Contacts of the strand formed by residues 432 - 442 (chain A) in PDB entry 2VR2
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 VAL 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLU* 3.6 19.9 - - - +
411A THR* 4.3 26.9 - - + -
412A ARG 3.5 5.4 - - - +
413A THR* 4.1 16.6 - - + +
430A GLY 3.3 8.4 + - - +
431A MET* 1.3 76.3 - - - +
433A CYS* 1.3 62.3 + - - +
434A HIS* 5.4 5.2 - - + -
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Residues in contact with CYS 433 (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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357A SER* 3.8 39.7 - - - +
358A VAL 4.1 0.4 - - - -
361A GLU* 3.8 7.0 - - - -
411A THR* 3.4 2.9 - - - -
412A ARG* 2.7 47.4 + - + +
414A ILE* 3.6 30.5 - - + -
431A MET* 3.7 26.5 - - - -
432A VAL* 1.3 74.7 - - - +
434A HIS* 1.3 63.1 + - - +
435A GLY 4.0 0.3 + - - +
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Residues in contact with HIS 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER 3.8 6.9 - - - +
360A TRP* 3.2 26.5 - - + +
361A GLU* 2.8 32.9 + - - +
365A HIS* 3.3 44.5 + + + +
408A PRO 3.6 9.4 - - - +
409A LYS* 3.6 19.4 + - - -
410A GLY 3.5 3.4 - - - -
411A THR* 3.4 28.5 - - + +
432A VAL* 5.4 5.3 + - + -
433A CYS* 1.3 75.8 - - - +
435A GLY* 1.3 62.6 + - - +
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Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER* 2.7 27.9 + - - -
360A TRP* 3.8 3.8 - - - -
406A TRP* 3.3 30.8 - - - -
407A ASP 3.2 12.1 + - - -
408A PRO* 3.7 3.2 + - - -
410A GLY 3.2 10.5 + - - -
412A ARG* 4.9 0.7 - - - -
433A CYS 4.6 1.2 - - - +
434A HIS* 1.3 75.2 - - - +
436A VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 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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357A SER* 4.8 0.2 - - - -
406A TRP* 3.7 3.7 - - - -
407A ASP* 3.0 34.3 + - + +
410A GLY* 3.6 17.7 - - - +
411A THR 3.3 30.3 - - - +
412A ARG* 3.7 18.2 - - + +
435A GLY* 1.3 75.7 - - - +
437A PRO* 1.4 79.0 - - + +
438A LEU* 3.3 16.8 + - + +
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Residues in contact with PRO 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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92A SER 3.7 22.7 - - - +
93A GLY* 3.8 17.9 - - - +
404A VAL* 3.9 13.7 - - + -
405A ILE 3.8 6.3 - - - +
406A TRP* 3.9 22.6 - - + -
412A ARG* 4.4 13.5 - - - +
435A GLY 4.2 2.2 - - - +
436A VAL* 1.4 92.5 - - + +
438A LEU* 1.3 63.8 + - - +
439A VAL 3.5 1.3 - - - -
440A THR* 4.3 11.9 - - - +
448A TYR* 3.7 15.6 - - + -
450A ALA* 5.3 0.5 + - - -
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Residues in contact with LEU 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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57A LYS* 3.9 40.4 - - + +
405A ILE* 3.0 21.9 + - + +
407A ASP* 3.9 20.0 - - + +
436A VAL* 4.0 18.4 - - + +
437A PRO* 1.3 75.1 - - - +
439A VAL* 1.3 71.2 + - + +
448A TYR* 3.9 1.8 - - - +
449A GLU* 3.5 3.5 - - - +
450A ALA* 3.3 28.1 + - - +
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Residues in contact with VAL 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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52A LEU* 3.8 24.9 - - + -
403A ILE 3.9 0.3 - - - +
404A VAL* 3.4 5.9 - - - +
405A ILE* 2.9 50.6 + - + -
438A LEU* 1.3 89.9 - - + +
440A THR* 1.3 66.1 + - - +
441A ILE* 4.0 14.5 - - + +
446A VAL* 3.8 20.4 - - + -
448A TYR 3.3 2.9 - - - -
449A GLU* 4.0 24.2 - - + +
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Residues in contact with THR 440 (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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91A LEU* 2.9 44.0 + - + +
94A GLY* 4.3 9.9 - - - -
96A THR* 3.7 26.0 - - + -
403A ILE 3.7 2.0 - - - -
404A VAL* 4.2 9.8 - - + +
437A PRO* 4.3 5.5 - - - +
439A VAL* 1.3 75.0 + - - +
441A ILE* 1.3 63.4 + - - +
446A VAL* 3.7 2.6 - - - +
447A VAL* 2.9 27.9 + - + +
448A TYR* 2.9 29.5 + - - +
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Residues in contact with ILE 441 (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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7A LEU* 3.8 22.4 - - + -
9A ILE* 3.8 31.2 - - + -
27A VAL* 5.4 1.6 - - + -
52A LEU* 4.8 4.0 - - + -
96A THR* 3.7 6.4 - - - +
401A ALA* 3.5 18.6 - - + +
402A ASP* 3.3 5.2 - - - -
403A ILE* 2.7 50.3 + - + +
405A ILE* 5.1 3.4 - - + -
439A VAL* 4.0 19.5 - - + -
440A THR* 1.3 77.1 - - - +
442A SER* 1.3 62.1 + - - +
444A GLY* 3.7 7.9 - - - -
445A LYS 3.5 21.8 - - - +
446A VAL* 4.1 7.2 - - + -
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Residues in contact with SER 442 (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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91A LEU* 3.9 13.5 - - - -
96A THR* 4.6 5.1 + - - -
126A CYS 4.1 4.4 + - - -
127A CYS* 3.9 22.0 - - - +
128A ASP 4.4 1.7 + - - -
402A ASP* 3.9 6.1 + - - -
441A ILE* 1.3 73.0 - - - +
443A ARG* 1.3 81.4 + - - +
444A GLY 3.2 1.1 - - - -
445A LYS* 2.9 24.9 + - - +
447A VAL* 3.7 26.4 - - - +
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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