Contacts of the strand formed by residues 232 - 238 (chain A) in PDB entry 4X3G
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 ARG 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASN* 3.4 3.5 - - - +
229A GLY* 3.1 28.0 + - - +
230A HIS* 3.2 25.2 + - - +
231A ARG* 1.4 81.4 - - - +
233A ARG* 1.3 62.9 + - - +
266A LEU* 3.6 40.2 + - - +
267A PHE* 3.7 17.0 - - + -
236B TRP* 4.0 15.0 - - + -
237B GLU 3.4 7.6 - - - -
238B ALA* 4.7 1.3 - - + -
241B ARG* 4.4 5.4 - - - +
255B ASP* 2.7 41.9 + - - +
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Residues in contact with ARG 233 (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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226A GLU* 3.3 34.3 + - + +
227A LEU 3.3 11.9 - - - +
228A ASN* 3.3 23.2 + - - +
232A ARG* 1.3 76.4 - - - +
234A LEU* 1.3 63.1 + - - +
235A THR* 3.5 14.6 + - - +
267A PHE* 4.0 1.0 - - - -
235B THR 4.1 0.5 - - - +
236B TRP* 3.4 10.0 - - - -
237B GLU* 2.8 80.5 + - + +
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Residues in contact with LEU 234 (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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225A LEU 3.7 1.0 - - - +
226A GLU* 3.2 4.3 - - - -
227A LEU* 2.9 56.5 + - + +
233A ARG* 1.3 72.3 - - - +
235A THR* 1.3 59.1 + - - +
257A LEU* 4.0 19.7 - - + +
258A VAL 4.9 3.6 - - - +
259A PHE* 4.4 8.3 - - + -
263A ILE* 4.0 22.4 - - + -
267A PHE* 4.2 10.9 - - + -
234B LEU* 4.2 16.4 - - + -
235B THR 3.4 15.3 - - - +
236B TRP* 4.0 20.0 - - + -
256B CYS 5.6 0.4 - - - +
257B LEU* 4.3 13.0 - - + -
258B VAL 5.7 4.7 - - - +
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Residues in contact with THR 235 (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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224A ARG* 3.7 33.9 - - + -
225A LEU 3.3 5.6 - - - +
226A GLU* 4.1 7.1 - - + +
233A ARG* 3.5 24.4 + - - +
234A LEU* 1.3 75.1 + - - +
236A TRP* 1.3 62.0 + - - +
237A GLU* 4.1 13.5 - - - +
257A LEU* 4.8 1.3 - - - -
233B ARG 4.1 0.6 - - - +
234B LEU* 3.6 8.8 - - - +
235B THR* 2.8 52.6 + - - +
237B GLU* 4.4 3.6 + - - -
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Residues in contact with TRP 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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223A TYR* 3.2 35.6 + + - +
224A ARG* 3.4 2.8 - - - -
225A LEU* 2.8 43.5 + - + +
235A THR* 1.3 73.5 - - - +
237A GLU* 1.3 63.0 + - - +
238A ALA* 3.6 21.4 - - + +
254A SER 4.8 2.7 - - - -
255A ASP* 3.7 15.3 - - - -
256A CYS* 3.5 35.4 - - - +
257A LEU* 3.7 35.4 - - + -
232B ARG* 3.9 24.0 - - + -
233B ARG 3.6 14.4 - - - -
234B LEU* 4.1 16.2 - - + -
263B ILE* 5.2 4.5 - - + -
266B LEU* 5.3 1.8 - - + -
267B PHE* 3.6 28.0 - + - -
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Residues in contact with GLU 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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223A TYR 3.4 5.6 - - - +
224A ARG* 3.7 34.7 - - + +
235A THR* 4.1 10.2 - - + +
236A TRP* 1.3 81.3 - - - +
238A ALA* 1.3 63.6 + - - +
231B ARG 5.3 0.2 - - - -
232B ARG* 3.4 2.4 - - - -
233B ARG* 2.8 84.2 + - + +
235B THR* 4.2 5.9 + - - -
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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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222A ALA* 3.5 6.9 - - - +
223A TYR* 2.9 43.2 + - + +
236A TRP* 3.6 29.1 - - + +
237A GLU* 1.3 75.8 - - - +
239A THR* 1.3 65.3 + - - +
255A ASP* 5.2 2.9 - - - +
231B ARG 3.3 16.2 - - - +
232B ARG* 4.4 4.5 - - + -
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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