Contacts of the strand formed by residues 403 - 413 (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 ILE 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.8 15.9 - - + -
25A VAL* 4.0 11.9 - - + -
27A VAL* 3.9 18.8 - - + -
32A VAL* 3.9 26.9 - - + -
59A VAL* 3.6 27.4 - - + -
60A LEU 3.5 4.9 - - - +
395A ILE* 3.9 18.2 - - + -
400A ASP 5.3 0.4 - - - +
401A ALA* 3.6 7.6 - - + -
402A ASP* 1.3 80.4 - - - +
404A VAL* 1.3 72.3 + - - +
405A ILE* 4.7 2.0 - - + +
439A VAL 3.9 0.9 - - - +
440A THR* 3.6 0.5 - - - -
441A ILE* 2.7 53.1 + - + +
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Residues in contact with VAL 404 (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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58A LEU 3.4 2.8 - - - +
59A VAL* 3.7 1.6 - - - -
60A LEU* 2.9 41.8 + - + +
62A GLY* 4.1 11.7 - - - -
94A GLY* 3.3 33.0 - - - +
96A THR* 4.7 0.7 - - + -
356A MET* 4.9 3.4 - - + -
403A ILE* 1.3 79.7 - - - +
405A ILE* 1.3 66.0 + - - +
406A TRP* 3.6 30.3 + - + -
437A PRO* 3.9 16.2 - - + -
439A VAL 3.4 8.7 - - - +
440A THR* 4.2 11.7 - - + +
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Residues in contact with ILE 405 (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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9A ILE* 4.1 28.9 - - + -
52A LEU* 4.0 24.7 - - + -
53A ASP 5.5 2.2 - - - +
54A ALA* 4.1 14.6 - - + -
57A LYS* 4.0 23.3 - - + -
58A LEU 3.3 5.8 - - - +
59A VAL* 4.8 3.4 - - + -
403A ILE* 4.3 6.9 - - + -
404A VAL* 1.3 71.7 - - - +
406A TRP* 1.3 60.9 + - - +
437A PRO* 3.8 2.3 - - - +
438A LEU* 3.0 42.5 + - + +
439A VAL* 2.9 38.2 + - + +
441A ILE* 5.1 2.0 - - + -
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Residues in contact with TRP 406 (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* 3.7 3.6 - - - +
58A LEU* 2.7 47.9 + - + +
60A LEU* 3.6 32.3 - - + -
93A GLY 3.9 11.2 - - - -
356A MET* 3.6 34.3 - - + -
357A SER* 3.8 9.2 - - - -
360A TRP* 3.4 43.4 - + + -
374A PHE* 4.5 2.5 - + - -
404A VAL* 3.7 20.0 - - + +
405A ILE* 1.3 73.2 - - - +
407A ASP* 1.3 67.5 + - - +
408A PRO* 3.4 8.6 - - - +
435A GLY* 3.3 39.1 - - - -
436A VAL 3.7 3.6 - - - -
437A PRO* 3.9 25.4 - - + -
438A LEU* 5.1 0.2 - - - -
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Residues in contact with ASP 407 (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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56A GLY 4.7 1.2 - - - +
57A LYS* 3.4 37.1 + - + +
405A ILE 4.2 0.6 + - - -
406A TRP* 1.3 73.1 - - - +
408A PRO* 1.3 63.4 - - - +
409A LYS* 3.4 17.0 + - - +
410A GLY* 3.3 25.1 + - - +
435A GLY* 3.2 4.3 + - - -
436A VAL* 3.0 41.2 + - + +
438A LEU* 3.9 17.8 - - + +
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Residues in contact with PRO 408 (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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56A GLY 4.8 10.5 - - - +
58A LEU* 3.7 32.5 - - + -
360A TRP* 3.5 31.1 + - + +
365A HIS* 4.9 2.9 + - - -
406A TRP* 3.4 9.2 - - + +
407A ASP* 1.3 86.5 - - - +
409A LYS* 1.3 66.9 + - + +
410A GLY 3.4 0.6 + - - -
434A HIS* 3.6 25.1 - - - +
435A GLY* 3.7 3.2 + - - -
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Residues in contact with LYS 409 (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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407A ASP* 3.4 9.6 + - - +
408A PRO* 1.3 82.7 - - + +
410A GLY* 1.3 59.6 + - - +
411A THR* 3.9 2.3 + - - +
434A HIS* 3.6 13.4 + - - -
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Residues in contact with GLY 410 (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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407A ASP* 3.3 22.1 + - - +
408A PRO 3.4 0.6 - - - -
409A LYS* 1.3 80.8 - - - +
411A THR* 1.3 61.7 + - - -
434A HIS* 3.5 3.5 - - - -
435A GLY 3.2 24.4 + - - -
436A VAL* 3.6 9.3 - - - +
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Residues in contact with THR 411 (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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409A LYS 4.6 1.8 - - - +
410A GLY* 1.3 73.0 - - - -
412A ARG* 1.3 65.7 + - - +
432A VAL* 4.3 18.6 - - + -
433A CYS 3.4 6.5 - - - +
434A HIS* 3.4 37.5 - - + +
436A VAL* 3.3 9.9 - - - +
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Residues in contact with ARG 412 (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 5.5 2.7 - - - -
93A GLY* 4.9 3.8 + - - -
353A GLU* 3.9 26.2 + - - +
354A ASP* 2.8 32.9 + - - +
357A SER* 2.8 35.6 + - - -
411A THR* 1.3 80.4 + - - +
413A THR* 1.3 68.1 + - - +
414A ILE* 3.9 15.7 + - - +
419A HIS* 5.8 1.0 - - - +
431A MET 3.6 1.6 - - - +
432A VAL* 3.5 2.1 - - - -
433A CYS* 2.7 41.5 + - + +
435A GLY 4.9 0.2 - - - -
436A VAL* 3.7 25.8 - - + -
437A PRO* 4.4 14.1 - - - +
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Residues in contact with THR 413 (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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412A ARG* 1.3 80.3 + - - +
414A ILE* 1.3 72.3 + - - +
415A SER* 3.7 6.7 + - - -
418A THR* 4.1 9.0 + - - -
430A GLY* 3.9 18.6 - - - +
431A MET 3.5 10.5 - - - +
432A VAL* 4.1 14.3 - - + +
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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