Contacts of the strand formed by residues 431 - 436 (chain A) in PDB entry 2V9V
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 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ASP* 3.7 22.6 - - - +
427A ARG* 3.4 8.7 + - - +
428A VAL 2.9 30.8 + - - +
429A GLU 4.1 0.3 - - - +
430A ASN* 1.3 81.2 + - - +
432A LEU* 1.3 61.2 + - - +
433A TYR* 4.2 7.0 - - + -
480A ARG* 2.8 37.5 + - - +
1516A NA 2.7 23.4 - - - -
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASP* 3.4 6.0 + - - +
396A TRP* 2.9 64.4 + - + +
414A LEU* 6.0 1.3 - - + -
425A LEU* 4.4 19.1 - - + -
426A LEU 3.7 26.9 - - - +
427A ARG* 4.1 14.6 - - + +
431A ASP* 1.3 75.7 - - - +
433A TYR* 1.3 69.6 + - - +
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU 5.1 2.0 - - - -
393A GLY* 4.1 8.5 - - - -
394A LEU* 3.3 26.5 - - - -
395A ASP* 3.8 17.3 - - + +
396A TRP* 4.9 0.7 - - - -
424A THR 3.7 0.5 - - - +
425A LEU* 3.4 7.2 - - - +
426A LEU* 2.8 38.1 + - + +
428A VAL* 3.7 30.3 - - + -
431A ASP* 4.2 8.3 - - + -
432A LEU* 1.3 81.5 - - - +
434A ALA* 1.3 58.1 + - - +
435A ILE* 4.2 15.7 - - + -
478A PRO* 4.5 11.1 - - + +
480A ARG* 3.1 32.4 + - - -
481A VAL* 3.8 25.8 - - + +
1513A CL 4.2 10.8 - - + +
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Residues in contact with ALA 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 4.2 15.2 - - + +
393A GLY* 3.2 2.8 - - - -
394A LEU* 2.9 39.1 + - + +
396A TRP* 4.5 5.8 - - + +
399A ALA* 5.7 1.1 - - + -
414A LEU* 3.9 33.0 - - + -
423A VAL* 4.0 5.2 - - + -
424A THR 3.6 4.7 - - - -
425A LEU* 4.2 5.4 - - + -
432A LEU 4.3 0.6 + - - -
433A TYR* 1.3 72.0 - - - +
435A ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 4.0 4.9 - - - -
392A GLU 4.1 7.9 - - - +
393A GLY* 4.1 15.3 - - - +
423A VAL* 3.5 3.2 - - - +
424A THR* 2.8 46.7 + - + +
426A LEU* 4.2 34.1 - - + -
433A TYR* 4.4 11.4 - - + -
434A ALA* 1.3 80.1 - - - +
436A SER* 1.3 75.1 + - - +
439A ARG* 4.8 4.3 - - + -
440A TYR* 4.3 12.3 - - + +
443A TRP* 3.9 37.5 - - + -
481A VAL* 5.1 4.9 - - + -
485A LEU* 4.8 3.8 - - + -
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Residues in contact with SER 436 (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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387A ILE* 3.8 18.5 + - - +
388A GLN* 3.0 29.0 + - - +
390A HIS 5.3 1.0 + - - -
422A GLN 3.9 6.5 - - - -
435A ILE* 1.3 74.2 - - - +
437A THR* 1.3 64.0 + - - +
438A GLU* 3.4 7.4 + - - +
439A ARG* 3.1 40.5 + - - +
440A TYR* 3.0 21.2 + - - +
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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