Contacts of the strand formed by residues 33 - 40 (chain A) in PDB entry 2W5H
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 ILE 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.7 25.1 - - + -
24A LYS* 4.1 21.3 - - + -
25A ILE 3.6 4.3 - - - +
26A ARG* 3.8 19.5 - - + -
31A GLY 3.1 9.3 + - - +
32A LYS* 1.3 83.6 + - - +
34A LEU* 1.3 69.1 + - - +
88A TYR* 3.9 33.3 + - + +
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Residues in contact with LEU 34 (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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8A TYR* 4.1 18.4 - - + -
24A LYS* 3.5 5.0 - - - +
25A ILE* 2.7 42.0 + - + +
27A ARG* 4.1 22.9 - - + +
32A LYS* 3.5 22.6 + - + +
33A ILE* 1.3 80.2 - - - +
35A VAL* 1.3 65.1 + - - +
71A TYR* 3.5 44.6 - - + -
85A VAL* 4.0 16.8 - - + -
86A MET 3.5 10.8 - - - -
87A GLU* 4.2 3.1 - - - -
88A TYR* 3.9 7.3 - - - +
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Residues in contact with VAL 35 (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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14A ILE* 3.6 19.7 - - + -
22A CYS* 4.4 15.0 - - - -
23A GLN 3.1 11.0 - - - +
24A LYS* 4.2 0.4 - - - -
25A ILE* 3.7 4.5 - - - -
34A LEU* 1.3 79.7 - - - +
36A TRP* 1.3 59.5 + - - +
37A LYS* 5.7 2.2 - - + -
85A VAL* 3.3 7.6 - - - +
86A MET* 2.7 55.2 + - + -
87A GLU 3.5 11.7 - - - +
88A TYR* 3.4 30.9 - - + +
89A CYS 5.3 0.2 - - - +
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Residues in contact with TRP 36 (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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5A ALA* 4.4 20.0 - - + -
8A TYR* 4.0 22.4 - + + -
10A VAL* 3.3 26.0 - - + -
21A ARG 3.8 0.2 - - - +
22A CYS* 3.5 3.6 - - - -
23A GLN* 2.8 60.8 + - + +
25A ILE* 3.5 23.8 - - + -
35A VAL* 1.3 77.6 - - - +
37A LYS* 1.3 65.7 + - - +
38A GLU* 4.7 2.0 - - + +
74A ILE* 4.1 20.9 - - + -
83A TYR* 3.6 44.1 - + + -
84A ILE 3.0 21.8 - - - +
85A VAL* 3.9 4.9 - - + +
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Residues in contact with LYS 37 (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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21A ARG 3.6 4.5 - - - +
22A CYS* 5.0 14.1 - - + -
35A VAL* 5.7 2.5 - - + -
36A TRP* 1.3 76.7 - - - +
38A GLU* 1.3 60.5 + - - +
39A LEU* 3.7 9.1 + - + +
82A LEU 3.2 8.0 - - - +
83A TYR* 3.3 2.1 - - - -
84A ILE* 2.8 34.1 + - + +
86A MET* 5.0 6.3 - - + -
160A PHE* 4.0 43.3 - - + -
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Residues in contact with GLU 38 (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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20A GLY* 3.2 26.2 - - - -
21A ARG* 2.8 66.6 + - + +
23A GLN* 3.8 9.1 - - - +
36A TRP* 4.0 1.3 + - + -
37A LYS* 1.3 70.9 - - - +
39A LEU* 1.3 62.4 + - - +
40A ASP 4.2 1.1 + - - +
81A THR* 3.4 25.1 - - + +
82A LEU 3.8 2.0 - - - -
83A TYR* 3.5 26.5 + - + -
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Residues in contact with LEU 39 (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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19A TYR* 3.3 24.5 - - + +
20A GLY* 5.0 0.4 - - - -
37A LYS* 3.8 13.0 - - + +
38A GLU* 1.3 84.9 - - - +
40A ASP* 1.3 60.1 + - - +
41A TYR* 3.3 5.3 + - + -
44A MET* 5.5 8.5 - - + -
52A LEU* 5.3 9.9 - - + -
81A THR* 4.3 2.7 - - - -
82A LEU* 2.7 58.5 + - + +
84A ILE* 3.5 33.4 - - + -
160A PHE* 4.0 15.7 - - + -
162A LEU* 5.6 0.4 - - + -
163A ALA* 4.4 15.5 - - + +
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Residues in contact with ASP 40 (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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19A TYR 5.1 1.4 + - - -
20A GLY* 6.0 0.4 - - - -
38A GLU* 4.2 2.4 + - - +
39A LEU* 1.3 68.1 - - - +
41A TYR* 1.3 57.3 + - - +
42A GLY* 2.8 32.7 + - - -
43A SER* 4.5 2.6 + - - -
44A MET* 4.2 8.2 - - - +
79A ASN 3.5 13.4 - - - +
80A THR* 3.0 16.2 + - - -
81A THR* 4.4 6.6 + - - +
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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