Contacts of the strand formed by residues 231 - 236 (chain B) in PDB entry 3OEE
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.4 0.2 - - - +
107B GLY* 3.0 24.3 + - - -
108B ARG 4.1 1.0 + - - +
185B ILE* 4.5 8.5 - - - +
203B CYS* 3.0 24.2 - - - -
205B TYR* 5.9 1.1 - - - -
222B LEU* 4.5 6.9 - - - +
227B ALA 2.7 25.1 + - - -
228B MET* 3.1 21.5 + - - +
229B LYS 3.5 0.6 - - - -
230B TYR* 1.3 83.5 - - - +
232B ILE* 1.3 64.1 + - - +
233B ILE* 4.9 10.1 - - - -
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLY 5.0 0.9 - - - +
105B LEU* 3.9 37.0 - - + +
106B LEU* 3.7 26.2 - - + -
108B ARG* 3.8 7.0 - - + +
110B VAL* 5.0 3.1 - - + -
203B CYS 2.7 11.6 + - - +
204B VAL* 3.4 10.4 - - + +
205B TYR 2.8 28.1 + - - +
231B SER* 1.3 78.4 - - - +
233B ILE* 1.3 74.9 + - - +
234B VAL* 4.5 8.1 - - + -
255B ILE* 3.4 34.8 - - + -
259B PHE* 3.8 16.2 - - + -
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG 3.2 6.8 + - - +
109B VAL* 3.5 28.2 - - + -
110B VAL* 2.9 32.3 + - - +
205B TYR* 3.6 29.8 - - + +
207B ALA* 5.5 0.2 - - + -
215B VAL* 4.1 22.2 - - + -
218B LEU* 5.4 0.4 - - + -
219B VAL* 3.7 19.5 - - + -
222B LEU* 3.8 26.2 - - + -
228B MET* 4.3 11.2 - - + -
231B SER* 4.9 3.1 - - - -
232B ILE* 1.3 86.3 - - - +
234B VAL* 1.3 68.6 + - - +
235B ALA* 4.1 0.7 - - + -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.3 16.6 - - + -
111B ASP 4.2 14.4 - - - +
112B ALA* 4.3 5.6 - - - -
204B VAL* 4.5 8.7 - - + -
205B TYR 3.0 9.0 + - - +
206B VAL* 3.4 4.8 - - + +
207B ALA* 2.9 26.3 + - - +
232B ILE* 4.5 2.9 - - + -
233B ILE* 1.3 78.9 - - - +
235B ALA* 1.3 61.5 + - - +
248B ALA* 4.0 33.2 - - + +
251B THR* 4.6 3.1 - - - +
252B ALA* 4.0 18.2 - - + -
255B ILE* 4.0 20.9 - - + -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 5.0 0.2 - - + -
110B VAL 2.9 13.9 + - - +
111B ASP* 3.5 23.4 - - - +
112B ALA 3.9 2.9 + - - -
117B ILE* 4.2 18.7 - - + +
207B ALA* 3.5 6.5 - - + -
215B VAL* 4.2 24.0 - - + -
233B ILE* 4.8 4.3 - - + -
234B VAL* 1.3 76.1 - - - +
236B ALA* 1.3 60.2 + - - +
237B THR* 3.9 13.9 - - + -
240B GLU* 4.0 4.6 - - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 4.6 2.2 - - + -
207B ALA 2.8 9.7 + - - +
208B VAL* 3.4 2.6 - - - -
209B GLY 2.7 24.8 + - - -
235B ALA* 1.3 73.8 - - - +
237B THR* 1.3 62.3 + - - +
240B GLU* 3.5 7.9 - - - -
244B LEU* 3.4 32.8 - - + +
245B GLN* 3.5 18.2 - - + +
248B ALA* 3.8 12.3 - - + +
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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