Contacts of the helix formed by residues 203 - 207 (chain A) in PDB entry 2OB2
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 LEU 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.5 44.6 - - + +
105A GLY* 4.0 5.6 - - - -
176A LEU* 3.6 12.6 - - + -
200A SER* 4.1 16.3 - - - -
201A GLU 4.1 2.0 - - - +
202A SMC 1.3 78.3 + - - -
204A LEU* 1.3 71.4 + - + +
205A CYS 3.1 1.3 - - - -
206A TYR* 2.9 20.9 + - - +
207A MET* 4.0 9.8 + - - +
215A LEU* 4.3 15.3 - - + -
232A ASP* 3.9 0.4 + - - -
1801A SAH 3.4 50.0 - - + +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A SER* 3.7 22.4 - - - +
203A LEU* 1.3 79.9 - - + +
205A CYS* 1.3 55.7 + - - +
206A TYR 3.1 0.2 - - - -
207A MET* 2.9 43.1 + - - +
212A SER* 3.7 23.1 - - - +
215A LEU* 4.0 16.8 - - + -
216A ILE* 4.0 10.8 - - + -
228A TRP* 4.5 3.4 - - + +
230A SER* 3.8 3.4 - - - +
232A ASP* 3.4 13.5 + - - +
261A THR* 4.8 1.6 + - - -
271A TYR* 4.2 0.7 - - - +
274A ARG* 4.1 20.5 + - - +
275A TRP* 3.5 39.7 - - + -
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Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SMC 3.9 13.5 - - - -
203A LEU 3.1 1.2 + - - -
204A LEU* 1.3 74.8 - - - +
206A TYR* 1.3 91.3 + - - +
207A MET 3.3 0.7 - - - -
232A ASP* 3.1 31.5 + - + +
233A PRO* 3.9 22.2 - - + +
259A MET* 3.2 38.6 - - + +
260A PRO* 3.3 6.1 - - - +
261A THR* 5.0 7.2 + - - +
262A LEU* 5.6 3.6 - - + +
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Residues in contact with TYR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.1 32.2 - - + +
8A THR* 3.6 41.6 - - + +
202A SMC 3.2 33.3 - - + +
203A LEU 2.9 11.2 + - - +
205A CYS* 1.3 87.4 - - - +
207A MET* 1.3 61.3 + - - +
208A HIS* 4.4 2.3 + - - -
257A LEU* 4.2 15.5 - - + +
258A GLU 3.6 18.2 - - - +
259A MET* 3.7 30.0 - - + +
260A PRO* 3.9 9.8 - - - +
1801A SAH 3.8 21.8 - + + +
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.2 29.2 - - + +
177A ASN* 3.1 33.0 - - - +
203A LEU* 4.1 21.3 - - + +
204A LEU* 2.9 39.9 + - - +
206A TYR* 1.3 81.9 - - - +
208A HIS* 1.3 69.9 + - - +
211A GLU* 3.9 14.1 - - + -
212A SER* 4.0 6.6 + - - -
215A LEU* 4.0 14.4 - - + -
260A PRO* 3.4 16.8 - - - +
261A THR* 3.7 10.7 - - - +
1801A SAH 4.7 7.0 - - - +
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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