Contacts of the strand formed by residues 231 - 236 (chain A) in PDB entry 3OEH
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 SER 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.7 0.2 - - - -
107A GLY* 2.8 33.4 + - - -
108A ARG 3.9 0.9 + - - +
185A ILE* 3.9 10.8 - - - +
203A CYS* 3.0 21.6 - - - +
205A TYR* 6.1 1.1 - - - -
222A LEU* 4.6 7.6 - - - +
227A ALA 2.8 23.8 + - - -
228A MET* 2.7 27.7 + - - +
229A LYS 3.6 0.6 + - - -
230A TYR* 1.3 75.7 - - - +
232A ILE* 1.3 65.1 + - - +
233A ILE* 5.4 2.0 - - - -
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Residues in contact with ILE 232 (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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105A LEU* 3.4 35.4 - - + +
106A LEU* 4.1 10.5 - - + -
108A ARG 3.7 9.2 - - - +
110A VAL* 4.6 7.2 - - + -
203A CYS 2.6 12.1 + - - +
204A VAL* 3.4 13.9 - - + +
205A TYR* 2.8 27.7 + - - +
231A SER* 1.3 77.1 - - - +
233A ILE* 1.3 72.2 + - - +
234A VAL* 4.0 11.8 + - + -
255A ILE* 3.5 34.1 - - + -
259A PHE* 3.8 25.1 - - + -
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Residues in contact with ILE 233 (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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108A ARG 3.1 6.5 + - - -
109A VAL* 3.3 27.7 - - + -
110A VAL* 2.9 30.7 + - - +
205A TYR* 3.4 39.7 - - + +
207A ALA* 4.8 0.4 - - + -
215A VAL* 3.9 22.0 - - + -
218A LEU* 4.5 4.5 - - + -
219A VAL* 3.8 21.1 - - + -
222A LEU* 4.1 21.5 - - + -
228A MET* 4.3 10.5 - - - -
231A SER* 5.4 2.2 - - - -
232A ILE* 1.3 74.4 - - - +
234A VAL* 1.3 63.9 + - - +
235A ALA* 4.2 6.5 - - + -
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Residues in contact with VAL 234 (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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110A VAL* 3.6 19.5 - - + -
111A ASP 4.2 9.9 - - - +
112A ALA* 4.2 2.5 - - - -
204A VAL* 4.6 2.5 - - + -
205A TYR 3.0 9.0 + - - +
206A VAL* 3.4 4.3 - - + +
207A ALA 2.7 32.9 + - - +
232A ILE* 4.0 7.7 + - + -
233A ILE* 1.3 71.1 - - - +
235A ALA* 1.3 53.9 + - - +
248A ALA* 4.0 23.8 - - + +
251A THR* 3.9 21.8 - - + -
252A ALA* 3.5 26.0 - - + -
255A ILE* 3.9 16.8 - - + -
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Residues in contact with ALA 235 (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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109A VAL* 4.6 0.4 - - + -
110A VAL 3.0 14.8 + - - +
111A ASP* 4.0 16.1 - - - +
112A ALA 4.9 0.9 - - - -
117A ILE* 4.5 17.5 - - + +
207A ALA* 3.4 10.8 - - + -
215A VAL* 4.0 26.7 - - + -
233A ILE* 3.9 5.6 - - + -
234A VAL* 1.3 73.9 - - - +
236A ALA* 1.3 60.8 + - - +
237A THR* 3.8 11.8 + - + +
240A GLU* 3.3 11.1 - - - +
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Residues in contact with ALA 236 (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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112A ALA* 4.2 7.6 - - + +
207A ALA 2.8 11.4 + - - +
208A VAL* 3.3 1.8 - - - -
209A GLY 2.9 22.3 + - - -
234A VAL 4.1 1.0 + - - -
235A ALA* 1.3 69.9 - - - +
237A THR* 1.3 62.6 + - - +
240A GLU* 3.3 7.4 - - - +
244A LEU* 3.4 37.2 - - + +
245A GLN* 3.7 10.0 - - + +
248A ALA* 3.6 16.9 - - + +
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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