Contacts of the strand formed by residues 292 - 295 (chain D) in PDB entry 1VLP
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 GLY 292 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D LEU* 3.3 12.7 - - - +
268D ALA* 2.9 20.4 + - - +
290D TYR* 3.3 11.0 - - - +
291D VAL* 1.3 84.7 - - - +
293D VAL* 1.3 65.8 + - - +
311D TYR* 3.5 13.1 + - - -
323D ILE 3.1 15.5 - - - -
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 3.6 5.6 - - - +
268D ALA* 3.1 10.1 - - + +
270D THR* 3.7 18.8 - - + -
282D PHE* 4.0 15.3 - - + -
292D GLY* 1.3 79.4 - - - +
294D ARG* 1.3 59.7 + - - +
303D TYR* 3.5 25.6 - - + +
307D ILE* 4.0 17.0 - - + -
311D TYR* 3.6 15.5 - - + +
323D ILE 3.0 12.6 + - - +
324D ILE* 3.3 19.2 - - + +
325D CYS* 2.9 24.9 + - - +
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Residues in contact with ARG 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR* 6.4 0.4 - - - -
177D PHE* 4.2 25.0 - - - -
180D ARG* 5.3 2.6 - - - +
229D THR* 3.9 29.8 - - + +
230D VAL 3.0 26.3 + - - -
231D ALA* 4.3 6.1 - - - +
232D HIS* 5.6 2.2 + - - -
267D LEU* 4.2 2.2 - - + +
268D ALA 2.7 16.7 + - - +
269D LEU* 3.9 35.2 - - + +
270D THR* 4.2 3.3 + - - -
271D ASP* 4.9 1.2 - - - +
293D VAL* 1.3 72.1 - - - +
295D GLN* 1.3 61.4 + - - +
296D ASP* 3.7 22.8 + - - -
303D TYR* 3.5 11.8 + - - -
325D CYS* 3.4 19.3 - - + +
327D SER* 3.0 30.4 + - - +
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Residues in contact with GLN 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL 4.0 1.8 + - - -
294D ARG* 1.3 69.8 - - - +
296D ASP* 1.3 59.4 + - - +
297D SER* 2.9 37.5 + - - +
298D GLY 3.8 9.1 + - - -
300D PRO* 3.7 21.7 - - + +
303D TYR* 3.3 45.3 - - + -
324D ILE* 3.8 9.4 - - + +
325D CYS 2.7 14.1 + - - +
326D TYR* 3.5 24.8 - - + +
327D SER* 3.1 29.3 + - - -
328D ASP* 3.9 9.7 + - - +
330D LEU* 5.6 0.3 - - - +
338D TYR* 5.1 1.0 - - - -
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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