Contacts of the strand formed by residues 530 - 539 (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 ILE 530 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B PRO* 4.7 13.0 - - + -
521B GLU* 4.5 5.8 - - - +
522B PRO* 3.8 33.0 - - + +
523B GLU 4.3 3.1 - - - +
524B ALA* 4.2 25.1 - - + +
528B VAL 5.3 0.2 - - - +
529B PRO* 1.3 77.7 - - - +
531B LEU* 1.3 59.4 - - - +
532B LYS 3.9 8.7 - - - +
533B TYR* 3.8 37.7 - - + +
552B ALA* 3.5 13.4 - - + +
578B ALA* 4.1 8.1 - - + -
579B LEU 3.3 16.4 - - - +
580B ASN* 4.2 1.8 - - + -
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Residues in contact with LEU 531 (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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529B PRO* 3.8 28.3 - - + +
530B ILE* 1.3 75.7 - - - +
532B LYS* 1.3 77.9 + - + +
551B ASP* 4.1 3.5 - - - +
552B ALA* 3.0 22.1 + - - +
553B LYS 4.7 0.2 + - - -
579B LEU* 2.7 21.0 + - + +
580B ASN* 4.1 9.0 - - - +
581B GLY* 4.0 20.2 - - - +
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Residues in contact with LYS 532 (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* 3.9 2.4 - - - +
531B LEU* 1.3 95.1 - - + +
533B TYR* 1.3 66.3 + - - +
549B TRP* 3.5 26.9 - - + -
550B TYR 3.4 8.5 - - - +
551B ASP* 3.1 42.1 + - - +
552B ALA* 4.0 1.3 - - - +
578B ALA* 3.6 2.6 - - - -
579B LEU* 2.7 51.9 + - + +
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Residues in contact with TYR 533 (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* 4.2 9.4 - - + -
519B PHE* 4.0 29.4 - + + -
521B GLU* 2.5 46.6 + - + +
522B PRO* 3.8 10.3 - - + +
530B ILE* 3.8 13.2 - - + +
532B LYS* 1.3 73.3 - - - +
534B LYS* 1.3 62.0 + - - +
535B ALA 3.9 0.8 + - - -
548B LYS 3.8 0.3 - - - +
549B TRP* 3.5 9.5 - - - -
550B TYR* 3.0 42.9 + - + +
552B ALA* 3.8 33.7 - - + -
555B ALA* 4.4 6.7 - - + -
561B VAL* 5.4 1.8 - - + -
576B LEU* 5.7 7.4 - - + -
577B ALA 3.1 15.0 - - - +
578B ALA* 3.7 23.6 - - + -
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Residues in contact with LYS 534 (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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533B TYR* 1.3 73.2 - - - +
535B ALA* 1.3 62.5 + - - +
536B GLU* 3.4 32.8 + - + +
547B SER* 3.4 23.4 + - - -
548B LYS 3.9 5.2 - - - +
549B TRP* 3.7 42.0 - - + +
575B ARG 3.7 0.7 - - - +
576B LEU* 3.2 8.1 - - - -
577B ALA* 2.6 49.0 + - + +
584B LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 535 (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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533B TYR 3.9 1.0 + - - -
534B LYS* 1.3 71.9 - - - +
536B GLU* 1.3 62.1 + - - +
537B TRP* 3.3 4.7 - - + -
547B SER* 3.1 25.6 - - - -
548B LYS 3.2 10.7 + - - -
550B TYR* 3.4 30.5 - - + -
561B VAL* 5.3 2.0 - - + -
563B ILE* 4.4 17.3 - - + -
574B VAL* 5.2 1.3 - - + -
576B LEU* 3.6 22.0 - - + -
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Residues in contact with GLU 536 (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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534B LYS* 3.4 27.5 - - + +
535B ALA* 1.3 78.7 - - - +
537B TRP* 1.3 61.7 + - - +
545B TRP* 3.9 13.9 - - + -
546B HIS 3.3 12.1 - - - +
547B SER* 4.2 9.2 - - - -
573B ALA 3.8 0.2 - - - +
574B VAL* 3.1 6.1 - - - +
575B ARG* 2.6 85.8 + - + +
584B LEU* 5.8 0.2 - - - +
587B ILE* 3.5 17.3 - - - +
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Residues in contact with TRP 537 (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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535B ALA* 3.3 25.6 - - + -
536B GLU* 1.3 76.5 - - - +
538B ARG* 1.3 62.4 + - - +
545B TRP* 3.7 2.7 - - - -
546B HIS* 2.8 61.3 + + + +
547B SER* 3.6 25.4 - - - -
548B LYS* 3.8 13.9 - - + -
550B TYR* 5.0 1.1 - - - -
563B ILE* 4.0 32.8 - - + -
564B VAL* 4.0 20.0 + - + -
565B GLY 5.2 2.8 + - - -
566B LEU* 3.5 28.1 - - + +
572B TYR* 4.3 13.9 - + + -
573B ALA 3.1 11.9 - - - +
574B VAL* 4.5 10.1 - - + -
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Residues in contact with ARG 538 (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* 1.3 78.6 - - - +
539B ALA* 1.3 77.8 + - - +
540B VAL* 3.1 5.3 + - - +
541B GLY 5.6 0.6 - - - +
542B GLU* 3.4 20.7 + - + -
543B GLU* 2.7 52.2 + - - +
544B VAL 3.4 17.9 - - - +
545B TRP* 2.9 51.6 - - + +
546B HIS* 4.9 2.7 - - - -
572B TYR* 3.7 4.5 - - - -
573B ALA* 3.1 27.8 + - - +
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Residues in contact with ALA 539 (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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538B ARG* 1.3 75.5 - - - +
540B VAL* 1.3 68.5 + - - +
541B GLY 3.0 0.2 + - - -
542B GLU* 2.9 42.9 + - + +
546B HIS* 5.4 2.8 + - - -
567B LYS* 6.4 1.3 - - + -
570B THR* 4.0 15.9 - - + -
571B THR 3.4 6.7 - - - -
572B TYR* 3.4 25.6 - - + +
642D SER* 5.2 3.6 - - - -
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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