Contacts of the strand formed by residues 263 - 270 (chain A) in PDB entry 2OA2
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 LEU 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MSE 3.5 2.3 - - - +
196A SER* 3.4 3.6 - - - -
197A ILE* 2.9 51.5 + - + +
217A VAL* 3.8 25.4 - - + -
219A GLU 3.5 16.4 - - - +
220A GLY* 3.9 1.3 - - - -
221A ARG 3.8 24.5 - - - +
222A GLY* 4.3 4.3 - - - +
239A VAL* 5.6 0.4 - - + -
255A VAL* 4.0 26.9 - - + -
256A ARG 4.6 0.2 - - - -
257A ASN* 3.3 35.7 - - + +
261A ARG 4.3 0.4 - - - -
262A PRO* 1.3 72.7 - - - +
264A LYS* 1.3 58.1 + - - +
265A LEU* 4.0 7.1 + - + -
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Residues in contact with LYS 264 (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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174A THR* 3.8 28.0 - - + +
175A LYS* 3.5 21.0 + - - -
176A ARG 4.7 0.2 - - - -
177A ASN 2.7 26.1 + - - +
178A ARG* 4.3 9.3 - - - +
195A MSE 3.5 2.7 - - - -
196A SER* 3.2 25.6 + - - +
217A VAL* 3.7 2.3 - - - +
218A GLU* 2.8 24.8 + - + -
219A GLU* 2.9 45.1 + - + +
262A PRO* 4.0 20.5 - - - +
263A LEU* 1.3 72.3 - - - +
265A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 265 (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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174A THR* 3.5 12.6 - - - +
194A LEU* 3.7 0.7 - - - -
195A MSE 2.8 58.7 + - + +
197A ILE* 3.6 24.7 - - + -
203A ILE* 4.8 1.3 - - + -
215A LEU* 3.8 28.7 - - + -
216A ARG 3.1 20.6 - - - +
217A VAL* 4.0 11.0 - - + -
245A ILE* 5.7 0.9 - - + -
255A VAL* 4.7 9.0 - - + -
263A LEU* 4.3 15.3 - - + -
264A LYS* 1.3 75.6 - - - +
266A TYR* 1.3 74.7 + - - +
267A SER 4.2 0.2 - - - +
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Residues in contact with TYR 266 (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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170A ILE* 3.6 32.5 - - + +
174A THR* 3.5 15.9 - - - +
192A VAL* 4.6 8.3 - - + -
193A THR 3.2 12.3 - - - +
194A LEU* 3.9 15.0 - - + -
214A PHE* 4.0 14.6 - + - -
215A LEU* 3.2 3.5 - - - -
216A ARG* 2.9 69.2 + - + +
218A GLU* 3.6 22.6 + - + -
265A LEU* 1.3 78.4 - - - +
267A SER* 1.3 60.8 + - - +
268A ILE* 4.3 22.2 - - + -
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Residues in contact with SER 267 (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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191A GLN 3.5 1.1 - - - +
192A VAL* 3.2 5.9 - - - +
193A THR* 2.8 45.1 + - - +
195A MSE 4.7 5.2 - - - -
213A GLN* 2.7 33.9 + - - +
214A PHE 3.3 4.3 - - - -
215A LEU* 4.1 9.0 - - - -
265A LEU* 4.4 5.4 - - - -
266A TYR* 1.3 74.4 - - - +
268A ILE* 1.3 63.8 + - - +
269A TYR* 3.3 13.7 - - - -
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Residues in contact with ILE 268 (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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190A LEU* 4.2 25.4 - - + -
191A GLN 3.2 7.2 - - - +
192A VAL* 4.1 18.4 - - + -
212A ASP 3.8 0.3 - - - +
213A GLN* 3.2 6.2 - - - +
214A PHE* 2.7 64.5 + - + +
266A TYR* 4.3 17.9 - - + -
267A SER* 1.3 78.8 + - - +
269A TYR* 1.3 69.4 + - - +
270A ALA* 5.1 3.1 - - + +
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Residues in contact with TYR 269 (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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181A ARG* 3.9 15.8 + - - -
190A LEU* 3.3 6.1 - - - +
191A GLN* 2.9 48.8 + - + +
193A THR* 3.9 15.1 + - + -
195A MSE 5.3 2.8 - - - -
208A HIS* 4.4 11.2 - + - -
211A LEU* 3.9 16.6 - - + -
212A ASP 3.7 3.1 - - - -
213A GLN* 3.7 31.9 + - - -
267A SER* 3.3 14.7 + - - -
268A ILE* 1.3 73.9 - - - +
270A ALA* 1.3 58.9 + - - +
271A PRO 3.3 15.1 - - - +
272A PRO* 4.3 1.3 - - + -
273A GLN* 3.5 30.1 - - + +
274A HIS* 3.0 32.2 + + - -
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Residues in contact with ALA 270 (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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189A HIS 3.6 10.8 - - - +
190A LEU* 4.6 6.3 - - + -
211A LEU* 3.2 1.5 - - - +
212A ASP* 2.9 40.8 + - + +
268A ILE* 4.2 3.8 + - + -
269A TYR* 1.3 73.9 - - - +
271A PRO* 1.3 66.5 + - - +
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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