Contacts of the strand formed by residues 566 - 570 (chain B) in PDB entry 4WGK
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 566 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 4.2 16.8 - - + +
247B LYS* 2.8 41.2 + - - +
282B ILE* 4.1 20.6 - - + -
417B GLN* 5.8 1.7 + - - -
531B SER 3.0 11.8 + - - -
532B LEU* 3.4 13.7 - - + +
533B ALA 2.8 26.0 + - - -
564B ASN 3.6 4.3 + - - -
565B MET* 1.3 71.2 - - - +
567B VAL* 1.3 62.6 + - - +
568B VAL* 4.6 0.4 - - + -
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 4.9 2.9 - - - +
533B ALA* 3.3 19.5 - - + +
535B THR* 3.8 29.2 - - + +
549B LEU* 5.6 0.2 - - + -
550B ARG* 3.2 41.3 - - + +
553B VAL* 4.1 15.3 - - + -
554B GLN* 4.1 27.3 - - + +
557B PHE* 4.7 0.7 - - + -
565B MET* 3.6 15.3 + - + +
566B THR* 1.3 79.4 - - - +
568B VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 3.6 39.3 - - + -
299B TRP* 3.8 35.9 - - + +
348B SER* 5.8 0.2 - - - +
532B LEU* 4.2 16.4 - - + -
533B ALA 2.9 17.2 + - - +
534B ILE* 3.8 23.6 - - + -
535B THR* 2.9 30.4 + - - -
550B ARG* 4.7 1.8 - - - +
566B THR* 4.6 0.4 - - + -
567B VAL* 1.3 76.1 - - - +
569B ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 569 (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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299B TRP* 3.6 7.3 - - - -
347B SER 3.4 1.7 - - - +
348B SER* 3.1 36.8 + - - +
349B ASN* 3.8 22.9 - - + +
535B THR* 3.5 16.4 - - - +
537B ILE* 3.8 26.7 - - + -
541B PHE* 4.4 7.4 - - + -
546B GLY* 4.0 24.0 - - - +
549B LEU* 3.7 23.3 - - + -
550B ARG* 3.9 25.9 - - + +
568B VAL* 1.3 72.6 - - - +
570B SER* 1.3 61.4 + - - +
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Residues in contact with SER 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.5 14.8 - - - -
189B ILE* 5.2 0.2 - - - -
191B SER* 3.4 10.9 + - - -
299B TRP* 3.9 9.3 + - - +
347B SER 3.5 4.4 + - - -
534B ILE* 3.9 22.7 - - - -
535B THR 2.9 16.0 + - - -
536B ALA* 4.5 0.4 - - - -
537B ILE* 2.8 31.5 + - - +
568B VAL 3.6 1.0 + - - -
569B ILE* 1.3 74.5 - - - +
571B GLY* 1.3 56.7 + - - +
573B CYS* 3.2 22.4 - - - -
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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