Contacts of the strand formed by residues 2282 - 2287 (chain A) in PDB entry 2W0P
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 GLU2282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2280A LYS* 4.2 22.8 - - - +
2281A ALA* 1.3 75.7 - - - +
2283A ILE* 1.3 60.5 + - - +
2284A SER 4.1 0.2 + - - -
2296A ALA 3.9 0.3 - - - +
2297A TYR* 3.2 4.7 - - - -
2298A VAL* 3.0 43.7 + - + +
2276B GLU* 4.2 8.8 - - - +
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Residues in contact with ILE2283 (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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2273A ILE* 4.3 17.9 - - + +
2274A ALA 4.5 0.4 - - - -
2275A VAL* 3.9 17.3 - - + +
2281A ALA* 4.0 8.2 + - + -
2282A GLU* 1.3 76.9 + - - +
2284A SER* 1.3 71.0 + - - +
2285A PHE* 5.6 2.5 - - + -
2295A VAL* 4.1 14.8 - - + -
2296A ALA 3.4 8.3 - - - +
2297A TYR* 4.0 14.1 - - + -
2276B GLU* 5.3 1.8 + - - -
11C SER* 3.6 37.5 - - - +
13C VAL* 3.9 29.0 - - + +
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Residues in contact with SER2284 (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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2282A GLU 4.1 0.8 + - - -
2283A ILE* 1.3 75.5 - - - +
2285A PHE* 1.3 63.5 + - - +
2294A GLY 4.5 0.2 - - - -
2295A VAL* 3.4 8.5 - - - +
2296A ALA* 2.8 48.6 + - - +
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Residues in contact with PHE2285 (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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2271A LEU* 3.7 21.1 - - + -
2273A ILE* 4.0 19.7 - - + -
2283A ILE* 5.6 3.4 - - + -
2284A SER* 1.3 78.1 - - - +
2286A GLU* 1.3 59.6 - - - +
2287A ASP* 3.7 28.0 - - + -
2293A CYS* 3.7 40.2 - - + -
2294A GLY 3.3 11.7 - - - -
2295A VAL* 4.3 4.3 - - + -
2313B GLU* 3.1 26.4 + - - +
15C ILE* 3.6 45.8 - - + -
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Residues in contact with GLU2286 (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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2285A PHE* 1.3 77.0 - - - +
2287A ASP* 1.3 64.7 + - - +
2288A ARG* 3.4 37.5 + - + +
2293A CYS* 3.4 4.2 - - - +
2294A GLY* 2.7 46.3 + - - +
2313B GLU* 5.1 1.6 - - - +
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Residues in contact with ASP2287 (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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2285A PHE* 3.7 24.4 - - + -
2286A GLU* 1.3 76.8 - - - +
2288A ARG* 1.3 69.4 + - - +
2289A LYS* 5.2 2.6 - - - +
2293A CYS* 4.1 14.3 - - - -
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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