Contacts of the strand formed by residues 210 - 216 (chain D) in PDB entry 6WNX
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 VAL 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.5 15.1 - - - +
172D CYS* 3.8 2.5 - - - -
183D GLY* 3.6 31.9 - - - -
184D SER 3.0 9.2 + - - +
187D SER 3.2 32.1 - - - +
188D THR 4.0 5.6 - - - +
189D VAL* 3.9 14.4 - - + -
206D HIS* 3.7 24.2 - - + -
209D ALA* 1.3 69.4 - - - +
211D LEU* 1.3 63.0 + - - +
212D HIS 3.9 11.7 - - - +
213D LEU* 4.9 0.9 - - + -
222D THR* 4.5 7.4 - - - -
223D CYS 3.8 11.4 - - - +
224D SER* 4.2 0.7 - - - -
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.8 21.2 - - + +
172D CYS* 3.7 13.4 - - - +
209D ALA* 3.9 12.3 - - + +
210D VAL* 1.3 72.8 - - - +
212D HIS* 1.3 66.9 + - - +
223D CYS 3.0 5.5 + - - -
225D LYS* 3.7 30.3 - - + +
252D ALA* 4.1 4.7 - - + -
253D VAL 3.6 22.4 - - - +
254D ASN* 3.4 32.5 - - - +
33F SEP 3.3 26.0 - - - +
34F GLY 3.4 20.1 - - - +
35F ILE* 4.6 2.0 - - - -
36F HIS* 4.7 3.6 - - - +
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Residues in contact with HIS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU 5.9 0.2 + - - -
172D CYS* 3.6 16.5 - - + +
210D VAL* 3.6 5.1 - - - +
211D LEU* 1.3 82.2 + - - +
213D LEU* 1.3 84.6 + - - +
214D ARG* 5.4 0.6 - - + +
222D THR* 3.6 1.0 - - - -
223D CYS* 3.1 45.5 + - - +
254D ASN 3.5 13.1 + - - +
255D VAL* 3.6 18.3 - - + +
256D VAL* 3.3 27.3 + - - +
384D ARG* 3.4 35.9 + - - -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D CYS* 3.6 17.9 - - + +
173D LEU 5.1 2.1 - - - +
174D GLN* 4.4 17.9 - - + +
181D VAL* 3.8 33.9 - - + +
182D THR* 3.6 11.7 - - - +
183D GLY* 3.4 32.3 - - - +
189D VAL* 4.4 8.7 - - + -
210D VAL* 4.9 0.7 - - + -
212D HIS* 1.3 92.0 + - - +
214D ARG* 1.3 70.4 + - - +
215D PHE* 4.4 4.9 - - + -
220D MET* 4.7 2.5 - - + -
221D VAL 3.1 15.7 - - - +
222D THR* 4.1 10.8 - - + -
256D VAL* 4.2 2.9 - - - -
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Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLN* 3.2 23.8 + - - +
212D HIS* 5.4 0.7 - - + +
213D LEU* 1.3 76.0 - - - +
215D PHE* 1.3 63.9 + - - +
216D SER* 4.1 21.3 + - - -
220D MET* 3.3 3.4 - - - +
221D VAL 2.8 34.1 + - - +
256D VAL* 4.5 11.6 - - + +
257D ASP* 3.0 33.4 + - - +
258D PHE* 3.3 42.0 + - + +
259D ASP* 5.8 0.6 - - - +
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Residues in contact with PHE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLN* 2.8 74.8 + - + -
175D TYR* 4.1 15.3 - - - -
176D ASP* 3.5 26.7 - - + -
178D ARG* 4.6 0.7 - - - -
179D VAL* 4.4 4.0 - - + -
181D VAL* 3.4 33.7 - - + -
213D LEU* 4.4 3.6 - - + -
214D ARG* 1.3 80.0 + - - +
216D SER* 1.3 67.4 + - - +
219D LEU 3.0 12.3 - - - +
220D MET* 3.7 14.6 - - + -
234D MET* 3.5 29.4 - - + -
258D PHE* 4.1 3.1 - - - -
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Residues in contact with SER 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 4.1 20.8 + - - -
215D PHE* 1.3 80.5 - - - +
217D ASN* 1.3 88.7 + - - +
218D GLY 3.2 2.9 - - - -
219D LEU* 2.8 24.8 + - - +
234D MET* 5.7 0.4 - - - +
258D PHE* 3.8 15.1 - - - -
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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