Contacts of the strand formed by residues 210 - 216 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.5 14.7 - - - +
172A CYS* 3.8 1.7 - - - -
183A GLY* 3.6 32.5 - - - -
184A SER 3.0 9.6 + - - +
187A SER 3.3 31.6 - - - +
188A THR 3.9 6.1 - - - +
189A VAL* 3.9 14.4 - - + -
206A HIS* 3.7 24.7 - - + -
209A ALA* 1.3 69.6 - - - +
211A LEU* 1.3 62.7 + - - +
212A HIS 3.9 11.2 - - - +
213A LEU* 4.9 1.3 - - + -
222A THR* 4.6 7.6 - - - -
223A CYS 3.8 11.7 - - - +
224A SER* 4.2 0.7 - - - -
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Residues in contact with LEU 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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171A LEU* 3.8 19.6 - - + +
172A CYS* 3.7 11.6 - - - +
209A ALA* 3.9 12.3 - - + +
210A VAL* 1.3 72.4 - - - +
212A HIS* 1.3 68.8 + - - +
223A CYS 3.0 6.1 + - - -
225A LYS* 3.7 28.3 - - + +
252A ALA* 4.1 5.4 - - + -
253A VAL 3.6 22.0 - - - +
254A ASN* 3.3 32.4 - - - +
33C SEP 3.3 26.0 - - - +
34C GLY* 3.5 19.3 - - - +
36C HIS* 4.4 7.9 - - - +
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Residues in contact with HIS 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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171A LEU 5.7 0.4 + - - -
172A CYS* 3.6 17.6 - - + +
210A VAL* 3.6 4.9 - - - +
211A LEU* 1.3 82.0 + - - +
213A LEU* 1.3 83.7 + - - +
214A ARG* 5.5 0.4 - - + +
222A THR* 3.6 0.9 - - - -
223A CYS* 3.1 41.8 + - - +
254A ASN 3.5 16.7 + - - +
255A VAL* 3.6 18.7 - - + +
256A VAL* 3.3 27.3 + - + +
384A ARG* 3.4 35.6 + - - -
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Residues in contact with LEU 213 (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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172A CYS* 3.6 17.1 - - + +
173A LEU 4.6 2.2 - - - +
174A GLN* 4.3 20.7 - - + +
181A VAL* 3.8 34.1 - - + +
182A THR* 3.6 12.6 - - - +
183A GLY* 3.3 32.1 - - - +
189A VAL* 4.5 8.1 - - + -
210A VAL* 4.9 0.4 - - + -
212A HIS* 1.3 91.7 + - - +
214A ARG* 1.3 67.8 + - - +
215A PHE* 4.5 3.8 - - + -
220A MET* 4.9 2.2 - - + -
221A VAL 3.1 14.6 - - - +
222A THR* 4.2 11.9 - - + -
256A VAL* 4.2 3.4 - - - -
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Residues in contact with ARG 214 (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 GLN* 3.2 21.5 + - - +
212A HIS* 5.5 0.2 - - + -
213A LEU* 1.3 76.6 - - - +
215A PHE* 1.3 68.4 + - - +
216A SER* 4.2 16.8 + - - -
220A MET* 3.3 3.4 - - - +
221A VAL 2.8 32.2 + - - +
256A VAL* 4.5 12.1 - - + +
257A ASP* 3.0 32.0 + - - +
258A PHE* 3.5 41.6 + - + +
337A ARG* 6.1 1.2 - - - +
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Residues in contact with PHE 215 (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 GLN* 2.8 74.8 + - + +
175A TYR* 4.1 16.2 - - - -
176A ASP* 3.7 26.5 - - + -
179A VAL* 4.4 7.9 - - + -
181A VAL* 3.4 33.9 - - + -
213A LEU* 4.5 3.4 - - + -
214A ARG* 1.3 79.9 + - - +
216A SER* 1.3 67.5 - - - +
219A LEU 3.0 13.2 - - - +
220A MET* 3.8 14.8 - - + -
234A MET* 3.8 21.5 - - + -
258A PHE* 4.1 2.0 - - - -
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Residues in contact with SER 216 (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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214A ARG* 4.2 18.6 + - - -
215A PHE* 1.3 79.6 - - - +
217A ASN* 1.3 88.7 + - - +
218A GLY 3.2 2.9 - - - -
219A LEU* 2.8 24.1 + - - +
258A PHE* 3.8 17.0 - - - -
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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