Contacts of the strand formed by residues 229 - 234 (chain R) in PDB entry 5A31
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 TYR 229 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R TYR* 4.9 3.1 - - - -
192R LEU* 4.4 13.6 - - - +
204R ALA* 4.1 17.5 - - + +
206R GLY 3.4 13.6 + - - +
207R LYS 3.3 36.3 - - - -
208R SER* 3.8 3.1 - - - -
209R ILE* 3.7 24.7 - - + -
223R CYS* 3.4 31.0 - - - +
224R ASP 3.0 22.0 + - - -
225R THR* 3.6 18.2 - - + -
228R GLU* 1.3 81.7 - - - +
230R THR* 1.3 60.4 + - - +
231R SER 5.2 1.1 - - - +
243R VAL* 3.1 30.7 - - + -
244R GLY 3.6 1.1 - - - +
245R GLN* 3.8 20.4 - - + -
251R GLU* 4.2 4.7 + - - -
253R TYR* 4.0 4.3 + - - -
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Residues in contact with THR 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190R TYR* 3.4 40.1 + - + +
191R SER 4.8 0.2 + - - -
192R LEU* 3.6 15.9 - - - +
228R GLU* 3.3 4.5 + - - +
229R TYR* 1.3 79.3 + - - +
231R SER* 1.3 63.4 + - - +
244R GLY 3.0 4.6 + - - -
245R GLN 3.9 12.1 - - - -
246R ALA* 3.3 20.8 + - - +
270R ARG* 4.0 15.7 - - + -
271R VAL 3.1 25.4 - - - +
272R ALA* 3.5 11.3 - - - +
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Residues in contact with SER 231 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R SER 5.0 3.4 - - - -
192R LEU* 4.1 7.2 - - - +
209R ILE* 5.7 0.2 - - - +
229R TYR* 5.3 1.3 - - - +
230R THR* 1.3 82.0 + - - +
232R LEU* 1.3 65.8 + - - +
243R VAL* 3.5 5.5 - - - +
244R GLY* 3.0 26.7 + - - +
271R VAL* 2.8 20.4 + - - +
272R ALA 3.4 21.1 - - - -
273R CYS* 3.7 5.8 - - - -
274R LEU* 3.2 25.8 - - - +
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Residues in contact with LEU 232 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191R SER 4.3 8.8 + - - +
192R LEU* 3.9 8.3 - - - +
193R ILE 3.5 23.6 - - - +
194R ASP* 3.6 25.5 - - + +
202R ALA* 4.0 19.1 - - + +
203R VAL 4.1 2.7 - - - -
204R ALA* 3.7 36.1 - - + +
209R ILE* 4.7 9.4 - - + -
231R SER* 1.3 77.1 - - - +
233R SER* 1.3 66.3 + - - +
241R LEU* 4.1 12.3 - - + -
242R ALA 3.2 12.6 - - - +
243R VAL* 4.8 3.1 - - + -
274R LEU* 4.0 7.1 + - - +
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Residues in contact with SER 233 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R ASP* 3.5 10.0 + - - -
232R LEU* 1.3 78.4 - - - +
234R TRP* 1.3 62.2 + - - +
241R LEU* 3.7 4.2 - - - +
242R ALA* 3.0 30.4 + - - -
274R LEU* 3.9 31.7 + - - -
275R SER* 4.2 4.3 - - - -
276R TRP* 3.1 27.5 + - - -
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Residues in contact with TRP 234 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194R ASP* 2.9 56.8 + - + +
195R TRP 5.3 0.2 - - - +
196R SER* 3.3 28.3 - - - -
197R SER 5.4 0.2 - - - +
200R VAL* 3.2 39.7 + - + -
202R ALA* 3.4 23.5 - - + +
211R LEU* 4.0 5.8 - - + -
233R SER* 1.3 74.0 + - - +
235R ILE* 1.3 71.0 + - - +
236R GLY 3.7 0.3 + - - -
238R GLY 3.2 29.8 - - - -
240R HIS 3.6 18.6 - - - -
241R LEU* 4.0 8.1 - - + -
255R VAL* 3.4 37.9 - - + -
276R TRP* 3.1 13.3 - - - +
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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