Contacts of the helix formed by residues 203 - 211 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C ASP 3.4 4.7 - - - -
191C TYR* 2.8 27.7 + - - +
193C CYS* 3.7 0.7 - - - -
194C PHE* 3.1 28.2 + - - +
197C ASN 4.6 0.9 - - - -
198C LYS 4.4 4.9 - - - -
200C SER* 2.9 15.7 + - - -
202C ALA* 1.3 73.6 - - - +
204C SER* 1.3 63.3 - - - +
206C ALA* 3.2 14.1 + - - +
207C ARG* 3.3 31.3 + - - +
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Residues in contact with SER 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C HIS* 3.6 23.7 + - - -
162C SER* 4.4 9.0 - - - -
164C SER* 3.8 3.8 - - - -
165C TYR* 3.7 12.9 + - - +
189C ASP 3.1 2.6 + - - -
199C TYR 6.2 0.7 - - - -
200C SER 3.6 2.8 + - - -
201C HIS 3.9 15.3 - - - -
203C SER* 1.3 77.6 - - - +
205C PHE* 1.3 66.2 + - - +
207C ARG* 3.4 10.7 - - - +
208C ILE* 3.2 37.3 + - - +
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Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C HIS* 3.8 18.4 - + - -
164C SER* 4.4 4.7 - - - -
168C VAL* 5.8 0.9 - - + -
181C ILE* 3.9 15.7 - - + -
183C HIS* 3.4 44.0 - + - -
188C PRO 4.0 4.3 - - - +
189C ASP* 2.9 20.1 + - + +
190C ILE* 3.5 14.6 - - + -
204C SER* 1.3 80.8 - - - +
206C ALA* 1.3 58.9 - - - +
207C ARG 3.4 0.2 - - - -
208C ILE* 3.7 21.8 - - + +
209C MET* 2.9 35.9 + - - +
217C LEU* 3.6 38.8 - - + -
266C TYR* 6.2 0.2 - + - -
268C SER* 3.8 16.2 - - - -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE* 3.3 26.5 - - - +
191C TYR 3.2 27.8 - - - +
203C SER 3.2 5.9 + - - +
205C PHE* 1.3 73.7 - - - +
207C ARG* 1.3 63.1 + - - +
209C MET* 3.6 1.4 + - - +
210C GLU* 2.6 45.3 + - - +
232C GLN* 4.1 8.7 - - - +
236C PHE* 4.3 5.9 - - + -
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C TYR* 3.6 44.6 + - + -
192C ASP* 2.4 38.0 + - - -
198C LYS* 3.3 52.3 + - - +
199C TYR* 5.6 2.2 - - + -
203C SER* 3.3 19.8 + - - +
204C SER* 3.4 11.0 - - - +
206C ALA* 1.3 79.6 - - - +
208C ILE* 1.3 58.1 + - - +
210C GLU* 2.6 47.1 + - - +
211C GLY* 3.1 22.9 + - - -
213C TYR* 4.4 0.2 - - - -
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C SER* 4.3 5.4 - - - +
165C TYR* 3.7 31.6 - - + +
168C VAL* 3.8 31.0 - - + -
181C ILE* 4.2 4.7 - - + -
204C SER* 3.2 30.8 + - - +
205C PHE* 3.7 33.0 - - + +
206C ALA 3.3 0.2 - - - -
207C ARG* 1.3 71.8 - - - +
209C MET* 1.3 69.6 + - - +
211C GLY 3.4 2.4 + - - -
212C GLY 3.3 13.7 + - - -
213C TYR* 3.3 14.1 + - + -
214C ALA* 3.9 23.7 + - + +
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Residues in contact with MET 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE* 4.7 2.2 - - + -
205C PHE 2.9 21.9 + - - +
206C ALA 4.1 1.3 - - - +
208C ILE* 1.3 73.7 - - - +
210C GLU* 1.3 57.6 + - - +
212C GLY* 2.9 25.7 + - - -
214C ALA* 3.8 32.5 - - - +
215C ARG 3.7 22.2 - - - +
217C LEU* 4.1 30.5 - - + -
236C PHE* 3.3 59.6 - - + +
238C VAL* 5.4 0.4 - - + -
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Residues in contact with GLU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ASP* 3.8 10.9 - - - +
206C ALA* 2.6 27.3 + - - +
207C ARG* 2.6 47.9 + - - +
209C MET* 1.3 75.7 - - - +
211C GLY* 1.3 57.8 + - - +
212C GLY 3.6 0.5 + - - -
232C GLN* 5.5 0.2 + - - -
235C ARG* 4.8 9.0 + - - +
236C PHE* 4.0 18.3 - - + -
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Residues in contact with GLY 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ARG 3.1 8.4 + - - -
208C ILE 3.4 0.2 + - - -
209C MET 3.2 0.2 - - - -
210C GLU* 1.3 77.3 - - - +
212C GLY* 1.3 64.2 + - - +
213C TYR* 3.2 38.6 + - - -
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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