Contacts of the strand formed by residues 432 - 437 (chain A) in PDB entry 6VSB
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 CYS 432 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 6.3 0.7 - - - -
377A PHE* 4.6 4.0 - - - -
378A LYS 3.4 5.8 - - - +
379A CYS* 2.0 43.3 - - - +
380A TYR* 5.2 0.4 - - - -
387A LEU* 4.8 17.3 - - - -
430A THR* 3.6 1.5 - - - -
431A GLY* 1.3 82.6 - - - +
433A VAL* 1.3 62.5 + - - +
434A ILE* 4.0 19.3 - - + -
512A VAL* 3.7 0.9 - - - -
513A LEU* 3.0 43.4 + - + +
515A PHE* 5.3 3.1 - - - -
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Residues in contact with VAL 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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376A THR* 4.2 5.1 - - + +
377A PHE* 4.0 1.0 - - - -
378A LYS* 2.6 59.3 + - + +
380A TYR* 3.8 21.1 - - + -
407A VAL 5.5 0.9 - - - +
410A ILE* 3.7 36.1 - - + +
425A LEU* 5.4 3.8 - - + -
430A THR* 4.1 15.5 - - + -
432A CYS* 1.3 74.2 - - - +
434A ILE* 1.3 61.1 + - - +
435A ALA* 6.0 1.1 - - + -
510A VAL* 4.7 7.0 - - + -
511A VAL 4.1 2.2 - - - -
512A VAL* 4.3 12.8 - - + +
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Residues in contact with ILE 434 (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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342A PHE* 4.2 8.5 - - + -
368A LEU* 3.6 17.7 - - + -
374A PHE* 3.4 35.0 - - + -
376A THR 3.2 15.5 - - - +
377A PHE* 3.6 33.9 - - + -
378A LYS 5.0 0.2 - - - +
432A CYS* 4.0 17.9 - - + -
433A VAL* 1.3 79.8 - - - +
435A ALA* 1.3 61.6 + - - +
436A TRP* 4.3 2.0 - - - -
509A ARG 4.2 0.2 - - - +
510A VAL* 3.6 2.8 - - - +
511A VAL* 2.9 37.7 + - - +
513A LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 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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374A PHE* 3.5 2.0 - - - +
375A SER* 3.0 3.7 + - - -
376A THR* 2.6 56.7 + - + +
407A VAL* 5.1 8.1 - - + -
433A VAL* 6.0 0.9 - - + -
434A ILE* 1.3 75.6 - - - +
436A TRP* 1.3 62.8 - - - +
508A TYR* 4.9 9.0 - - + -
509A ARG 3.4 12.6 - - - +
510A VAL* 3.9 19.3 - - + -
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Residues in contact with TRP 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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342A PHE* 3.4 31.2 + + - -
347A PHE* 3.9 6.3 - + - -
373A SER 3.7 9.0 - - - +
374A PHE* 3.3 53.2 - + - -
375A SER* 3.6 7.4 - - - +
434A ILE 4.3 5.4 - - - -
435A ALA* 1.3 77.7 - - - +
437A ASN* 1.3 85.0 + - - +
438A SER* 3.1 13.5 + - - -
508A TYR* 3.3 10.1 - - - -
509A ARG* 3.2 69.0 + - + +
511A VAL* 3.6 32.5 - - + -
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Residues in contact with ASN 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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375A SER* 3.7 13.8 + - - +
436A TRP* 1.3 88.6 - - - +
438A SER* 1.3 69.5 + - - +
439A ASN* 2.7 26.9 + - - +
440A ASN* 3.5 16.9 + - - +
503A VAL* 5.3 0.4 - - - +
506A GLN* 2.9 26.0 + - - +
508A TYR* 3.1 38.6 + - + -
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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