Contacts of the strand formed by residues 265 - 270 (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 VAL 265 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP* 3.0 14.8 - - + +
182C LEU* 4.4 4.0 - - + +
258C LEU* 3.4 28.9 - - + +
259C GLY* 3.4 37.0 - - - +
264C GLY* 1.3 68.3 - - - +
266C TYR* 1.3 68.1 + - - +
267C ILE* 4.6 7.9 - - + -
302C LEU* 5.0 1.6 - - + -
304C ALA* 3.7 27.4 - - + -
305C ASP* 3.1 8.4 + - + +
306C VAL* 3.2 11.8 - - + +
307C VAL* 3.1 26.9 + - - +
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Residues in contact with TYR 266 (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* 5.1 0.2 - - - -
167C VAL* 3.2 37.1 - - + +
168C VAL* 3.7 27.4 - - + -
171C VAL* 4.2 15.7 - - + -
179C VAL* 3.9 20.8 - - + +
180C ASP 2.8 4.8 + - - -
181C ILE* 2.9 17.4 - - + +
182C LEU 2.8 30.8 + - - -
264C GLY 4.3 0.4 - - - -
265C VAL* 1.3 73.3 - - - +
267C ILE* 1.3 65.9 + - - +
268C SER* 3.9 8.3 - - - -
307C VAL* 5.2 1.6 - - + -
308C GLY* 3.1 30.1 - - - +
309C ALA 3.8 7.0 - - - -
310C ASP* 2.5 45.9 + - - +
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Residues in contact with ILE 267 (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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182C LEU* 3.1 22.7 - - + +
184C LEU* 4.8 1.3 - - + -
265C VAL* 4.6 3.1 - - + -
266C TYR* 1.3 75.2 - - - +
268C SER* 1.3 60.4 - - - +
269C ILE* 3.6 30.1 - - + -
299C LEU* 4.3 11.7 - - + -
302C LEU* 4.0 17.7 - - + -
306C VAL* 3.7 37.0 - - + -
308C GLY 3.1 4.9 + - - -
309C ALA* 3.0 11.2 - - + +
310C ASP 3.0 25.5 + - - +
336C LEU* 3.9 19.7 - - + -
339C LYS* 4.5 5.2 - - + -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C HIS* 3.0 21.8 + - - -
164C SER* 3.6 2.1 + - - -
181C ILE* 4.8 0.7 - - - -
182C LEU 2.8 11.3 + - - -
183C HIS* 3.4 8.5 - - - -
184C LEU 3.0 24.4 + - - +
205C PHE* 3.8 22.1 - - - -
266C TYR* 3.9 9.2 - - - -
267C ILE* 1.3 71.9 - - - +
269C ILE* 1.3 59.2 + - - +
270C ASP 3.8 0.2 - - - -
310C ASP* 2.5 30.5 + - - -
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LEU* 3.7 24.2 - - + -
267C ILE* 3.6 22.7 - - + -
268C SER* 1.3 69.7 - - - +
270C ASP* 1.3 74.0 - - - +
271C VAL* 3.6 1.0 + - - -
273C CYS* 4.2 16.2 - - - -
295C VAL* 5.0 0.7 - - + -
299C LEU* 4.0 19.5 - - + -
310C ASP* 3.0 17.0 + - - +
311C VAL* 3.4 9.0 - - + +
312C VAL* 3.0 26.5 + - - -
332C LEU* 4.4 27.8 - - + -
336C LEU* 3.7 20.9 - - + -
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C HIS* 3.4 23.4 + - + -
184C LEU 2.9 11.8 + - - +
185C ASP* 3.0 26.8 - - - +
187C HIS* 4.6 0.9 + - - -
268C SER 3.7 2.6 + - - -
269C ILE* 1.3 72.6 - - - +
271C VAL* 1.3 83.0 + - - +
272C ASP* 3.0 31.8 + - - +
273C CYS* 3.1 18.5 + - - +
312C VAL* 3.7 8.9 - - - +
313C GLU* 3.0 28.8 - - - +
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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