Contacts of the strand formed by residues 434 - 439 (chain A) in PDB entry 2VDQ
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.6 2.2 - - - -
25A PHE* 3.8 6.4 - - + -
363A LEU* 5.2 2.3 - - - +
366A LEU* 5.8 0.4 - - - -
423A GLY* 3.3 22.5 - - - -
424A ALA 3.9 0.3 + - - -
425A VAL 2.9 14.6 + - - +
426A ASP* 3.4 0.2 - - - +
427A ILE* 2.9 38.6 + - + +
428A ASP* 3.2 5.8 - - - +
432A TYR 3.2 1.9 - - - +
433A PRO* 1.3 73.5 - - - +
435A LEU* 1.3 62.2 + - - +
447A VAL* 5.1 2.2 - - + -
448A TYR 3.4 10.8 - - - +
449A ARG* 3.4 8.7 - - - -
450A ALA 2.9 24.5 + - - +
2007A CA 2.5 29.9 - - - -
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Residues in contact with LEU 435 (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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3A LEU* 3.7 32.3 - - + +
361A ALA* 4.8 0.9 - - + -
363A LEU* 3.7 21.3 - - + -
375A ALA* 4.3 10.5 - - + -
389A VAL* 4.3 13.0 - - + -
391A VAL* 5.1 0.7 - - + -
407A LEU* 3.8 19.7 - - + -
421A LEU* 4.2 12.8 - - + -
422A ARG 3.3 20.4 - - - +
434A ASP* 1.3 74.6 - - - +
436A ILE* 1.3 71.3 + - - +
437A VAL* 3.9 15.0 - - + -
446A ALA 3.9 0.9 - - - +
447A VAL* 3.5 2.5 - - - +
448A TYR* 2.8 40.7 + - + +
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Residues in contact with ILE 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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23A LEU* 3.8 18.6 - - + +
24A ASP 4.1 11.7 - - - -
25A PHE* 3.7 33.4 - - + -
35A ILE* 3.7 42.2 - - + -
421A LEU* 3.4 5.9 - - - -
422A ARG* 2.8 55.4 + - + +
435A LEU* 1.3 78.1 - - - +
437A VAL* 1.3 63.9 + - - +
445A VAL* 4.4 4.3 - - + -
446A ALA 3.5 3.8 - - - +
447A VAL* 3.9 14.6 - - + -
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Residues in contact with VAL 437 (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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23A LEU* 4.1 3.4 - - - -
389A VAL* 4.2 7.0 - - + -
407A LEU* 5.1 0.2 - - + -
411A PHE* 5.4 0.9 - - - -
417A PHE* 3.4 28.7 - - + -
418A GLY* 3.4 33.7 - - - +
420A SER 3.6 2.5 - - - -
421A LEU* 3.3 18.6 - - + -
435A LEU* 3.9 20.6 - - + -
436A ILE* 1.3 75.0 - - - +
438A GLY* 1.3 62.6 + - - +
439A ALA 4.0 0.2 + - - -
445A VAL* 3.3 2.5 - - - +
446A ALA* 2.8 41.6 + - + +
448A TYR* 4.0 15.9 - - + -
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Residues in contact with GLY 438 (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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20A GLY* 3.6 10.5 - - - -
23A LEU* 3.8 9.6 - - - +
416A ALA 3.6 4.0 - - - +
418A GLY 3.1 23.3 + - - -
419A PHE* 3.8 4.4 + - - -
420A SER* 3.0 28.5 + - - +
437A VAL* 1.3 73.2 - - - +
439A ALA* 1.3 59.3 + - - -
440A TYR 3.8 2.5 - - - -
444A GLN 3.8 5.6 - - - -
445A VAL* 4.3 0.4 - - - -
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Residues in contact with ALA 439 (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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20A GLY 4.3 0.2 + - - -
411A PHE* 3.6 37.5 - - + -
415A SER* 3.1 26.2 - - - +
416A ALA 4.2 0.2 - - - -
417A PHE* 3.9 7.0 - - + +
437A VAL 4.0 0.6 + - - -
438A GLY* 1.3 73.2 - - - +
440A TYR* 1.3 66.2 + - - +
442A ALA* 2.9 11.2 + - + -
443A ASN 3.1 8.5 + - - -
444A GLN 2.9 17.7 + - - +
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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