Contacts of the strand formed by residues 562 - 566 (chain A) in PDB entry 2ZT5
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A PHE* 3.3 8.8 - - - -
561A LYS* 1.3 76.3 - - - +
563A SER* 1.3 70.8 + - - +
564A VAL* 4.6 0.7 - - - -
584A LEU* 4.5 13.9 - - + -
589A VAL* 4.1 15.5 - - + -
590A SER 2.9 12.4 + - - +
591A HIS* 2.9 35.3 - - + +
592A LYS 3.3 0.3 + - - -
612A VAL* 3.9 0.2 - - - -
614A PHE* 3.3 17.0 - - - -
616A VAL* 3.9 27.4 - - - -
652A VAL* 4.1 14.6 - - + -
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Residues in contact with SER 563 (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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560A PHE* 3.9 7.3 - - - -
562A CYS* 1.3 74.0 - - - +
564A VAL* 1.3 62.1 + - - +
565A LEU* 3.8 5.5 + - - +
592A LYS 3.8 9.7 + - - -
594A ASP* 4.3 13.2 - - - +
604A TYR* 4.6 3.5 - - - -
607A THR* 3.3 25.5 + - - -
612A VAL* 3.7 14.6 - - - -
614A PHE 2.8 16.1 + - - -
615A GLY* 3.1 4.4 - - - -
616A VAL 2.9 24.6 + - - -
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Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A CYS* 4.1 4.9 - - - -
563A SER* 1.3 73.9 - - - +
565A LEU* 1.3 56.6 + - - +
566A PRO* 5.0 1.8 - - + -
577A VAL* 4.5 17.9 - - + +
580A LEU* 3.6 29.2 - - + -
581A SER* 5.4 1.8 - - - -
584A LEU* 3.6 30.7 - - + -
591A HIS* 4.3 14.1 - - + -
592A LYS 3.1 8.6 + - - +
593A VAL* 3.0 13.1 - - + +
594A ASP 2.7 30.4 + - - -
616A VAL* 3.9 5.2 - - + +
618A ILE* 4.1 15.3 - - + -
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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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563A SER* 3.8 4.9 + - - +
564A VAL* 1.3 74.6 - - - +
566A PRO* 1.3 63.7 - - - +
567A LEU* 5.4 1.8 - - + -
594A ASP* 3.4 24.2 - - + +
600A ILE* 4.1 21.5 - - + -
603A ARG* 3.7 42.2 - - + +
604A TYR* 3.4 43.7 - - + +
607A THR* 5.1 0.4 - - - +
616A VAL 3.1 11.3 + - - +
617A THR* 4.3 9.3 - - + +
618A ILE* 3.3 18.2 + - - -
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Residues in contact with PRO 566 (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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564A VAL* 3.9 6.1 - - + +
565A LEU* 1.3 87.4 - - - +
567A LEU* 1.3 65.4 + - - +
568A SER 3.8 17.5 - - - +
569A GLN* 4.4 17.5 - - - +
573A PHE* 3.9 10.3 - - + -
577A VAL* 3.9 28.0 - - + -
593A VAL* 4.1 8.3 - - + -
594A ASP 3.8 13.5 - - - +
603A ARG* 3.0 24.2 + - - -
618A ILE* 3.5 13.2 - - + +
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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