Contacts of the strand formed by residues 562 - 565 (chain A) in PDB entry 3FZP
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 CYS 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A PRO 4.3 0.7 - - - -
485A HIS* 3.7 23.8 - - + -
529A TYR* 4.3 2.2 - - - -
532A GLN* 3.5 5.6 + - - +
558A ALA* 3.0 28.3 + - + -
559A SER* 2.9 23.8 + - - +
560A PRO 3.5 0.8 + - - -
561A GLU* 1.3 81.3 - - - +
563A VAL* 1.3 66.0 + - - +
564A LYS* 3.8 28.7 - - - -
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Residues in contact with VAL 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A HIS* 3.0 26.7 + - - +
510A LEU* 4.2 15.3 - - + -
529A TYR* 3.7 48.9 - - + +
532A GLN* 3.1 16.4 + - + +
533A ILE* 3.7 22.7 - - + -
555A ILE* 3.7 8.7 - - + -
556A LEU 3.3 12.8 - - - +
557A VAL* 4.2 7.2 - - + -
562A CYS* 1.3 77.6 - - - +
564A LYS* 1.3 67.8 + - - +
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Residues in contact with LYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A HIS 5.3 0.2 + - - -
484A PRO* 2.9 31.2 + - - +
485A HIS 3.4 5.4 - - - -
486A ILE 3.7 16.0 + - - +
487A VAL* 3.6 22.6 - - + +
488A LYS* 5.9 1.0 - - - +
503A GLU* 4.5 5.0 + - - -
505A TYR* 3.6 39.4 + - + +
555A ILE* 3.4 4.8 - - - -
556A LEU* 2.8 38.7 + - + +
558A ALA* 3.8 17.0 - - + -
562A CYS* 3.8 11.1 - - - -
563A VAL* 1.3 76.0 - - - +
565A LEU* 1.3 64.0 - - - +
566A GLY 3.4 0.3 + - - -
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Residues in contact with LEU 565 (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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485A HIS 2.8 17.6 + - - +
486A ILE* 3.6 12.5 - - + +
487A VAL* 3.1 22.2 + - - +
533A ILE* 3.8 17.6 - - + +
536A ALA* 4.3 13.9 - - + -
537A MET* 3.7 30.5 - - + -
540A LEU* 4.4 6.3 - - + -
547A HIS* 3.6 35.0 - - + +
549A ASP 4.4 5.4 - - - +
550A ILE* 4.6 12.8 - - + -
554A ASN* 4.1 8.7 - - - +
555A ILE* 4.2 11.2 - - + -
564A LYS* 1.3 70.0 - - - +
566A GLY* 1.3 65.4 + - - +
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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
------------------------------------------------------------
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