Contacts of the strand formed by residues 187 - 191 (chain A) in PDB entry 2OZO
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 PHE 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 3.6 37.7 - + + +
177A LEU* 4.7 2.2 - - - -
185A GLY 3.2 18.6 - - - +
186A LYS* 1.3 77.9 - - - +
188A LEU* 1.3 67.4 - - - +
189A LEU* 4.1 12.6 - - + -
200A LEU* 4.0 8.3 - - + -
201A SER 3.2 13.0 - - - +
202A LEU* 3.7 11.4 - - + -
236A VAL* 3.9 25.4 - - + -
240A LYS* 4.4 7.4 - - - -
250A LEU* 3.8 24.9 - - + -
251A LYS 3.5 22.0 - - - -
252A GLU 3.1 12.7 + - - -
253A ALA* 3.6 6.5 - - + -
254A CYS* 2.9 27.0 + - - +
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Residues in contact with LEU 188 (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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163A TRP 3.3 15.0 - - - +
165A HIS* 3.8 22.2 - - + +
168A LEU* 3.7 26.7 - - + -
173A ALA* 4.0 15.7 - - + -
176A LYS* 4.3 3.6 - - + -
177A LEU* 4.0 20.2 - - + -
187A PHE* 1.3 81.6 - - - +
189A LEU* 1.3 86.9 + - - +
190A ARG* 4.3 4.5 - - + +
200A LEU* 3.5 1.0 - - - +
201A SER* 3.1 47.5 + - - +
254A CYS* 4.1 8.5 - - + +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TRP* 2.9 39.7 + - + +
164A TYR* 3.6 8.5 - - + -
165A HIS* 2.9 28.8 + - - +
187A PHE* 4.1 10.8 - - + -
188A LEU* 1.3 88.9 - - - +
190A ARG* 1.3 62.6 + - - +
198A TYR* 5.3 3.6 - - + -
199A ALA 3.3 11.2 - - - +
200A LEU* 3.6 20.2 - - + -
213A ILE* 3.9 23.3 - - + -
232A LEU* 4.1 20.4 - - + -
235A LEU* 5.6 0.4 - - + -
236A VAL* 4.2 17.9 - - + -
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Residues in contact with ARG 190 (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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165A HIS 3.7 8.1 - - - +
168A LEU* 3.9 29.6 + - + +
169A THR* 4.1 2.4 - - - +
170A ARG* 2.8 65.8 - - - +
173A ALA* 3.7 24.7 - - - +
188A LEU* 4.4 3.4 - - + -
189A LEU* 1.3 77.3 - - - +
191A PRO* 1.3 70.1 + - + +
192A ARG* 4.2 8.3 - - - +
198A TYR* 3.1 5.3 - - - +
199A ALA* 2.7 48.5 + - + +
201A SER* 3.2 14.7 + - - -
210A HIS* 3.2 20.2 + - - -
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Residues in contact with PRO 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.3 26.0 - - + +
165A HIS 3.5 15.5 - - - +
166A SER* 4.1 14.6 - - - +
167A SER* 4.9 0.9 - - - +
168A LEU 4.7 7.5 - - - +
190A ARG* 1.3 88.5 + - + +
192A ARG* 1.3 64.8 + - - +
197A THR 4.0 1.8 - - - +
198A TYR* 3.3 29.4 - - + -
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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