Contacts of the strand formed by residues 23 - 32 (chain E) in PDB entry 2Q6W
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 ARG 23 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E PHE* 3.4 2.3 - - - -
18E PHE* 2.7 58.2 + - + +
21E THR 4.6 0.3 - - - -
22E GLU* 1.3 79.4 - - + +
24E VAL* 1.3 62.1 + - - +
80E ARG* 4.3 0.2 - - - +
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Residues in contact with VAL 24 (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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16E HIS 3.1 7.9 - - - +
17E PHE* 3.5 29.4 - - + -
18E PHE* 5.1 0.2 - - - -
21E THR 3.7 6.1 - - - +
23E ARG* 1.3 76.9 - - - +
25E ARG* 1.3 63.0 + - - +
42E SER* 4.2 1.7 + - - -
43E ASP* 4.8 4.3 - - - +
75E VAL* 3.6 31.7 - - + +
79E CYS* 3.3 37.7 - - + -
80E ARG* 3.5 34.4 - - + +
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Residues in contact with ARG 25 (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 GLU 3.3 1.4 - - - +
15E CYS* 3.3 3.8 - - - -
16E HIS* 2.7 52.9 + - + +
18E PHE* 4.2 13.2 - - + -
24E VAL* 1.3 74.3 - - - +
26E TYR* 1.3 63.1 + - - +
27E LEU* 3.6 27.8 - - + +
39E ARG* 4.6 8.3 - - - +
41E ASP* 2.8 35.5 + - - +
42E SER* 3.7 4.5 - - - +
43E ASP* 3.1 38.5 + - - +
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Residues in contact with TYR 26 (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 SER* 3.9 0.7 - - - -
14E GLU 3.2 10.5 - - - -
25E ARG* 1.3 73.1 - - - +
27E LEU* 1.3 79.9 + - - +
28E ASP* 3.5 10.7 - - + +
40E PHE* 3.5 35.2 - + - +
41E ASP* 3.5 0.9 - - - -
42E SER* 2.7 47.0 + - - +
71E LYS* 2.9 20.8 + - + +
74E ARG* 3.6 24.7 - - + -
75E VAL* 3.8 9.6 - - + +
78E TYR* 3.5 20.4 - + - -
79E CYS* 3.6 24.5 - - - -
28F ASP* 2.0 40.3 + - - -
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Residues in contact with LEU 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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141D GLU* 5.8 0.9 - - - +
12E LYS 3.4 0.3 - - - +
13E SER* 3.0 3.8 - - - -
14E GLU* 2.6 63.8 + - + +
16E HIS* 4.1 10.8 - - + +
25E ARG* 3.6 37.7 - - + +
26E TYR* 1.3 97.1 - - - +
28E ASP* 1.3 59.3 + - - +
29E ARG* 3.9 26.7 - - + +
39E ARG* 4.5 20.4 - - - +
40E PHE 3.1 7.2 - - - +
41E ASP* 3.8 7.6 - - - +
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Residues in contact with ASP 28 (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 ARG* 2.8 35.0 + - - +
12E LYS 3.5 1.7 - - - +
13E SER* 3.6 3.3 + - - +
26E TYR* 3.5 17.2 - - + +
27E LEU* 1.3 71.4 - - - +
29E ARG* 1.3 59.2 + - - +
30E TYR* 2.8 26.8 + - + -
38E LEU 3.7 0.2 - - - +
39E ARG* 2.9 6.4 - - - +
40E PHE* 2.8 46.4 + - + -
47E TYR* 3.2 8.1 + - - -
71E LYS* 2.8 26.9 + - - +
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Residues in contact with ARG 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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141D GLU* 2.4 38.1 + - - -
143D HIS* 4.9 4.8 + - - -
11E ARG* 3.2 8.7 - - - +
12E LYS* 2.8 42.1 + - + +
14E GLU* 2.9 27.8 + - - +
27E LEU* 3.9 22.4 - - + +
28E ASP* 1.3 79.6 + - - +
30E TYR* 1.3 62.9 + - - +
31E PHE* 3.5 29.6 - - + -
36E GLU* 2.6 51.6 + - - +
38E LEU 3.3 4.9 - - - -
39E ARG* 3.2 20.5 - - + +
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Residues in contact with TYR 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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66D ASP* 5.5 0.7 - - - -
69D ASN* 4.4 13.2 - - + -
9E GLU* 5.5 4.0 - - + -
10E LEU 3.6 2.9 - - - -
11E ARG* 3.5 29.2 + - + -
28E ASP* 2.8 37.2 + - - -
29E ARG* 1.3 74.6 - - - +
31E PHE* 1.3 60.8 + - - +
36E GLU* 3.1 7.8 - - - +
37E PHE* 3.0 46.9 + + + -
38E LEU* 2.7 31.5 + - + -
47E TYR* 3.9 6.3 - + - -
61E TRP* 3.4 37.6 - + - -
30F ALA* 4.6 0.2 - - - -
31F LEU* 3.9 14.1 + - - +
33F LEU* 4.1 14.6 - - + -
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Residues in contact with PHE 31 (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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143D HIS* 3.5 37.2 - + + -
9E GLU* 3.5 9.7 - - - +
10E LEU* 2.8 62.5 + - + +
12E LYS* 3.8 24.5 - - + -
29E ARG* 3.5 55.9 - - + -
30E TYR* 1.3 76.2 - - - +
32E HIS* 1.3 59.8 + - - +
33E ASN 4.1 7.6 - - - +
35E GLU 2.9 7.4 - - - +
36E GLU* 3.4 31.4 - - + -
37E PHE* 3.6 3.4 - - - -
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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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70D LEU* 3.5 7.3 - - + +
73D MET* 3.5 26.8 + - + -
74D THR* 3.4 26.9 + - - -
77D SER* 3.4 20.3 + - - -
80D THR 4.2 4.3 - - - -
7E PHE* 4.0 6.0 - + - +
8E LEU 3.1 15.6 + - - -
9E GLU* 2.6 28.3 - - - +
31E PHE* 1.3 72.4 - - - +
33E ASN* 1.3 82.4 + - - +
34E GLN 2.9 0.7 + - - -
35E GLU* 2.6 41.8 + - + +
37E PHE* 3.5 15.6 - - + -
53E LEU* 4.6 5.8 - - + -
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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