Contacts of the helix formed by residues 203 - 211 (chain B) in PDB entry 6VSU
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 SER 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ASP 3.4 2.9 - - - -
191B TYR* 2.7 27.7 + - - +
193B CYS 3.7 1.4 + - - -
194B PHE* 3.1 26.9 + - - +
198B LYS 3.9 5.4 - - - -
200B SER* 2.9 12.9 + - - -
202B ALA* 1.3 74.6 - - - +
204B SER* 1.3 67.1 + - - +
205B PHE 3.2 3.1 - - - -
206B ALA* 3.1 13.5 + - - +
207B ARG* 3.1 32.3 + - - +
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B HIS* 2.8 30.7 + - - +
162B SER* 4.0 18.6 - - - -
164B SER* 4.9 1.8 - - - -
165B TYR* 3.8 14.9 - - - +
189B ASP 3.4 1.4 + - - -
199B TYR* 6.2 0.4 - - - +
200B SER 3.4 4.7 + - - -
201B HIS 3.8 8.0 + - - -
203B SER* 1.3 76.8 - - - +
205B PHE* 1.3 70.9 + - - +
207B ARG* 3.4 7.8 + - - +
208B ILE* 3.0 30.0 + - - +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B HIS* 3.4 29.8 - + - -
164B SER* 4.3 8.5 - - - -
168B VAL* 5.7 0.7 - - + -
181B ILE* 4.1 24.7 - - + -
183B HIS* 3.4 43.1 - + - -
188B PRO 4.0 2.5 - - - +
189B ASP* 3.0 20.5 + - + +
190B ILE* 3.6 13.2 - - + -
204B SER* 1.3 77.4 - - - +
206B ALA* 1.3 61.7 + - - +
208B ILE* 3.8 21.9 - - + +
209B MET* 2.9 33.4 + - - +
217B LEU* 3.9 26.0 - - + -
268B SER* 3.8 11.0 - - - -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ASP 3.7 0.6 + - - -
190B ILE* 3.5 22.6 - - - +
191B TYR 3.6 20.0 - - - +
203B SER 3.1 9.7 + - - +
205B PHE* 1.3 73.9 - - - +
207B ARG* 1.3 78.2 + - - +
209B MET* 3.3 0.7 + - - +
210B GLU* 2.9 34.5 + - - +
232B GLN* 4.1 10.3 - - - +
236B PHE* 4.2 8.7 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TYR* 3.4 50.3 + - + -
192B ASP* 2.6 40.0 + - - +
198B LYS* 2.9 55.6 + - - +
199B TYR* 5.5 1.1 - - + -
203B SER* 3.1 17.6 + - - +
204B SER* 3.4 9.9 - - - +
206B ALA* 1.3 80.7 - - - +
208B ILE* 1.3 61.7 + - - +
210B GLU* 2.9 46.9 + - - +
211B GLY* 3.3 17.0 + - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B SER* 3.7 26.0 - - - +
165B TYR* 3.8 18.4 - - + -
168B VAL* 4.0 23.3 - - + -
181B ILE* 3.9 10.1 - - + -
204B SER 3.0 21.7 + - - +
205B PHE* 3.8 33.9 - - + +
206B ALA 3.2 0.6 - - - -
207B ARG* 1.3 76.7 - - - +
209B MET* 1.3 66.0 + - - +
211B GLY 3.4 8.8 + - - -
213B TYR* 3.4 24.3 + - + -
214B ALA* 3.9 26.9 + - + +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ILE* 5.2 0.4 - - + -
205B PHE 2.9 25.2 + - - +
206B ALA 3.3 0.6 + - - +
208B ILE* 1.3 74.1 - - + +
210B GLU* 1.3 65.9 + - - +
212B GLY* 3.2 14.3 + - - -
213B TYR 5.3 0.2 - - - +
214B ALA* 3.7 38.7 - - - +
215B ARG 4.2 11.2 - - - +
217B LEU* 4.0 33.9 - - + +
236B PHE* 3.4 58.7 - - + +
237B GLY 5.7 0.4 - - - -
238B VAL* 4.6 2.5 - - + -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ASP* 3.7 10.2 - - - +
206B ALA* 2.9 22.2 + - - +
207B ARG* 2.9 48.2 + - - +
209B MET* 1.3 77.6 - - - +
211B GLY* 1.3 58.8 - - - +
212B GLY 3.3 0.9 + - - -
232B GLN* 5.5 0.2 + - - -
235B ARG* 4.4 15.2 + - - +
236B PHE* 3.8 20.0 - - + -
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ARG 3.3 7.8 + - - -
208B ILE 3.4 0.6 + - - -
209B MET 3.3 1.2 - - - -
210B GLU* 1.3 77.9 - - - +
212B GLY* 1.3 61.7 + - - +
213B TYR* 3.2 39.4 + - - -
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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