Contacts of the strand formed by residues 530 - 539 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A PRO* 4.7 5.2 - - + -
521A GLU* 4.8 7.0 - - + +
522A PRO* 3.5 36.6 - - + +
525A THR* 4.3 30.0 - - + +
528A VAL 4.6 0.7 - - - +
529A PRO* 1.3 74.4 - - - +
531A LEU* 1.3 62.3 + - - +
532A LYS 3.8 17.9 - - - +
533A TYR* 3.8 19.7 - - + +
552A ALA* 3.3 18.4 - - + +
553A LYS* 6.0 0.3 + - - -
578A ALA* 3.9 17.0 - - + -
579A LEU 3.9 5.8 - - - +
580A ASN* 4.4 1.6 - - - -
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Residues in contact with LEU 531 (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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528A VAL* 5.8 1.8 - - + -
529A PRO* 3.9 18.6 - - + +
530A ILE* 1.3 72.7 - - - +
532A LYS* 1.3 87.2 + - + +
551A ASP* 3.8 1.4 - - - +
552A ALA* 2.9 21.8 + - - +
579A LEU* 2.9 22.6 + - + +
580A ASN* 4.1 3.6 - - - -
581A GLY* 3.9 24.2 - - - +
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Residues in contact with LYS 532 (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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530A ILE* 3.8 4.5 - - - +
531A LEU* 1.3 101.2 + - + +
533A TYR* 1.3 69.1 + - - +
549A TRP* 3.7 28.7 - - + -
550A TYR 3.2 9.6 - - - +
551A ASP* 2.5 49.7 + - - +
552A ALA 4.0 0.9 - - - +
578A ALA* 3.8 1.4 - - - -
579A LEU* 3.0 37.4 + - + -
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Residues in contact with TYR 533 (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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503A PRO* 4.2 12.1 - - + -
519A PHE* 3.4 34.5 - + + -
521A GLU* 3.7 24.6 - - - +
522A PRO* 3.7 10.6 - - + +
530A ILE* 3.8 13.2 - - + +
532A LYS* 1.3 76.7 - - - +
534A LYS* 1.3 60.0 + - - +
548A LYS 3.6 1.2 - - - +
549A TRP* 3.4 6.6 - - - -
550A TYR* 2.8 43.1 + - + +
552A ALA* 3.9 35.2 - - + +
555A ALA* 4.0 13.7 - - + -
556A SER* 4.4 5.1 + - - -
561A VAL* 5.3 2.2 - - + -
576A LEU* 4.7 13.7 - - + -
577A ALA 3.4 14.6 - - - +
578A ALA* 3.9 17.7 - - + -
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Residues in contact with LYS 534 (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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533A TYR* 1.3 73.2 - - - +
535A ALA* 1.3 65.5 + - - +
536A GLU* 3.3 27.9 + - - +
547A SER* 3.6 25.2 + - - -
548A LYS 3.6 6.3 - - - +
549A TRP* 3.6 39.0 - - + +
575A ARG 3.8 0.3 - - - +
576A LEU* 3.5 7.5 - - - -
577A ALA* 3.0 37.2 + - + +
584A LEU* 3.7 26.7 - - + -
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Residues in contact with ALA 535 (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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533A TYR 3.8 1.6 + - - -
534A LYS* 1.3 75.1 - - - +
536A GLU* 1.3 60.4 + - - +
537A TRP* 3.6 4.5 - - + -
547A SER* 3.0 28.1 - - - -
548A LYS 2.9 9.0 + - - +
550A TYR* 3.4 30.3 - - + -
561A VAL* 5.4 1.8 - - + -
563A ILE* 4.3 18.2 - - + -
574A VAL* 5.5 2.9 - - + -
575A ARG 3.8 4.9 - - - +
576A LEU* 3.9 13.0 - - + -
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Residues in contact with GLU 536 (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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534A LYS* 3.3 35.5 - - + +
535A ALA* 1.3 79.0 - - - +
537A TRP* 1.3 60.6 + - - +
545A TRP* 3.7 20.1 - - + -
546A HIS 3.1 9.9 - - - +
547A SER* 4.4 3.1 - - - -
574A VAL* 3.2 4.5 - - - +
575A ARG* 2.7 80.9 + - + +
576A LEU 6.4 0.2 - - - -
577A ALA* 6.1 0.2 - - - -
584A LEU* 5.5 1.0 - - - +
587A ILE* 4.5 14.5 - - - +
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Residues in contact with TRP 537 (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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535A ALA* 3.6 8.7 - - + -
536A GLU* 1.3 77.9 - - - +
538A ARG* 1.3 62.1 + - - +
545A TRP* 3.6 3.1 - - - -
546A HIS* 2.9 63.0 + + + +
547A SER 3.5 36.8 - - - -
548A LYS* 3.9 13.9 - - + -
550A TYR* 5.1 0.9 - - - -
563A ILE* 4.0 35.0 - - + -
564A VAL 4.6 12.9 + - - -
565A GLY 5.8 0.2 + - - -
566A LEU* 3.5 31.2 - - + +
572A TYR* 4.1 14.3 - + + -
573A ALA 3.1 11.4 - - - +
574A VAL* 4.2 11.4 - - + -
593A PHE* 5.3 0.9 - - + -
1696A SO4 5.0 2.9 - - - -
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Residues in contact with ARG 538 (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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537A TRP* 1.3 77.9 - - - +
539A ALA* 1.3 76.9 + - - +
540A VAL* 3.4 2.3 + - - +
541A GLY 5.5 1.0 - - - +
542A GLU* 3.3 26.3 + - + -
543A GLU* 3.5 21.0 + - - +
544A VAL 3.3 15.9 - - - +
545A TRP* 3.3 49.7 - - + +
546A HIS* 5.0 2.7 - - - -
572A TYR* 3.2 6.6 - - - -
573A ALA* 2.8 43.1 + - + +
1695E SO4 2.7 41.8 + - - -
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Residues in contact with ALA 539 (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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538A ARG* 1.3 77.5 - - - +
540A VAL* 1.3 62.6 + - - +
541A GLY 2.8 0.2 + - - -
542A GLU* 2.8 50.4 + - + +
546A HIS* 5.3 4.1 - - + +
570A THR* 4.3 11.9 - - + -
571A THR 3.5 8.5 - - - +
572A TYR* 3.6 21.4 - - + +
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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