Contacts of the strand formed by residues 546 - 551 (chain B) in PDB entry 2VKW
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 HIS 546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B GLU* 3.1 5.0 - - - -
537B TRP* 2.9 70.3 + + + +
538B ARG* 4.3 7.9 - - + +
539B ALA 5.9 0.2 - - - -
542B GLU* 6.2 3.4 - - + -
544B VAL* 3.9 20.5 + - + +
545B TRP* 1.3 75.1 - - - +
547B SER* 1.3 60.6 + - - +
1695B SO4 3.1 32.7 + - - +
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Residues in contact with SER 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LYS* 4.0 25.3 - - - -
535B ALA 3.0 12.3 - - - -
536B GLU* 4.2 7.6 - - - -
537B TRP* 3.6 7.3 - - - -
545B TRP* 4.1 2.1 + - - -
546B HIS* 1.3 76.4 - - - +
548B LYS* 1.3 65.8 + - - +
549B TRP* 5.7 3.5 + - - -
1693B SO4 3.9 9.6 + - - -
1695B SO4 2.9 21.5 + - - -
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Residues in contact with LYS 548 (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* 3.5 1.9 - - - -
535B ALA 2.9 30.5 + - - -
537B TRP* 3.5 22.7 - - + -
547B SER* 1.3 78.0 - - - +
549B TRP* 1.3 88.2 + - - +
550B TYR* 3.3 35.9 + - + +
562B THR 4.5 4.9 + - - -
564B VAL* 4.8 17.8 - - + +
1693B SO4 3.6 20.6 - - - +
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Residues in contact with TRP 549 (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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532B LYS* 3.8 18.8 - - + -
533B TYR 3.4 11.2 - - - -
534B LYS* 3.4 51.3 - - + +
547B SER* 5.7 3.4 + - - -
548B LYS* 1.3 91.5 - - - +
550B TYR* 1.3 61.5 + - - +
579B LEU* 3.8 37.5 - - + -
584B LEU* 3.9 14.8 - - + -
1692B SO4 4.9 10.2 + - - +
1693B SO4 2.7 36.2 + - - +
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Residues in contact with TYR 550 (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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532B LYS* 3.3 8.7 - - - +
533B TYR* 2.8 45.6 + - + +
535B ALA* 3.7 19.1 - - + -
537B TRP* 4.3 0.5 - - - -
548B LYS* 3.3 57.2 + - + +
549B TRP* 1.3 75.8 - - - +
551B ASP* 1.3 65.9 + - - +
554B GLU* 5.5 7.2 - - - +
555B ALA* 5.1 0.7 - - + -
561B VAL* 3.7 41.5 - - + -
562B THR 2.9 33.6 + - - -
563B ILE* 3.8 12.1 - - - +
576B LEU* 6.1 0.2 - - + -
1692B SO4 4.3 1.3 - - - -
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Residues in contact with ASP 551 (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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639A ARG* 3.9 8.7 + - - +
644A GLU* 5.4 1.0 - - - +
645A TRP* 2.7 35.7 + - - -
531B LEU 4.0 2.6 - - - +
532B LYS* 2.8 34.9 + - - +
550B TYR* 1.3 73.4 - - - +
552B ALA* 1.3 59.7 + - - +
553B LYS 3.3 4.1 + - - -
554B GLU* 3.0 34.3 + - + +
555B ALA* 3.0 26.9 + - - +
1692B SO4 3.7 19.1 + - - +
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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