Contacts of the strand formed by residues 209 - 213 (chain C) in PDB entry 2OX4
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 ASP 209 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU 5.0 1.9 - - - +
186A PRO* 4.8 9.0 - - - +
187A SER 5.0 7.3 + - - -
125C ARG* 2.7 35.0 + - - +
161C ASP 2.9 8.8 + - - +
162C ALA* 3.2 7.2 - - + -
163C VAL* 2.9 30.7 + - - +
201C ARG* 4.7 2.7 + - - +
206C PRO 4.9 5.4 - - - +
207C ASP 5.3 2.7 - - - +
208C VAL* 1.3 77.7 - - - +
210C ILE* 1.3 59.2 + - - +
211C ILE* 4.2 0.9 - - + -
234C ASN* 4.4 13.9 - - - +
236C PHE* 3.4 36.7 - - + +
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Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 3.5 10.8 - - + +
165C VAL* 4.5 13.5 - - + -
197C VAL* 4.3 12.1 - - + +
200C ILE* 3.8 22.7 - - + -
201C ARG* 3.4 64.8 - - + +
204C VAL* 4.5 2.7 - - + -
208C VAL 4.1 1.6 - - - +
209C ASP* 1.3 78.9 - - - +
211C ILE* 1.3 69.4 + - - +
212C VAL* 4.4 12.6 - - + -
233C PHE 4.9 1.3 - - - +
234C ASN 4.8 0.2 + - - -
235C ILE* 3.6 13.2 - - + +
236C PHE* 2.8 29.6 + - - +
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Residues in contact with ILE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C TYR* 3.6 42.8 - - + -
162C ALA* 5.1 2.7 - - + -
163C VAL 2.9 14.1 + - - +
164C LYS* 3.3 22.5 - - + +
165C VAL* 3.0 30.5 + - - +
209C ASP 5.5 0.4 - - - -
210C ILE* 1.3 75.9 - - - +
212C VAL* 1.3 67.0 - - - +
236C PHE* 4.0 21.8 - - + -
237C PHE* 3.4 52.5 - - + +
239C GLU* 4.6 1.6 - - + +
338C ILE* 4.9 2.9 - - + -
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 3.5 9.2 - - + +
167C VAL* 4.3 7.0 - - + -
197C VAL* 4.1 15.5 - - + -
210C ILE* 4.4 5.8 - - + -
211C ILE* 1.3 77.7 - - - +
213C GLU* 1.3 60.4 + - - +
214C ASN* 3.7 19.5 - - - +
226C PHE* 4.1 15.7 - - + -
230C ILE* 3.9 8.7 - - + -
235C ILE* 3.9 30.3 - - + +
237C PHE 3.1 8.1 + - - +
238C TYR* 3.4 22.6 - - + -
239C GLU* 2.9 26.2 + - - +
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Residues in contact with GLU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 3.1 22.0 + - - +
164C LYS* 3.6 19.5 + - + -
165C VAL 2.9 17.2 + - - +
166C ASP* 3.1 28.6 - - + +
167C VAL 4.3 0.9 + - - -
212C VAL* 1.3 72.4 - - - +
214C ASN* 1.3 64.0 + - - +
215C HIS* 2.9 52.4 + - + +
239C GLU* 3.0 22.6 - - - +
240C GLU* 4.0 1.4 - - - +
402C MG 2.2 31.8 - - - -
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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