Contacts of the strand formed by residues 202 - 212 (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 ARG 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER* 4.2 3.8 + - - -
198A PRO* 2.9 53.2 + - + +
199A GLY* 3.3 20.8 - - - +
200A PRO* 3.1 10.2 - - - +
201A GLY* 1.3 85.5 + - - +
203A LEU* 1.3 71.4 + - - +
251A ASP* 3.3 28.1 + - - -
252A VAL 3.3 11.2 - - - +
253A ALA* 4.5 7.6 - - + +
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Residues in contact with LEU 203 (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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194A SER* 6.5 1.1 - - - -
197A SER* 5.6 0.4 - - - +
198A PRO* 3.5 7.4 - - - +
202A ARG* 1.3 81.7 - - - +
204A GLN* 1.3 62.2 + - - +
205A LEU* 3.9 13.2 - - + -
250A LEU 3.8 0.2 - - - +
251A ASP* 3.3 4.2 - - - -
252A VAL* 2.6 38.4 + - + +
254A ASP* 3.7 28.3 - - - +
257A ALA* 3.6 16.4 - - + -
278A TRP* 4.3 13.2 - - + +
280A HIS* 3.6 32.1 - - + +
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Residues in contact with GLN 204 (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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194A SER* 3.2 11.2 - - - -
195A GLY* 2.9 34.6 + - - -
196A PRO* 3.0 43.0 - - - +
197A SER* 5.2 0.6 - - - +
198A PRO* 3.8 11.9 - - + +
203A LEU* 1.3 75.6 - - - +
205A LEU* 1.3 71.9 + - - +
206A VAL* 4.5 0.7 - - + -
232A GLN* 6.1 1.0 - - - +
249A THR* 3.2 33.9 + - - +
250A LEU 3.3 12.5 + - - +
251A ASP* 5.1 3.7 - - - +
278A TRP* 4.6 0.2 - - - -
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Residues in contact with LEU 205 (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* 3.9 11.9 - - + -
204A GLN* 1.3 79.3 - - - +
206A VAL* 1.3 59.0 + - - +
221A TRP* 3.4 34.6 + - + -
249A THR* 3.1 8.7 - - - -
250A LEU* 2.8 39.0 + - + +
252A VAL* 3.8 24.9 - - + -
257A ALA* 4.6 2.2 - - + +
260A LEU* 3.7 32.1 - - + -
278A TRP* 3.7 43.7 - - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.3 10.2 - - - +
193A SER* 2.8 40.0 + - - +
194A SER 3.6 1.6 - - - +
195A GLY* 3.5 33.0 - - - +
196A PRO* 5.3 0.9 - - + -
204A GLN* 4.5 2.0 - - + -
205A LEU* 1.3 76.7 - - - +
207A CYS* 1.3 63.8 + - - +
208A HIS* 3.0 31.9 - - + +
221A TRP* 3.9 2.1 - - - -
247A ARG* 4.1 19.1 - - + -
248A ALA 3.6 2.5 - - - -
249A THR* 3.6 20.9 - - + -
278A TRP* 4.7 0.2 - - - -
1099A MET 5.0 3.6 - - - +
1100A GLY* 4.9 1.6 - - - -
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Residues in contact with CYS 207 (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 ALA* 5.2 0.2 - - - -
191A TRP 3.6 3.6 - - - -
192A LEU* 3.8 7.2 - - + -
206A VAL* 1.3 75.0 - - - +
208A HIS* 1.3 69.2 + - - +
209A VAL* 4.6 5.2 - - - +
219A VAL* 4.2 6.5 - - - -
221A TRP* 3.8 9.6 - - + +
246A LEU 3.9 0.2 - - - +
247A ARG* 3.1 5.9 - - - -
248A ALA* 2.8 43.3 + - + +
262A CYS* 2.0 53.2 - - + -
264A VAL* 4.6 2.7 - - - -
276A LEU* 5.1 4.0 - - - -
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Residues in contact with HIS 208 (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 ALA* 2.9 29.9 - - - +
191A TRP* 2.8 70.0 + + + -
193A SER* 2.9 25.0 + - - -
206A VAL* 3.0 26.9 - - + +
207A CYS* 1.3 74.9 - - - +
209A VAL* 1.3 61.2 + - - +
210A SER 4.1 0.4 - - - -
245A TYR* 2.6 29.5 + - + +
246A LEU 3.6 3.8 - - - -
247A ARG* 4.2 2.8 - - - -
1100A GLY* 3.7 24.2 - - - -
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Residues in contact with VAL 209 (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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188A PRO* 3.4 28.5 - - + -
189A GLU 3.7 4.0 - - - +
190A ALA* 5.0 1.6 - - + -
207A CYS* 4.6 2.7 - - - +
208A HIS* 1.3 77.4 - - - +
210A SER* 1.3 59.7 + - - +
212A PHE* 3.4 19.2 - - + -
217A VAL* 4.5 4.0 - - + -
219A VAL* 3.3 36.1 - - + -
245A TYR* 3.4 1.3 - - - -
246A LEU* 2.8 45.2 + - + +
264A VAL* 3.7 33.2 - - + -
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Residues in contact with SER 210 (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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187A LYS 4.6 0.2 - - - +
188A PRO* 3.1 3.3 - - - +
189A GLU* 3.0 35.0 + - - +
191A TRP* 3.6 17.7 - - - -
209A VAL* 1.3 76.8 - - - +
211A GLY* 1.3 58.4 + - - +
212A PHE 3.4 3.1 - - - -
239A ASN* 3.2 18.2 + - - -
244A TRP 3.5 3.6 - - - -
245A TYR* 3.8 12.5 - - - -
1012A ARG* 2.8 33.5 + - - +
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Residues in contact with GLY 211 (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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186A VAL* 3.5 10.0 - - - +
187A LYS 3.5 12.5 - - - +
188A PRO* 4.0 3.1 - - - -
210A SER* 1.3 75.6 + - - +
212A PHE* 1.3 59.1 + - - -
239A ASN* 3.3 3.1 - - - +
243A THR* 3.1 34.8 - - - +
244A TRP 2.6 13.7 + - - -
1012A ARG* 5.6 3.4 - - - -
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Residues in contact with PHE 212 (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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186A VAL 3.4 5.8 - - - -
188A PRO* 3.5 24.7 - - + -
209A VAL* 3.4 44.6 - - + -
210A SER 3.4 1.0 + - - -
211A GLY* 1.3 77.8 - - - +
213A TYR* 1.3 60.9 + - - +
214A PRO 3.6 11.9 - - - -
215A LYS* 3.2 23.3 - - - -
217A VAL* 3.7 21.5 - - + -
236A ILE* 4.2 6.1 - - + -
244A TRP* 3.1 55.7 + + + -
245A TYR 4.1 1.3 - - - -
246A LEU* 3.8 14.6 - - + -
266A HIS* 3.8 12.6 - + + +
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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