Contacts of the strand formed by residues 168 - 175 (chain C) in PDB entry 3VA2
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 GLN 168 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ASP 4.9 2.0 - - - +
167C THR* 1.3 80.6 + - - +
169C TYR* 1.3 77.8 + - - +
170C PHE* 4.2 21.0 - - + -
187C LYS* 4.5 4.8 - - - +
191C GLY 3.1 23.0 + - - -
192C ARG* 4.0 3.1 - - - +
193C ASN* 2.7 49.0 + - - +
217C GLY* 3.4 4.9 - - - -
218C SER* 3.2 33.5 + - - +
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Residues in contact with TYR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C THR 3.1 22.5 + - - -
128C SER* 4.0 0.4 + - - -
129C ILE* 3.5 28.7 - - + -
157C TRP* 3.9 7.9 - - + +
159C VAL* 2.6 49.8 + - + -
163C ALA* 3.8 8.5 - - - +
167C THR* 4.7 12.1 - - + +
168C GLN* 1.3 86.3 + - - +
170C PHE* 1.3 71.2 + - - +
185C TYR* 4.2 0.6 - - - -
192C ARG* 5.1 3.6 - - + -
193C ASN* 2.6 60.1 + - + +
215C VAL* 4.1 11.2 - - + -
216C ASN 3.3 13.5 - - - +
217C GLY* 4.3 2.2 - - - -
224C ILE* 4.3 12.3 - - + -
225C ARG 5.6 0.4 - - - -
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Residues in contact with PHE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C TRP* 5.9 0.2 - - - -
168C GLN* 4.2 23.3 - - + -
169C TYR* 1.3 80.5 - - - +
171C LEU* 1.3 60.9 + - - +
172C TYR* 3.5 30.3 - - + +
181C GLU* 4.2 13.0 - - - +
185C TYR* 3.5 10.8 - + - +
193C ASN* 5.0 1.6 - - - -
214C LEU 3.5 1.2 - - - +
215C VAL* 3.2 6.4 - - - -
216C ASN* 2.7 53.0 + - + +
217C GLY 4.3 2.0 - - - -
218C SER* 3.1 34.3 - - - -
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Residues in contact with LEU 171 (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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153C LEU* 5.2 4.3 - - + -
155C CYS* 5.0 6.7 - - + -
157C TRP* 4.4 11.4 - - + -
170C PHE* 1.3 71.2 - - - +
172C TYR* 1.3 80.1 + - - +
173C TYR* 4.3 4.3 - - + +
181C GLU* 3.4 6.1 - - - +
182C CYS* 3.0 33.6 + - + -
185C TYR* 2.9 15.0 + - + -
196C CYS* 3.8 19.5 - - + -
198C PHE* 3.6 31.2 - - + -
213C VAL* 3.6 18.4 - - + -
214C LEU 3.5 13.2 - - - +
215C VAL* 3.5 21.5 - - + -
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Residues in contact with TYR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.6 19.5 - - + -
170C PHE* 3.5 42.4 - - + +
171C LEU* 1.3 80.7 - - - +
173C TYR* 1.3 59.3 + - - +
179C THR* 4.7 6.5 - - + -
180C GLU 3.3 9.2 - - - +
181C GLU* 3.5 39.1 + - + -
213C VAL* 3.4 4.2 - - - +
214C LEU* 2.5 63.2 + - + +
216C ASN* 3.9 15.9 - - + +
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Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.5 3.8 - - - -
153C LEU* 3.9 18.6 - - + -
171C LEU* 4.8 2.2 - - + -
172C TYR* 1.3 74.8 - - - +
174C ARG* 1.3 64.3 + - - +
175C TYR* 4.1 11.4 - - + -
178C TRP 4.8 3.6 - - - -
179C THR* 3.3 8.3 - - - +
180C GLU* 2.4 74.2 + - + -
198C PHE* 3.6 32.1 - + - -
201C THR* 3.3 9.8 - - + -
202C PHE* 2.8 28.8 + + + -
203C ILE* 4.0 18.4 - - + -
211C LEU* 3.6 16.6 - - + -
212C ALA 3.2 10.8 - - - +
213C VAL* 4.2 8.3 - - + -
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Residues in contact with ARG 174 (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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42C GLY* 4.7 2.2 - - - -
43C LEU* 2.3 61.8 + - + +
44C ALA 4.1 3.4 + - - -
45C GLN* 3.6 37.1 + - - +
87C VAL* 4.7 12.3 - - - +
173C TYR* 1.3 80.1 - - - +
175C TYR* 1.3 60.8 + - - +
176C GLY* 2.8 35.6 + - - +
177C SER* 4.9 1.8 - - - +
178C TRP 3.3 12.6 - - - +
179C THR* 3.2 19.5 - - - +
209C ASP* 5.4 7.3 + - - -
210C TRP* 4.0 10.7 + - - +
211C LEU* 3.8 2.9 - - - +
212C ALA* 2.6 45.3 + - + +
230C LEU* 6.0 0.2 - - - +
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Residues in contact with TYR 175 (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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131B ILE* 4.2 15.8 - - + +
173C TYR* 4.0 6.3 - - + -
174C ARG* 1.3 72.4 - - - +
176C GLY* 1.3 65.6 + - - +
177C SER 3.3 3.6 + - - -
178C TRP* 3.1 31.3 + + - +
202C PHE* 4.0 6.5 - - + +
203C ILE* 4.0 41.1 - - + +
204C LEU* 3.8 25.1 - - + -
207C GLY* 3.1 8.9 - - - -
208C ARG 3.1 13.3 + - - -
209C ASP* 3.0 50.6 + - + +
210C TRP 3.2 20.4 - - - -
211C LEU* 4.3 7.4 - - + -
233C LEU* 3.7 14.6 - - + -
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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