Contacts of the strand formed by residues 195 - 202 (chain B) in PDB entry 4RN1
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 VAL 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 3.7 33.9 - - + -
166B ARG* 4.0 18.2 - - - +
172B ILE* 3.3 15.3 - - + +
174B TYR* 4.9 1.8 - - + -
189B PHE* 3.9 41.7 - - + +
192B THR* 3.9 6.5 + - + +
193B SER* 4.2 2.3 - - - +
194B LYS* 1.3 86.2 - - + +
196B MET* 1.3 63.5 + - - +
197B THR* 4.0 6.2 + - + -
225B TYR* 3.9 0.7 - - - +
255B PHE* 4.3 1.1 - - - -
403B K 2.6 28.4 - - - -
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Residues in contact with MET 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE 2.9 7.1 + - - -
173B LEU* 3.4 10.6 - - + +
174B TYR* 2.8 26.9 + - - +
195B VAL* 1.3 73.8 - - - +
197B THR* 1.3 68.8 + - - +
198B VAL* 4.3 2.7 - - + -
224B TYR 4.1 2.2 - - - +
225B TYR* 3.4 46.2 - - + +
227B VAL* 4.4 4.3 - - + -
251B VAL* 3.6 35.2 - - - -
255B PHE* 3.6 38.8 - - + -
373B LEU* 4.2 8.7 - - + -
376B VAL* 4.0 17.9 - - + -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B TYR* 3.5 15.7 - - + -
185B VAL* 3.9 36.8 - - + +
186B GLU* 3.9 20.2 + - - +
189B PHE* 4.7 7.0 - - + -
195B VAL* 4.4 11.0 - - + +
196B MET* 1.3 77.8 - - - +
198B VAL* 1.3 58.8 + - - +
199B SER* 5.7 0.7 - - - -
225B TYR 3.4 3.6 + - - -
226B SER* 3.6 20.4 + - - -
227B VAL* 2.8 33.5 + - - +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 3.9 18.4 - - + -
174B TYR* 2.7 14.4 + - - +
175B VAL* 3.4 7.6 - - + -
176B ASP* 2.7 34.0 + - - +
196B MET* 4.3 2.5 - - + -
197B THR* 1.3 79.2 - - - +
199B SER* 1.3 59.2 + - - +
200B LEU* 4.3 14.8 - - + -
227B VAL* 3.3 22.4 - - + +
229B VAL* 5.1 0.7 - - + -
247B VAL* 3.9 23.8 - - + -
248B LEU* 4.7 11.4 - - + -
251B VAL* 3.8 21.3 - - + -
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B TYR* 6.0 0.2 - - - -
176B ASP* 3.5 10.6 + - - +
181B HIS* 4.0 6.1 - - - -
182B GLY* 3.6 11.8 + - - -
186B GLU* 5.6 0.4 - - - -
197B THR* 5.7 0.9 - - - -
198B VAL* 1.3 77.8 - - - +
200B LEU* 1.3 63.1 + - - +
201B HIS* 2.8 26.9 + - - -
227B VAL 2.9 9.1 + - - -
228B ASN* 3.7 13.4 - - - -
229B VAL* 2.8 28.8 + - - +
402B K 2.9 17.2 - - - -
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B VAL* 5.6 0.7 - - + -
176B ASP 3.0 9.7 + - - +
177B LEU* 4.2 14.1 - - + -
178B ASP 2.9 8.8 - - - +
198B VAL* 4.3 14.1 - - + -
199B SER* 1.3 74.2 - - - +
201B HIS* 1.3 58.1 + - - +
229B VAL* 3.8 26.7 - - + -
231B ILE* 4.0 14.4 - - + -
240B TYR* 3.6 43.7 + - + +
243B ILE* 4.4 4.9 - - + -
244B CYS* 3.9 33.4 - - + +
247B VAL* 5.2 4.0 - - + -
248B LEU* 6.2 1.3 - - + -
277B PHE* 5.1 2.3 - - - -
402B K 2.7 21.7 - - - -
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Residues in contact with HIS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP 4.1 0.4 - - - -
179B LEU 3.4 14.1 - - - +
180B HIS 3.6 2.9 - - - -
181B HIS* 3.4 46.1 - + + +
199B SER* 2.8 33.8 + - - -
200B LEU* 1.3 74.1 - - - +
202B LYS* 1.3 76.0 + - - +
203B PHE* 4.2 7.1 - - + +
211B THR 4.5 2.2 - - - -
212B GLY* 2.6 33.7 + - - -
228B ASN* 3.4 13.7 - - + -
229B VAL 3.3 12.5 + - - +
231B ILE* 2.8 26.8 + - - +
277B PHE* 3.8 10.1 - - - -
402B K 3.7 0.4 - - - -
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A MET 5.6 1.4 + - - -
275A CYS* 4.9 13.1 + - - +
179B LEU* 3.0 19.9 + - + -
181B HIS* 5.2 1.7 + - - +
201B HIS* 1.3 80.2 - - - +
203B PHE* 1.3 64.6 + - - +
204B SER* 4.3 15.0 - - - -
207B PHE* 3.4 62.0 - - + -
208B PHE 4.9 1.0 - - - +
209B PRO* 6.0 0.3 - - - +
231B ILE 3.2 13.0 - - - +
232B GLN* 5.3 2.7 - - - -
233B ASP* 3.0 41.7 + - - +
275B CYS 5.6 0.4 + - - -
276B SER* 3.5 16.0 + - - +
277B PHE* 3.6 8.4 - - + -
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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
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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