Contacts of the strand formed by residues 199 - 205 (chain B) in PDB entry 2OIB
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 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU* 5.3 7.0 - - + +
191B LYS* 4.0 26.7 - - + -
193B GLY 3.3 13.9 - - - +
194B GLU* 3.9 26.9 - - + +
198B GLY* 1.3 75.2 - - - -
200B VAL* 1.3 65.0 + - - +
201B TYR* 3.3 34.0 - - + +
213B LYS* 3.8 1.0 - - - -
214B LYS 3.3 26.6 + - - -
216B ALA* 5.3 2.4 - - + +
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Residues in contact with VAL 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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190B ASN 3.9 0.2 - - - +
191B LYS* 3.9 2.9 - - - -
192B MET* 3.1 55.0 + - + +
193B GLY* 2.7 24.1 + - - +
194B GLU* 4.9 2.2 - - - +
198B GLY 4.1 4.9 - - - +
199B VAL* 1.3 77.9 - - - +
201B TYR* 1.3 64.3 + - - +
211B ALA* 4.0 12.8 - - + -
212B VAL 3.3 11.2 - - - +
213B LYS* 3.8 27.4 - - + +
262B TYR* 6.0 1.3 - - + -
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 3.8 18.8 - - + -
180B PHE* 3.6 37.7 - + + -
181B ASP 3.3 23.3 - - - -
182B GLU* 2.9 29.4 + - + -
190B ASN* 3.3 6.5 - - + +
191B LYS* 4.4 5.4 - - - -
192B MET* 3.7 4.0 - - - -
199B VAL* 3.3 41.3 + - + +
200B VAL* 1.3 76.6 - - - +
202B LYS* 1.3 63.6 + - - +
203B GLY 3.7 0.5 + - - -
210B VAL 3.5 0.3 - - - +
211B ALA* 3.4 4.5 - - - -
212B VAL* 2.8 49.8 + - - +
214B LYS* 3.4 28.5 + - + -
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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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177B THR* 4.3 0.7 - - - -
189B GLY 6.2 1.6 - - - +
190B ASN* 2.6 57.4 + - - +
192B MET* 3.5 14.8 - - + -
201B TYR* 1.3 74.0 - - - +
203B GLY* 1.3 58.1 + - - +
204B TYR* 3.7 25.0 + - + +
209B THR* 3.7 28.7 - - + -
210B VAL 3.5 4.3 - - - -
264B TYR* 4.0 32.0 + - + +
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Residues in contact with GLY 203 (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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176B VAL* 3.3 23.3 - - - -
177B THR* 4.5 2.0 - - - -
190B ASN* 4.6 0.4 - - - -
201B TYR 3.7 0.6 + - - -
202B LYS* 1.3 75.9 - - - +
204B TYR* 1.3 73.1 + - - -
209B THR* 3.4 10.4 - - - +
210B VAL* 2.9 34.5 + - - -
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Residues in contact with TYR 204 (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 ASN 5.0 0.7 - - - +
176B VAL* 3.2 27.7 + - - +
190B ASN* 6.0 3.1 - - - -
202B LYS* 3.7 28.4 + - + +
203B GLY* 1.3 82.8 - - - -
205B VAL* 1.3 67.0 + - - +
206B ASN 4.0 15.3 + - - +
207B ASN* 5.1 7.0 - - - -
208B THR 3.4 7.2 - - - +
209B THR* 3.5 25.4 - - + -
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Residues in contact with VAL 205 (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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166B HIS* 6.0 3.1 - - + +
168B PHE* 4.1 30.3 - - + -
176B VAL* 3.7 25.6 - - + -
204B TYR* 1.3 74.8 - - - +
206B ASN* 1.3 79.1 + - - +
208B THR* 2.9 39.0 + - - +
210B VAL* 4.2 19.7 - - + +
261B VAL* 5.3 1.3 - - + -
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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