7 + - - +
27B ARG* 2.9 61.5 + - - +
8C T 6.0 2.2 - - + +
13D G 5.3 0.4 - - + -
14D T 3.6 14.1 - - + +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 2.9 48.4 + - - +
21B ASP* 3.4 43.6 + - - +
22B ALA 3.1 0.2 - - - -
23B ALA* 1.3 78.4 - - - +
25B CYS* 1.3 55.8 + - - +
27B ARG* 3.2 5.1 + - - +
28B SER* 2.9 32.6 + - - +
12D C 3.2 39.3 + - + +
13D G 3.6 16.6 + - - +
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Residues in contact with CYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP 2.9 15.8 + - - +
22B ALA* 3.0 12.8 + - - +
24B ARG* 1.3 76.7 - - - +
26B ARG* 1.3 57.6 + - - +
28B SER* 3.2 10.9 + - - -
29B LYS* 3.0 38.9 + - - +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 3.9 11.5 + - - -
129A LEU* 3.4 34.6 - - + +
22B ALA 2.9 11.8 + - - +
23B ALA* 3.6 13.8 - - - +
24B ARG 3.3 0.2 - - - -
25B CYS* 1.3 74.1 - - - +
27B ARG* 1.3 63.0 + - + +
29B LYS* 3.1 10.6 + - - +
30B GLU* 2.8 30.5 + - + +
6C C 4.4 3.8 - - - +
7C G 2.9 48.3 + - - +
8C T 3.9 40.0 + - - +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 2.9 48.6 + - - +
24B ARG* 3.5 6.1 - - - +
26B ARG* 1.3 77.2 - - + +
28B SER* 1.3 62.7 + - - +
30B GLU* 2.9 28.9 - - - +
31B THR* 3.0 18.8 + - + +
9C A 4.7 4.2 - - - +
11D A 3.9 19.7 - - + +
12D C 3.1 51.0 + - - +
13D G 2.6 43.2 + - - -
14D T 3.6 6.3 + - - -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.9 16.4 + - - +
25B CYS* 3.2 14.0 - - - -
26B ARG 3.2 0.2 - - - -
27B ARG* 1.3 73.6 - - - +
29B LYS* 1.3 68.0 + - - +
31B THR* 2.7 23.2 + - - -
32B GLU* 3.0 11.7 + - - +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.0 19.1 - - + -
133A ARG* 6.2 1.8 - - - +
25B CYS* 3.0 26.3 + - - +
26B ARG* 3.1 11.2 + - - +
28B SER* 1.3 76.5 - - - +
30B GLU* 1.3 64.5 + - - +
32B GLU* 3.7 3.9 - - - +
33B VAL* 2.9 32.6 + - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 5.6 6.5 - - - -
129A LEU* 3.5 20.4 - - + +
132A LEU* 6.1 0.4 - - - -
26B ARG* 2.8 21.2 + - + +
27B ARG* 2.9 26.8 - - - +
29B LYS* 1.3 71.9 - - - +
31B THR* 1.3 85.2 + - - +
33B VAL* 3.1 3.5 + - - +
34B PHE* 2.9 51.8 + - + -
53B LYS* 4.9 5.9 - - - +
11D A 4.2 12.1 + - - +
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.0 15.9 + - + +
28B SER* 2.7 24.1 + - - -
30B GLU* 1.3 96.0 - - - +
32B GLU* 1.3 60.2 + - - +
34B PHE* 2.9 21.8 + - - +
35B TYR* 3.0 19.3 + - - +
11D A 3.5 28.0 - - - +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 5.9 0.7 + - - -
28B SER 3.0 13.6 + - - +
29B LYS* 3.9 3.7 - - - +
31B THR* 1.3 82.3 + - - +
33B VAL* 1.3 61.7 + - - +
35B TYR* 4.3 3.6 - - - +
36B GLU* 3.2 40.0 + - - +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.5 5.2 - - + -
132A LEU* 2.8 39.3 - - + +
133A ARG* 3.4 48.7 - - - +
136A VAL* 3.8 7.3 - - + +
29B LYS* 2.9 34.0 + - + +
30B GLU* 3.4 6.1 - - - +
32B GLU* 1.3 82.9 - - - +
34B PHE* 1.3 62.5 + - - +
36B GLU* 3.3 19.0 - - - +
37B LEU* 3.7 4.0 + - - +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 5.1 3.1 - - + -
128A LYS* 4.6 16.4 - - - -
132A LEU* 3.0 38.8 - - + -
30B GLU* 2.9 52.2 + - + -
31B THR* 2.9 8.9 + - - +
