Contacts of the strand formed by residues 231 - 235 (chain D) in PDB entry 4UC5
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 CYS 231 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 4.0 1.8 - - - +
178D ALA 4.9 0.9 - - - -
185D VAL* 3.1 15.9 - - - +
187D PHE* 3.9 19.1 - - + -
202D ILE* 3.8 25.6 - - + +
205D ALA* 3.8 18.4 - - - -
228D ASN* 3.5 42.4 - - - +
229D PRO 3.5 3.6 - - - +
230D ASP* 1.3 78.3 - - - +
232D HIS* 1.3 62.4 + - - +
261D THR* 3.5 17.7 - - - +
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Residues in contact with HIS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 3.9 26.4 - - + +
57D LEU* 5.3 1.2 - - + +
161D TRP* 3.1 33.6 + + - -
184D PRO* 5.6 0.2 - - + -
185D VAL 3.0 17.6 + - - +
186D GLY* 3.3 17.8 - - - -
187D PHE* 2.8 27.9 + - - +
202D ILE* 3.6 13.5 - - - -
230D ASP 4.4 2.0 - - - -
231D CYS* 1.3 75.9 - - - +
233D VAL* 1.3 77.2 + - - +
234D ILE* 3.9 1.8 - - + -
261D THR* 4.4 5.4 - - + -
263D LYS 3.7 18.2 - - - +
264D LEU* 4.7 1.0 - - - -
265D MET* 3.7 31.5 + - + +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PHE* 3.2 7.4 - - + +
195D LEU* 4.4 14.8 - - + -
198D ALA* 3.7 30.7 - - + +
199D ILE* 4.1 4.0 - - + +
202D ILE* 3.7 20.3 - - + +
232D HIS* 1.3 92.2 + - - +
234D ILE* 1.3 66.7 + - - +
235D LEU* 5.0 2.5 - - + -
251D ALA* 5.6 0.4 - - + -
255D LEU* 4.0 26.0 - - + +
261D THR 5.9 0.2 + - - -
263D LYS 4.7 1.4 + - - +
264D LEU* 3.7 25.4 - - + -
265D MET 3.2 14.2 + - - -
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Residues in contact with ILE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D TRP* 3.7 24.7 - - + -
163D ALA* 4.9 2.9 - - + -
186D GLY* 3.6 26.2 - - - +
187D PHE 2.7 8.9 + - - +
188D LYS* 3.5 34.3 - - + -
189D ASN* 3.2 24.6 + - - +
232D HIS* 3.9 13.7 - - + -
233D VAL* 1.3 82.0 - - - +
235D LEU* 1.3 65.4 + - - +
236D ARG 3.4 1.0 + - - -
265D MET* 3.3 22.7 - - + +
267D ASP* 4.1 24.0 - - + +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ASN* 3.5 5.8 - - - +
195D LEU* 4.3 25.1 - - + -
233D VAL* 5.0 1.6 - - + -
234D ILE* 1.3 69.9 - - - +
236D ARG* 1.3 58.8 + - - +
242D ASN* 3.3 44.9 - - + +
247D HIS* 4.9 1.6 - - + +
248D VAL* 4.1 18.6 - - + +
251D ALA* 4.4 11.4 - - + -
264D LEU* 3.7 35.4 - - + -
265D MET 2.8 14.1 + - - +
266D ILE* 3.7 9.4 - - + -
267D ASP 2.9 27.4 + - - -
272D ASN* 3.1 6.4 + - - -
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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
------------------------------------------------------------
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