Contacts of the strand formed by residues 235 - 239 (chain A) in PDB entry 4Y2H
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 GLU 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A HIS* 3.1 38.6 + - + +
234A SER* 1.3 84.4 - - - +
236A ILE* 1.3 67.9 + - - +
237A VAL* 3.5 3.8 + - + +
322A LEU 4.1 2.3 - - - +
324A TYR 5.5 0.5 + - - -
352A ARG* 5.2 9.3 + - - +
371A PHE* 3.9 10.5 - - - -
372A ALA 3.4 8.7 - - - +
374A GLU* 4.2 22.5 - - + +
375A ASP 5.1 2.5 + - - -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 1.3 70.6 - - - +
237A VAL* 1.3 61.1 + - - +
290A ILE* 6.2 0.2 - - + -
321A ALA* 3.7 30.1 - - + -
322A LEU 3.8 9.4 - - - +
323A LEU* 4.0 9.2 - - + -
353A LEU* 3.8 20.2 - - + +
355A VAL* 3.6 27.4 - - + -
371A PHE* 3.4 21.8 - - + -
372A ALA* 3.0 11.6 + - - -
373A MET* 3.5 39.1 - - + +
374A GLU* 3.0 29.3 + - - +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 3.9 15.5 - - + +
235A GLU* 3.8 12.6 - - + +
236A ILE* 1.3 74.1 - - - +
238A VAL* 1.3 70.2 + - - +
239A GLN* 3.4 23.2 + - + +
321A ALA* 3.5 1.1 - - - -
322A LEU* 2.6 42.7 + - + +
324A TYR* 3.8 31.0 - - + -
374A GLU* 3.6 17.5 - - - +
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Residues in contact with VAL 238 (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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159A TYR* 3.6 52.0 - - + -
237A VAL* 1.3 74.0 - - - +
239A GLN* 1.3 61.0 + - - +
318A TRP 3.7 22.4 - - - +
319A LYS* 4.0 19.9 + - + +
320A GLN 3.4 5.4 - - - +
321A ALA* 5.1 4.3 - - - -
373A MET* 4.0 14.4 - - + -
374A GLU* 3.3 18.1 + - + +
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Residues in contact with GLN 239 (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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198A ASP* 2.8 35.8 + - - -
200A MET* 4.1 15.0 - - - +
201A LEU* 4.7 2.4 - - - +
204A ARG* 5.9 0.7 + - - -
237A VAL* 3.4 15.4 + - + +
238A VAL* 1.3 75.0 - - - +
240A GLY* 1.3 72.4 + - - +
319A LYS* 3.8 8.3 - - - -
320A GLN* 3.1 27.7 + - - +
322A LEU* 3.9 18.4 - - + +
324A TYR* 3.8 7.3 + - - -
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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