Contacts of the strand formed by residues 244 - 253 (chain A) in PDB entry 3OV6
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 TRP 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP* 6.4 0.7 - - + -
34A GLU* 4.0 28.9 - - + -
210A SER* 3.4 1.4 - - - -
211A GLY 2.6 32.7 + - - -
212A PHE* 3.1 46.4 + + + +
213A TYR* 3.8 23.0 - + - -
215A LYS* 3.3 57.2 - - - +
236A ILE* 3.6 20.6 - - + -
237A LEU 3.4 19.3 - - - -
238A PRO* 3.8 27.1 - - + -
239A ASN* 3.1 3.0 + - - -
242A GLY 4.4 8.8 + - - -
243A THR* 1.3 82.4 - - - +
245A TYR* 1.3 59.8 + - - +
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Residues in contact with TYR 245 (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 TRP* 4.1 7.9 - + - -
208A HIS* 2.6 37.6 + - + -
209A VAL 3.4 4.9 - - - -
210A SER* 3.8 20.0 - - - -
212A PHE* 4.0 2.2 - - - -
236A ILE* 3.1 5.5 - - - +
237A LEU* 2.7 62.4 + - + +
239A ASN* 4.1 7.9 - - - +
244A TRP* 1.3 75.7 - - - +
246A LEU* 1.3 65.3 + - - +
247A ARG* 3.1 39.7 + - + -
1010A TYR* 3.6 40.5 - + + +
1011A SER 3.6 20.8 + - - -
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Residues in contact with LEU 246 (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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207A CYS 3.9 0.2 - - - +
208A HIS* 3.6 0.7 - - - -
209A VAL* 2.8 37.6 + - + +
212A PHE* 3.8 13.4 - - + -
217A VAL* 3.7 27.8 - - + +
219A VAL* 4.2 23.3 - - + +
233A LEU* 4.4 14.8 - - + -
234A GLY 3.2 33.7 - - - +
235A ASP 3.9 8.5 - - - +
236A ILE* 4.2 13.5 - - + -
245A TYR* 1.3 82.4 - - - +
247A ARG* 1.3 78.6 + - - +
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Residues in contact with ARG 247 (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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206A VAL* 4.1 21.1 - - + -
207A CYS 3.1 16.6 - - - +
208A HIS* 4.2 0.9 - - - +
209A VAL* 5.8 0.2 - - - -
232A GLN 3.9 0.5 - - - +
233A LEU* 3.8 0.5 - - - -
234A GLY* 2.8 33.4 + - - -
235A ASP 4.8 2.0 + - - +
237A LEU* 5.2 4.0 - - + +
245A TYR* 3.1 33.7 + - + +
246A LEU* 1.3 82.1 - - - +
248A ALA* 1.3 58.8 + - - +
249A THR* 4.3 6.5 + - + +
1008A GLN* 4.6 13.5 - - - +
1009A VAL 3.4 23.6 + - - +
1010A TYR* 3.7 7.4 - - - +
1099A MET 5.8 0.4 - - - -
1100A GLY* 2.6 31.0 + - - -
1102A GLY* 3.6 19.4 + - - -
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Residues in contact with ALA 248 (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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206A VAL* 3.6 0.9 - - - -
207A CYS* 2.8 35.6 + - + +
219A VAL* 3.7 26.0 - - + +
220A MET 5.0 0.4 - - - +
221A TRP* 3.1 13.1 + - + -
231A THR* 3.8 11.0 - - + -
232A GLN 3.3 4.3 - - - -
233A LEU* 3.6 26.2 - - + +
247A ARG* 1.3 73.7 - - - +
249A THR* 1.3 63.1 + - - +
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Residues in contact with THR 249 (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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204A GLN* 3.2 24.8 + - - +
205A LEU 3.1 4.5 - - - -
206A VAL* 3.6 33.0 - - + -
221A TRP* 3.8 2.2 - - - -
230A GLY 4.1 0.5 - - - +
231A THR* 3.2 7.8 - - - +
232A GLN* 2.9 50.3 + - - +
247A ARG* 4.2 7.6 - - + +
248A ALA* 1.3 78.0 - - - +
250A LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 250 (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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203A LEU 3.8 0.3 - - - +
204A GLN* 3.3 7.0 - - - -
205A LEU* 2.8 36.8 + - + +
221A TRP* 3.6 36.6 - - + +
228A GLN* 4.0 17.7 - - + +
230A GLY* 3.8 13.5 - - - -
231A THR* 3.7 26.9 - - - +
249A THR* 1.3 78.1 - - - +
251A ASP* 1.3 75.5 + - - +
252A VAL* 4.0 2.9 + - + -
260A LEU* 3.8 29.4 - - + -
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Residues in contact with ASP 251 (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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198A PRO* 4.0 20.2 - - + -
202A ARG* 3.3 27.5 + - - +
203A LEU 3.3 5.2 - - - -
204A GLN* 4.5 5.5 - - + +
230A GLY* 5.2 9.0 + - - +
232A GLN* 5.8 0.2 - - - +
250A LEU* 1.3 84.0 - - - +
252A VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 252 (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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202A ARG* 3.3 6.1 - - - +
203A LEU* 2.6 47.1 + - + +
205A LEU* 3.8 35.9 - - + -
223A ARG* 5.2 1.1 - - - +
250A LEU* 4.9 4.3 - - + +
251A ASP* 1.3 78.6 + - - +
253A ALA* 1.3 73.6 + - - +
256A GLU* 4.0 30.7 - - + +
257A ALA* 4.1 7.2 - - + -
260A LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 253 (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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201A GLY 3.5 8.3 - - - +
202A ARG* 4.3 7.3 - - + +
252A VAL* 1.3 82.3 - - - +
254A ASP* 1.3 69.4 + - - +
255A GLY 3.3 2.4 + - - +
256A GLU* 3.3 34.1 + - + +
257A ALA 3.6 5.9 + - - -
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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