Contacts of the strand formed by residues 235 - 239 (chain A) in PDB entry 4J2X
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 ASN 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A VAL* 3.1 7.8 - - - +
232A GLU 2.9 33.2 + - - +
233A GLY 3.0 25.1 + - - -
234A GLY* 1.4 79.6 - - - +
236A PHE* 1.3 66.3 + - - +
237A HIS* 3.7 4.4 + - + -
191B TRP* 3.1 31.2 + - + +
341C LYS* 3.7 20.8 + - - +
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Residues in contact with PHE 236 (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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229A LEU* 3.9 22.4 - - + -
230A HIS 3.5 3.8 - - - -
231A VAL* 3.6 20.9 - - + +
235A ASN* 1.3 75.0 - - - +
237A HIS* 1.3 60.4 + - - +
246A PHE* 3.5 27.6 - + - -
276A LEU 4.7 1.1 - - - -
283A MET* 3.5 29.8 - - + -
284A ALA* 3.7 20.9 - - - -
285A LEU* 3.8 30.5 - - + -
331A ILE* 3.9 14.7 + - + +
191B TRP* 3.5 57.8 - + + -
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Residues in contact with HIS 237 (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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228A TYR 3.7 0.3 - - - +
229A LEU* 3.8 1.9 - - - +
230A HIS* 2.7 82.7 + + + +
232A GLU* 3.4 38.4 + - + +
235A ASN* 4.1 4.6 + - + +
236A PHE* 1.3 75.0 - - - +
238A ALA* 1.4 58.5 + - - +
239A SER* 3.7 18.1 + - - -
329A GLU* 2.8 48.6 + - + +
330A ARG* 5.3 1.1 - - - -
331A ILE* 3.6 11.9 - - - +
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Residues in contact with ALA 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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227A ARG* 3.2 30.9 + - + -
228A TYR 3.3 7.6 - - - +
237A HIS* 1.4 72.4 - - - +
239A SER* 1.3 60.7 + - - +
326A LEU* 3.8 30.7 - - + -
328A GLN 4.1 2.5 - - - +
329A GLU* 2.7 21.8 + - - +
331A ILE* 3.8 18.1 - - + +
354A TRP* 4.6 3.8 - - + -
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Residues in contact with SER 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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227A ARG* 3.2 3.1 - - - +
228A TYR* 2.6 43.2 + - - -
230A HIS* 4.3 1.8 - - - -
232A GLU* 5.6 0.3 + - - -
237A HIS* 3.7 27.7 + - - -
238A ALA* 1.3 73.1 - - - +
240A SER* 1.3 59.8 + - - +
241A GLN* 3.3 4.9 + - - +
242A GLN* 3.1 40.3 + - - +
329A GLU* 5.0 0.9 - - - -
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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