Contacts of the strand formed by residues 532 - 539 (chain E) 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 LYS 532 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530E ILE* 3.5 8.2 - - - +
531E LEU* 1.3 96.6 - - + +
533E TYR* 1.3 66.7 + - - +
549E TRP* 3.7 28.0 - - + -
550E TYR 3.3 9.0 - - - +
551E ASP* 3.1 37.4 + - - +
552E ALA 3.9 1.8 - - - +
578E ALA* 3.6 0.5 - - - -
579E LEU* 2.8 40.8 + - + -
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Residues in contact with TYR 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503E PRO* 4.2 8.1 - - + -
519E PHE* 3.3 39.7 - + + -
521E GLU* 3.1 37.1 - - + +
522E PRO* 3.8 9.6 - - + +
530E ILE* 3.7 9.5 - - + +
532E LYS* 1.3 73.4 - - - +
534E LYS* 1.3 61.2 + - - +
549E TRP* 3.5 4.5 - - - -
550E TYR* 2.8 43.4 + - + +
552E ALA* 3.8 36.5 - - + +
555E ALA* 4.3 7.2 - - + -
556E SER* 5.7 1.3 - - - -
561E VAL* 5.2 1.6 - - + -
576E LEU* 4.6 13.0 - - + -
577E ALA 3.3 9.4 - - - +
578E ALA* 3.6 29.2 - - + -
579E LEU 4.8 0.2 - - - +
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Residues in contact with LYS 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E TYR* 1.3 72.1 - - - +
535E ALA* 1.3 66.6 + - - +
536E GLU* 3.2 32.6 + - + +
547E SER* 3.5 20.6 + - - -
548E LYS 3.7 7.6 - - - +
549E TRP* 3.8 49.0 - - + +
575E ARG 4.0 0.3 - - - +
576E LEU* 3.5 4.5 - - - -
577E ALA* 2.8 40.7 + - + +
584E LEU* 3.9 22.7 - - + -
587E ILE* 5.5 0.7 - - - +
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Residues in contact with ALA 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E TYR 3.9 0.6 + - - -
534E LYS* 1.3 73.2 - - - +
536E GLU* 1.3 62.1 + - - +
537E TRP* 3.5 9.3 - - + -
547E SER* 3.0 26.0 - - - -
548E LYS 3.0 11.6 + - - -
550E TYR* 3.7 25.4 - - + -
561E VAL* 5.1 2.5 - - + -
563E ILE* 4.7 8.7 - - + -
574E VAL* 5.1 3.6 - - + -
575E ARG 3.5 5.2 - - - +
576E LEU* 3.4 20.2 - - + -
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Residues in contact with GLU 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534E LYS* 3.2 28.8 - - + +
535E ALA* 1.3 80.0 - - - +
537E TRP* 1.3 61.2 + - - +
545E TRP* 3.6 21.4 - - + -
546E HIS 3.1 13.2 - - - +
547E SER* 3.9 7.7 - - - -
574E VAL* 3.1 4.3 - - - +
575E ARG* 2.7 78.0 + - + +
587E ILE* 4.4 11.3 - - + +
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Residues in contact with TRP 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535E ALA* 3.5 9.9 - - + -
536E GLU* 1.3 80.0 - - - +
538E ARG* 1.3 66.6 + - - +
545E TRP* 3.7 4.0 - - - -
546E HIS* 2.9 52.4 + + + +
547E SER* 3.4 40.4 - - - -
548E LYS* 3.7 14.6 - - + -
550E TYR* 5.0 1.3 - - - -
563E ILE* 4.2 31.9 - - + -
564E VAL* 4.3 18.4 + - + -
565E GLY 5.5 1.4 + - - -
566E LEU* 3.8 29.0 - - + +
572E TYR* 4.6 8.7 - + + -
573E ALA 2.9 14.8 - - - +
574E VAL* 4.1 12.1 - - + -
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Residues in contact with ARG 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E TRP* 1.3 83.3 - - - +
539E ALA* 1.3 69.0 + - - +
540E VAL* 3.2 11.8 + - - +
541E GLY 4.9 1.4 - - - +
542E GLU* 3.2 32.1 + - + -
543E GLU* 4.0 10.7 + - - +
544E VAL 3.5 22.7 - - - +
545E TRP* 3.5 52.9 - - + +
546E HIS* 5.1 5.8 - - + -
572E TYR* 3.2 7.5 - - - -
573E ALA* 2.9 42.9 + - + +
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Residues in contact with ALA 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642C SER* 4.4 11.0 - - - -
538E ARG* 1.3 76.2 - - - +
540E VAL* 1.3 70.3 + - - +
541E GLY 3.1 0.2 + - - -
542E GLU* 3.0 39.2 + - + +
546E HIS* 5.9 1.0 - - - -
570E THR* 4.5 6.3 - - + -
571E THR 3.5 10.1 - - - +
572E TYR* 3.5 20.8 - - + -
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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