Contacts of the strand formed by residues 182 - 186 (chain A) in PDB entry 4OG6
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 ALA 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 5.8 0.2 + - - -
155A SER* 3.9 21.7 - - - +
158A ALA* 3.7 20.9 - - + -
175A LEU* 4.3 2.5 - - + -
176A ALA 3.2 6.7 - - - +
177A LEU* 3.8 20.0 - - + -
181A HIS* 1.3 96.0 + - - +
183A TRP* 1.3 67.1 + - - +
195A GLU* 4.5 0.2 - - - +
197A THR* 3.5 12.0 - - + +
602A 2S9 3.7 0.6 - - - -
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Residues in contact with TRP 183 (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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158A ALA* 4.5 0.2 - - - -
175A LEU* 3.6 6.2 - - - +
176A ALA* 2.7 47.4 + - + +
177A LEU 4.5 0.7 - - - -
178A SER* 3.9 28.9 - - - -
181A HIS* 3.6 20.4 - + + -
182A ALA* 1.3 80.8 - - - +
184A VAL* 1.3 83.8 + - - +
193A THR* 3.9 18.0 - - - +
194A ALA 3.3 15.5 - - - +
195A GLU* 4.1 12.1 - - - +
196A VAL* 4.2 10.3 - - - -
211A VAL* 3.7 22.1 - - + +
221A LEU 4.5 0.2 - - - -
222A TYR* 3.7 26.5 - + - -
227A TYR* 3.4 50.8 - + + -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.7 29.4 - - + -
158A ALA 4.5 1.8 - - - +
161A VAL* 4.3 8.1 - - + -
162A VAL* 3.7 28.0 - - + -
173A VAL* 4.2 10.3 - - + -
174A HIS 3.1 7.0 - - - +
176A ALA* 4.4 0.2 - - - -
183A TRP* 1.3 86.4 - - - +
185A VAL* 1.3 66.2 + - - +
186A PHE* 4.5 5.8 - - + -
193A THR* 3.3 4.2 - - - -
194A ALA* 2.9 46.3 + - + +
196A VAL* 3.8 19.7 - - + +
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Residues in contact with VAL 185 (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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172A ASP 3.4 2.0 - - - +
173A VAL* 3.4 2.4 - - - +
174A HIS* 2.9 54.8 + - + +
175A LEU 4.9 3.1 - - - +
176A ALA* 4.1 15.7 - - + +
184A VAL* 1.3 78.0 - - - +
186A PHE* 1.3 66.5 + - - +
190A GLY* 3.8 12.8 - - - +
192A GLN 3.1 8.5 - - - +
193A THR* 3.9 8.7 - - + -
227A TYR* 4.6 1.6 - - + -
229A ARG* 4.4 20.9 - - + -
230A CYS 5.4 0.2 - - - +
607A DMS 3.6 24.7 - - + -
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Residues in contact with PHE 186 (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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113A SER 3.5 15.9 - - - -
114A SER* 3.7 2.5 - - - -
115A ARG* 3.5 50.0 - - + -
118A VAL* 3.9 18.2 - - + -
172A ASP* 3.4 17.0 - - - +
173A VAL* 4.0 17.3 - - + -
184A VAL* 4.5 2.9 - - + -
185A VAL* 1.3 80.6 - - - +
187A GLY* 1.3 76.6 + - - +
188A PRO* 5.8 0.2 - - + -
190A GLY* 3.9 4.8 + - - -
191A GLU 3.4 3.3 + - - -
192A GLN* 2.9 65.8 + - + +
193A THR 4.0 1.8 - - - -
194A ALA* 3.8 26.7 - - + -
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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