Contacts of the strand formed by residues 26 - 38 (chain E) in PDB entry 4ZXB
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 CYS 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLU 3.5 7.2 - - - +
8E CYS* 2.0 50.9 - - + -
22E GLU 4.0 4.5 - - - -
23E LEU* 3.1 39.8 + - + +
25E ASN* 1.3 74.9 - - - +
27E SER* 1.3 60.0 + - - +
28E VAL 4.1 7.2 - - - +
29E ILE* 4.5 9.2 - - + -
53E LYS* 3.4 5.3 - - - +
54E LEU* 3.3 27.3 + - + +
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Residues in contact with SER 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E TYR* 3.9 12.5 - - - -
4E PRO* 3.7 12.4 - - - +
5E GLY* 4.0 24.2 - - - -
6E GLU 2.8 10.5 + - - -
25E ASN 3.5 1.2 + - - -
26E CYS* 1.3 74.5 - - - +
28E VAL* 1.3 63.5 + - - +
53E LYS* 3.2 12.1 + - - -
54E LEU* 3.8 1.7 - - - +
55E ILE* 2.9 52.5 + - - +
56E MET 3.2 6.6 + - - -
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Residues in contact with VAL 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E TYR* 3.6 38.4 - - + -
6E GLU 3.4 2.3 + - - +
7E VAL* 3.4 10.9 - - + -
8E CYS* 2.8 26.2 + - - -
26E CYS* 4.1 2.1 - - - +
27E SER* 1.3 84.6 - - - +
29E ILE* 1.3 75.0 + - - +
30E GLU 4.2 2.0 - - - +
54E LEU* 4.3 0.7 - - - -
56E MET* 3.3 29.2 - - + -
58E THR* 4.2 2.2 - - + -
251E TRP* 3.8 34.3 - - + -
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Residues in contact with ILE 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E CYS* 3.4 4.0 - - + +
9E PRO 3.9 14.8 - - - +
10E GLY* 3.9 1.3 - - - -
11E MET* 5.8 0.2 - - + -
23E LEU* 3.7 31.0 - - + -
26E CYS* 4.5 6.1 - - + -
28E VAL* 1.3 73.9 - - - +
30E GLU* 1.3 60.3 + - - +
31E GLY 3.2 14.5 + - - +
32E HIS 3.8 22.9 - - - +
33E LEU* 3.9 29.2 - - + -
54E LEU* 3.8 24.2 - - + +
56E MET 2.9 9.1 + - - -
57E ILE* 3.5 11.8 - - + -
58E THR* 2.9 28.6 + - - +
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 3.7 16.1 - - + +
8E CYS 2.7 11.3 + - - +
9E PRO* 3.5 6.9 - - + +
10E GLY 3.3 14.1 + - - -
28E VAL* 3.7 1.6 + - + -
29E ILE* 1.3 68.5 - - - +
31E GLY* 1.3 56.8 + - - +
58E THR* 3.5 9.6 - - + +
248E PHE* 3.4 10.2 - - - -
249E GLN* 3.6 33.2 - - + +
251E TRP* 2.7 31.2 + - - +
252E ARG* 2.9 39.4 + - - -
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Residues in contact with GLY 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLY* 4.0 7.2 - - - -
29E ILE* 3.6 4.8 - - - +
30E GLU* 1.3 75.6 - - - +
32E HIS* 1.3 59.5 + - - -
57E ILE* 3.4 10.2 - - - +
58E THR* 3.0 6.9 + - - -
59E ASP* 3.1 40.5 + - - -
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Residues in contact with HIS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLY* 3.1 8.0 - - - -
11E MET 2.9 31.5 + - - -
12E ASP* 2.9 33.9 + - - -
29E ILE* 3.8 4.6 - - - +
31E GLY* 1.3 73.3 - - - -
33E LEU* 1.3 62.1 + - - +
34E GLN* 3.8 11.8 + - + -
57E ILE* 4.6 0.4 - - - -
59E ASP* 3.7 8.0 + - + -
60E TYR* 3.3 58.4 + + + +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET* 3.5 21.5 - - + +
13E ILE* 4.3 3.6 - - + -
23E LEU* 4.0 19.7 - - + -
29E ILE* 3.9 26.2 - - + -
32E HIS* 1.3 74.3 - - - +
34E GLN* 1.3 65.8 + - - +
35E ILE* 4.2 17.0 - - + -
57E ILE* 4.3 10.7 - - + +
60E TYR 2.9 7.4 + - - +
61E LEU* 3.4 22.0 - - + +
62E LEU 2.9 24.9 + - - -
76E PHE* 3.6 34.5 - - + -
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Residues in contact with GLN 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E MET 3.0 7.6 + - - +
12E ASP* 3.3 34.8 + - - +
13E ILE* 2.8 31.9 + - - +
14E ARG* 3.7 13.5 - - - +
32E HIS* 3.8 10.5 + - + -
33E LEU* 1.3 74.9 - - - +
35E ILE* 1.3 60.3 + - - +
36E LEU* 3.8 20.1 - - + +
60E TYR* 2.8 32.8 + - + -
62E LEU* 3.3 21.9 - - + +
88E PHE* 4.2 11.8 - - - -
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 3.3 7.9 - - + +
17E LEU* 5.3 4.3 - - + -
20E LEU* 4.1 25.4 - - + -
33E LEU* 4.2 15.5 - - + -
34E GLN* 1.3 77.7 - - - +
36E LEU* 1.3 62.5 + - - +
38E MET* 4.1 22.0 - - + -
46E PHE* 6.4 0.4 - - + -
62E LEU* 2.9 5.6 + - - +
63E LEU* 3.3 28.7 - - + -
64E PHE 3.1 22.0 + - - -
66E VAL* 3.5 20.9 - - + +
69E LEU* 6.2 2.2 - - + -
75E LEU* 4.9 8.5 - - + -
76E PHE* 4.1 23.1 - - + -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASP 4.9 0.2 - - - -
13E ILE 2.9 21.5 + - - +
14E ARG* 3.1 59.5 - - + +
15E ASN 3.5 0.3 + - - -
34E GLN* 3.8 34.3 - - + +
35E ILE* 1.3 79.9 - - - +
37E LEU* 1.3 84.5 + - + +
38E MET* 3.5 6.4 + - - +
62E LEU* 4.8 5.2 - - + -
64E PHE* 3.1 30.1 - - + +
66E VAL* 3.9 2.2 - - - -
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Residues in contact with LEU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ARG* 5.1 11.2 - - + +
15E ASN* 3.1 33.7 + - - +
36E LEU* 1.3 91.8 - - + +
38E MET* 1.3 58.3 + - - +
39E PHE* 3.6 39.5 + - + -
64E PHE* 3.0 42.2 + - + -
65E ARG* 3.3 8.5 + - + -
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Residues in contact with MET 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 3.7 36.1 - - + +
14E ARG 3.7 6.3 - - - -
15E ASN 3.4 18.6 - - - +
16E ASN 3.2 25.8 - - - +
17E LEU* 3.7 29.2 - - + -
35E ILE* 4.1 16.2 - - + -
36E LEU 3.7 4.0 - - - +
37E LEU* 1.3 74.2 - - - +
39E PHE* 1.3 60.7 + - - +
40E LYS 3.5 2.0 - - - -
41E THR* 3.2 17.7 + - + +
65E ARG 3.0 6.0 + - - -
66E VAL* 4.3 14.1 - - + -
67E TYR* 2.9 29.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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