Contacts of the strand formed by residues 28 - 32 (chain A) in PDB entry 2W8K
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 VAL 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.6 15.4 - - + +
16A GLU* 4.9 2.5 - - + -
17A GLU* 3.2 15.3 - - - +
23A LEU* 4.3 22.7 - - + +
26A LYS* 3.4 8.7 - - + +
27A PRO* 1.3 73.6 - - - +
29A VAL* 1.3 70.8 + - - +
30A VAL* 4.7 8.1 - - + +
46A ALA* 3.0 27.9 - - - +
47A ASN* 3.1 29.2 + - - +
50A ALA* 4.4 0.2 - - - +
72A VAL* 3.3 9.6 - - + +
74A LEU* 4.0 24.2 - - + -
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Residues in contact with VAL 29 (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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28A VAL* 1.3 79.2 - - - +
30A VAL* 1.3 61.2 + - - +
31A CYS* 3.2 13.6 + - - -
43A VAL* 3.4 42.8 - - + -
45A THR 3.7 2.2 - - - +
46A ALA* 4.2 0.7 - - + -
50A ALA* 4.4 11.7 - - + -
55A VAL* 3.8 13.9 - - + -
64A ALA* 5.3 0.2 - - + -
68A LEU* 5.9 0.4 - - + -
71A ALA* 3.9 16.2 - - + -
72A VAL 2.8 10.5 + - - +
73A TYR* 3.3 30.8 - - + -
74A LEU 3.0 22.9 + - - -
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Residues in contact with VAL 30 (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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12A TYR* 4.0 6.7 - - + +
13A ALA* 3.8 35.0 - - + +
16A GLU* 4.4 9.0 - - + -
28A VAL* 4.8 4.7 - - + -
29A VAL* 1.3 68.5 - - - +
31A CYS* 1.3 59.4 + - - +
43A VAL* 3.9 1.6 - - - -
44A ALA* 2.9 31.6 + - + +
45A THR* 2.9 20.5 + - + +
74A LEU* 3.0 15.9 - - + +
75A PRO 3.7 3.4 - - - +
76A MET* 3.5 34.1 - - + -
81A TYR* 3.7 12.8 - - + +
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Residues in contact with CYS 31 (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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29A VAL* 3.3 24.0 - - - -
30A VAL* 1.3 75.1 - - - +
32A VAL* 1.3 62.4 + - - +
33A PHE* 3.7 13.7 + - + -
42A ALA 3.5 4.5 - - - -
43A VAL* 4.6 2.7 - - - +
61A ILE* 3.3 33.2 - - + -
73A TYR* 3.3 34.8 - - - -
74A LEU 2.7 8.6 + - - +
75A PRO* 3.1 8.7 - - - +
76A MET 2.9 24.0 + - - -
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Residues in contact with VAL 32 (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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31A CYS* 1.3 76.2 - - - +
33A PHE* 1.3 66.5 + - - +
41A GLY* 2.9 24.9 - - - -
42A ALA 2.8 18.5 + - - +
44A ALA* 4.1 19.3 - - + +
76A MET* 4.2 22.7 - - + +
4T C 3.4 35.2 - - - +
5T N2G 3.2 32.1 - - - +
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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