Contacts of the strand formed by residues 296 - 300 (chain C) in PDB entry 2V90
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 ARG 296 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C GLY* 4.6 9.4 - - - -
275C GLN 3.7 12.6 - - - +
276C PHE* 3.7 30.7 - - + -
294C GLY 3.5 1.9 + - - +
295C ASP* 1.3 73.9 - - - +
297C LEU* 1.3 68.8 + - - +
298C VAL* 3.5 16.2 + - + +
306C GLU* 3.1 24.9 + - - +
328C VAL* 3.1 8.5 - - - -
329C VAL* 2.9 53.4 + - + +
266E GLU* 5.2 2.2 + - - +
267E LYS* 3.7 20.9 + - - +
268E GLY 4.5 7.7 + - - -
269E LEU* 4.2 18.6 - - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PHE* 5.5 0.4 - - + -
263C LEU* 4.3 15.7 - - + -
275C GLN* 3.0 25.4 + - + +
277C LEU* 4.7 10.6 - - + +
295C ASP 4.1 1.2 + - - -
296C ARG* 1.3 75.5 + - - +
298C VAL* 1.3 62.0 + - - +
299C ALA 3.5 20.4 - - - +
300C VAL* 3.7 20.2 - - + -
305C VAL* 3.8 16.0 - - + +
306C GLU* 4.5 5.4 - - - +
313C THR* 3.8 22.7 - - + -
317C ILE* 4.0 13.9 - - + -
326C LEU* 3.8 24.0 - - + -
327C THR 3.6 9.4 - - - +
328C VAL* 4.2 8.7 - - + +
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PRO* 4.6 3.8 - - + -
296C ARG* 3.8 15.7 - - - +
297C LEU* 1.3 78.8 - - - +
299C ALA* 1.3 60.2 + - + +
304C SER* 3.5 9.2 + - - -
305C VAL* 3.0 22.4 + - - -
306C GLU* 3.6 34.8 + - + +
327C THR* 2.7 50.5 + - + +
328C VAL* 4.0 5.2 - - - +
329C VAL* 3.7 26.7 - - + -
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Residues in contact with ALA 299 (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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297C LEU* 3.5 4.8 - - - +
298C VAL* 1.3 81.2 - - + +
300C VAL* 1.3 69.6 + - - +
301C ALA 4.3 0.4 - - - -
302C GLY* 4.3 7.4 - - - +
303C GLU 3.2 23.3 - - - +
304C SER* 4.2 1.8 - - - -
305C VAL* 4.0 2.7 - - - +
326C LEU* 3.4 4.9 - - - -
327C THR* 2.9 44.4 + - - +
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Residues in contact with VAL 300 (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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297C LEU* 3.7 25.6 - - + -
299C ALA* 1.3 79.6 - - - +
301C ALA* 1.3 78.8 + - + +
302C GLY 3.2 0.2 - - - -
303C GLU* 2.9 23.7 + - - +
305C VAL* 3.8 19.6 - - + +
313C THR* 4.8 3.4 - - + +
316C ARG* 4.0 34.2 + - + +
317C ILE* 3.9 15.5 - - + +
320C GLN* 4.4 4.9 - - + -
324C VAL* 4.4 2.5 - - + -
325C SER 3.5 6.1 - - - +
326C LEU* 3.8 8.3 - - + -
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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