Contacts of the strand formed by residues 295 - 300 (chain A) 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 ASP 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A PHE* 3.4 3.3 - - - +
277A LEU* 2.8 44.2 + - + +
291A MET* 3.7 10.4 - - - +
292A GLN* 2.9 40.9 + - - +
294A GLY* 1.3 77.9 - - - +
296A ARG* 1.3 59.2 + - - +
328A VAL* 3.5 28.8 - - + +
329A VAL 3.6 3.4 - - - -
330A ASP* 2.5 35.6 - - - +
331A PRO* 3.3 6.1 - - - +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLY* 4.2 15.2 - - - -
275A GLN 3.8 11.4 - - - +
276A PHE* 3.7 39.9 - - + -
294A GLY 3.5 1.8 + - - +
295A ASP* 1.3 73.7 - - - +
297A LEU* 1.3 65.6 + - - +
298A VAL* 3.5 24.5 + - + +
306A GLU* 5.9 2.0 - - - -
328A VAL* 3.2 7.2 - - - -
329A VAL* 2.9 47.0 + - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 5.5 2.0 - - + -
263A LEU* 4.0 13.0 - - + -
275A GLN* 3.0 27.1 + - + +
277A LEU* 4.0 13.7 - - + +
295A ASP 3.8 2.0 + - - -
296A ARG* 1.3 71.9 - - - +
298A VAL* 1.3 60.1 + - - +
299A ALA 3.6 20.6 - - - +
300A VAL* 3.9 10.5 - - + -
305A VAL* 3.4 21.0 - - + +
306A GLU* 5.4 0.9 - - - +
313A THR* 3.6 30.3 - - + -
317A ILE* 4.0 13.7 - - + -
326A LEU* 4.0 25.1 - - + -
327A THR 3.7 8.7 - - - +
328A VAL* 4.2 8.7 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A PRO* 4.7 5.4 - - + -
296A ARG* 3.5 30.3 + - + +
297A LEU* 1.3 72.1 - - - +
299A ALA* 1.3 62.7 + - + +
304A SER* 3.4 9.2 + - - -
305A VAL* 2.9 23.5 + - - -
306A GLU* 3.5 32.9 + - + +
327A THR* 2.8 38.9 + - + +
328A VAL* 4.4 2.5 - - - +
329A VAL* 4.0 23.1 - - + -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.6 6.4 - - - +
298A VAL* 1.3 81.8 - - + +
300A VAL* 1.3 62.4 + - - +
302A GLY* 4.4 8.1 - - - +
303A GLU 3.2 23.6 - - - +
304A SER* 4.2 2.0 - - - -
305A VAL* 3.7 2.6 - - - +
326A LEU* 3.6 3.5 - - - -
327A THR* 2.8 48.0 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.9 15.9 - - + -
299A ALA* 1.3 77.0 - - - +
301A ALA* 1.3 77.5 + - + +
302A GLY 3.0 1.6 - - - -
303A GLU* 2.9 23.4 + - - +
305A VAL* 3.9 22.1 - - + +
313A THR* 4.6 4.0 - - + +
316A ARG* 3.5 37.3 + - + +
317A ILE* 3.8 26.5 - - + +
324A VAL* 4.0 14.4 - - + -
325A SER 3.5 3.6 - - - -
326A LEU* 4.0 3.4 - - + -
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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