Contacts of the strand formed by residues 571 - 580 (chain B) in PDB entry 2VKX
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 THR 571 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A LYS* 4.4 8.1 + - - -
622A ILE* 4.4 13.1 - - + +
539B ALA* 3.4 5.4 - - - -
540B VAL* 2.7 43.9 + - + +
570B THR* 1.3 77.0 - - - +
572B TYR* 1.3 56.3 + - - +
592B GLU* 3.3 31.2 - - + +
593B PHE 3.4 10.5 - - - +
594B LYS* 4.1 16.3 - - - +
641D LEU* 4.1 20.1 - - + +
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Residues in contact with TYR 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B TRP* 4.3 17.3 - + + -
538B ARG 3.5 6.5 - - - +
539B ALA* 3.4 31.9 - - + +
540B VAL* 3.9 4.0 - - - -
546B HIS* 5.6 3.8 - + - -
565B GLY 5.1 0.3 + - - -
566B LEU* 3.6 17.0 - - + -
567B LYS* 2.7 47.7 + - - +
570B THR* 3.5 32.8 - - + +
571B THR* 1.3 74.6 - - - +
573B ALA* 1.3 63.2 + - - +
591B SER 3.8 0.2 - - - +
592B GLU* 3.2 6.6 - - - +
593B PHE* 2.9 66.4 + + + -
595B THR* 3.8 8.3 - - + -
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Residues in contact with ALA 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B TRP* 3.1 5.9 - - - +
538B ARG* 3.1 36.1 + - + +
540B VAL* 4.6 10.1 - - + -
545B TRP* 3.7 15.8 - - + -
572B TYR* 1.3 74.5 - - - +
574B VAL* 1.3 60.6 + - - +
590B ALA* 4.2 19.7 - - + -
591B SER 3.4 6.1 - - - +
592B GLU* 4.3 5.4 - - + +
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Residues in contact with VAL 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B ILE* 3.8 8.7 - - + +
508B VAL* 4.4 9.4 - - + -
517B VAL* 4.4 19.1 - - + -
535B ALA* 5.2 0.2 - - + -
536B GLU 3.1 17.3 - - - +
537B TRP* 4.5 6.5 - - + -
545B TRP* 4.7 0.2 - - - -
563B ILE* 4.8 10.1 - - + -
573B ALA* 1.3 75.4 - - - +
575B ARG* 1.3 71.7 + - - +
576B LEU* 4.7 7.9 - - + -
590B ALA* 3.4 1.6 - - - -
591B SER* 2.8 52.1 + - - +
593B PHE* 3.9 23.8 - - + -
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Residues in contact with ARG 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B ILE* 4.1 2.5 - - - -
534B LYS 3.7 0.7 - - - +
536B GLU* 2.6 65.5 + - + +
545B TRP* 3.0 58.1 - - + +
574B VAL* 1.3 77.0 - - - +
576B LEU* 1.3 67.8 + - - +
587B ILE* 3.2 34.1 - - + +
588B SER* 3.5 27.7 + - - +
589B ALA 4.0 4.9 - - - +
590B ALA* 4.4 4.3 - - - +
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B PRO* 3.2 25.4 - - + +
505B ILE* 4.2 13.5 - - + -
517B VAL* 4.1 11.4 - - + -
519B PHE* 3.6 49.8 - - + -
533B TYR* 5.7 7.4 - - + -
534B LYS 3.2 3.6 - - - +
535B ALA* 3.6 28.0 - - + +
550B TYR* 6.0 0.2 - - + -
561B VAL* 4.7 9.0 - - + -
574B VAL* 4.7 7.9 - - + -
575B ARG* 1.3 83.7 - - - +
577B ALA* 1.3 61.7 + - - +
587B ILE* 3.5 3.2 - - - -
588B SER* 3.0 33.6 + - - +
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Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B PRO* 4.0 7.0 - - - -
533B TYR* 3.1 7.3 - - - -
534B LYS* 2.6 46.7 + - + +
576B LEU* 1.3 75.6 - - - +
578B ALA* 1.3 60.4 + - - +
584B LEU* 3.7 28.0 - - + -
585B GLY 4.4 4.0 - - - +
586B GLU 4.3 2.7 - - - -
587B ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B PRO* 3.9 14.3 - - + +
501B SER 4.3 3.3 + - - +
503B PRO* 4.0 3.4 - - + +
522B PRO* 3.8 22.9 - - + -
530B ILE* 4.1 9.2 - - + -
532B LYS 3.7 3.6 - - - -
533B TYR* 3.7 22.7 - - + -
577B ALA* 1.3 75.1 - - - +
579B LEU* 1.3 61.9 + - - +
584B LEU* 3.4 2.7 - - - +
585B GLY* 2.8 32.1 + - - +
586B GLU 5.0 1.0 + - - -
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Residues in contact with LEU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ILE* 3.3 8.6 - - - +
531B LEU* 2.7 38.7 + - + -
532B LYS* 2.7 46.3 + - + +
549B TRP* 3.6 30.7 - - + -
578B ALA* 1.3 74.4 - - - +
580B ASN* 1.3 68.3 + - - +
583B GLY* 3.9 20.0 - - - -
584B LEU* 3.9 8.7 - - + +
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Residues in contact with ASN 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B ASP 3.3 23.0 + - - -
499B THR* 4.3 0.9 - - - -
500B PRO* 4.1 20.6 - - + +
525B THR 3.8 7.7 + - - -
528B VAL* 3.3 20.0 + - + +
529B PRO 3.4 22.0 - - - +
530B ILE* 4.2 1.6 - - + -
531B LEU* 4.1 9.3 - - - +
579B LEU* 1.3 81.9 - - - +
581B GLY* 1.3 61.3 + - - +
582B LYS* 2.9 5.9 + - - +
583B GLY* 2.8 48.8 + - - +
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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