33B VAL* 1.3 74.1 - - - +
35B TYR* 1.3 64.7 + - + +
36B GLU 3.0 4.3 - - - -
37B LEU* 2.8 35.0 + - + +
38B ALA* 3.0 10.4 + - - +
53B LYS* 3.4 43.7 - - + -
56B ILE* 4.3 11.1 - - + +
57B MET* 4.1 15.3 - - - -
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Residues in contact with TYR 35 (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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31B THR* 3.0 18.4 + - - +
32B GLU* 5.1 3.4 - - - +
34B PHE* 1.3 78.7 - - + +
36B GLU* 1.3 57.4 + - - +
37B LEU 3.5 0.2 - - - -
38B ALA* 3.8 6.4 - - + +
39B HIS* 2.9 24.8 + - - +
48B SER 5.0 0.7 - - - +
49B SER* 3.0 33.2 - - - +
50B HIS* 4.3 4.8 - - - -
51B LEU 2.7 32.1 + - - -
52B ASP* 4.9 3.1 - - - -
53B LYS* 5.2 5.3 + - + -
56B ILE* 4.0 14.8 - - + -
10D C 5.4 2.5 + - - -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 3.4 26.2 + - - -
136A VAL* 4.6 14.9 - - + +
32B GLU* 3.2 30.2 + - - +
33B VAL* 3.3 28.0 - - - +
35B TYR* 1.3 76.4 - - - +
37B LEU* 1.3 60.9 + - - +
38B ALA 3.3 0.2 - - - -
39B HIS* 3.5 12.7 + - + +
40B GLU* 2.9 28.1 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 5.1 7.0 - - + -
132A LEU* 5.5 3.8 - - + -
135A ALA* 4.7 4.7 - - + -
136A VAL* 3.6 33.4 - - + +
139A MET* 3.8 38.1 - - + -
33B VAL 4.0 2.9 - - - +
34B PHE* 2.8 21.2 + - + +
36B GLU* 1.3 82.8 - - - +
38B ALA* 1.3 63.3 + - - +
40B GLU* 3.1 28.9 + - - +
41B LEU* 3.2 4.0 + - + +
56B ILE* 3.7 22.0 - - + +
57B MET* 4.8 10.1 - - - -
60B ALA* 4.2 15.9 - - + -
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Residues in contact with ALA 38 (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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34B PHE 3.0 6.2 + - - +
35B TYR* 3.8 9.9 - - - +
37B LEU* 1.3 77.3 - - - +
39B HIS* 1.3 62.1 - - - +
41B LEU* 3.1 32.8 - - + +
48B SER* 3.2 30.7 - - - +
49B SER 4.9 1.1 - - - +
51B LEU* 4.4 0.7 - - + -
56B ILE* 3.5 37.0 - - + +
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Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 4.0 18.0 + - - -
35B TYR 2.9 20.1 + - - +
36B GLU* 3.5 13.8 + - + +
38B ALA* 1.3 74.7 - - - +
40B GLU* 1.3 67.5 + - - +
41B LEU 3.3 2.8 + - - +
45B HIS* 3.2 59.5 + + + -
48B SER* 3.5 14.1 + - - -
49B SER* 4.9 5.6 - - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 5.1 4.7 - - + +
139A MET* 3.3 52.9 - - + +
140A LYS* 3.5 45.8 + - + +
36B GLU 2.9 14.5 + - - +
37B LEU* 3.1 16.3 + - - +
39B HIS* 1.3 84.5 + - - +
41B LEU* 1.3 81.9 + - - +
42B PRO* 4.5 4.3 - - - +
45B HIS* 5.6 0.5 + - - -
63B PHE* 4.9 3.5 - - - -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 3.5 26.0 - - + -
158A PHE* 4.9 2.2 - - + -
37B LEU* 3.2 9.1 + - + +
38B ALA* 3.1 30.9 + - - +
39B HIS 3.8 2.6 - - - +
40B GLU* 1.3 92.1 + - - +
42B PRO* 1.3 70.7 - - + +
43B LEU* 2.8 34.5 - - + +
45B HIS* 5.7 0.3 + - - -
48B SER* 4.5 3.6 - - - -
51B LEU* 4.1 10.8 - - + -
56B ILE* 4.6 9.2 - - + +
59B LEU* 4.1 43.7 - - + +
60B ALA* 4.2 4.3 - - + +
63B PHE* 5.1 0.7 - - + -
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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