Contacts of the strand formed by residues 188 - 193 (chain A) in PDB entry 2OQ1
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 LYS 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.8 25.0 - - + +
182A GLY* 6.1 1.3 - - - -
183A ALA* 4.4 10.0 - - - +
184A GLN 4.1 8.6 - - - +
185A THR* 2.8 51.6 + - - +
186A ASP 3.3 0.6 + - - -
187A GLY* 1.3 75.4 - - - +
189A PHE* 1.3 58.3 + - - +
204A LEU* 3.1 2.6 - - - -
205A ILE* 2.9 37.9 + - + +
254A GLU* 3.2 37.8 + - + +
255A ALA 4.2 2.5 - - - +
256A CYS* 4.1 22.7 - - + +
257A PRO* 6.0 1.3 - - - -
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Residues in contact with PHE 189 (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 TRP* 3.7 29.2 - + + +
179A LEU* 4.3 1.8 - - - -
187A GLY 3.5 10.8 - - - +
188A LYS* 1.3 75.2 - - - +
190A LEU* 1.3 66.1 + - - +
191A LEU* 5.7 0.2 - - + -
202A LEU* 3.9 13.0 - - + -
203A SER 3.2 12.8 - - - +
204A LEU* 3.7 11.7 - - + -
238A VAL* 3.5 35.4 - - + -
242A LYS* 3.9 13.5 - - - -
252A LEU* 3.5 28.7 - - + -
253A LYS 3.7 16.2 - - - -
254A GLU 2.9 22.3 + - - -
255A ALA* 3.7 8.9 - - + -
256A CYS* 2.8 34.9 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TRP 3.4 7.2 - - - +
167A HIS* 3.7 24.2 - - + +
170A LEU* 3.7 26.0 - - + -
175A ALA* 4.1 18.8 - - + +
178A LYS* 4.5 2.5 - - + -
179A LEU* 4.2 14.1 - - + -
189A PHE* 1.3 85.2 - - - +
191A LEU* 1.3 64.5 + - - +
192A ARG* 4.1 12.6 - - + -
202A LEU* 3.7 5.0 - - - +
203A SER* 3.0 51.6 + - - +
256A CYS* 4.1 19.1 - - + -
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Residues in contact with LEU 191 (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 TRP* 2.8 36.6 + - + +
166A TYR* 3.6 20.4 - - + -
167A HIS* 3.0 27.9 + - - +
189A PHE* 5.7 0.2 - - + -
190A LEU* 1.3 74.0 - - - +
192A ARG* 1.3 73.1 + - - +
200A TYR* 3.8 25.8 - - + -
201A ALA 3.5 8.1 - - - +
202A LEU* 3.9 15.7 - - + -
215A ILE* 3.6 29.4 - - + -
234A LEU* 4.6 12.8 - - + -
237A LEU* 5.1 0.4 - - + -
238A VAL* 4.4 12.1 - - + -
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Residues in contact with ARG 192 (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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167A HIS* 3.7 6.3 - - + +
170A LEU* 3.6 31.3 + - + +
171A THR* 4.1 1.4 - - - +
172A ARG* 3.8 18.0 - - - +
175A ALA* 3.6 20.9 - - - +
190A LEU* 4.1 6.3 - - + -
191A LEU* 1.3 81.3 - - - +
193A PRO* 1.3 72.2 + - + +
194A ARG* 4.6 4.8 - - - +
200A TYR* 3.4 3.1 - - - +
201A ALA* 2.8 52.4 + - + +
203A SER* 3.1 15.7 + - - -
212A HIS* 3.0 27.7 + - - -
304B PTR 2.8 43.2 + - - -
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Residues in contact with PRO 193 (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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166A TYR* 3.6 24.0 - - + +
167A HIS 3.0 18.8 - - - +
168A SER 3.2 21.1 - - - +
169A SER* 4.7 2.2 - - - +
170A LEU 4.2 9.1 - - - +
192A ARG* 1.3 95.5 + - + +
194A ARG* 1.3 66.8 + - - +
199A THR 4.7 0.4 - - - +
200A TYR* 3.6 20.8 - - + -
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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