Contacts of the helix formed by residues 560 - 564 (chain A) in PDB entry 3ZNS
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 LEU 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A LEU* 2.8 33.0 + - + +
558A ARG* 4.1 14.4 - - + +
559A GLY* 1.3 74.2 - - - +
561A ARG* 1.3 63.9 + - - +
563A GLN* 3.1 35.4 + - - +
564A CYS* 3.7 10.8 - - - -
853A GLU* 3.4 45.1 - - + +
856A VAL* 4.0 12.8 - - + -
857A ALA* 4.1 15.0 - - + +
860A LEU* 4.0 10.7 - - + +
862A ASN* 5.2 4.9 - - - +
722B PRO* 6.1 4.0 - - + -
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LEU* 3.8 24.2 - - + -
552A TRP* 2.9 86.7 + - + +
553A SER* 4.0 3.2 - - - +
555A LEU* 2.9 19.8 + - + +
556A GLN* 3.5 41.9 + - + +
559A GLY 3.5 0.4 - - - -
560A LEU* 1.3 77.1 - - - +
562A SER* 1.3 63.4 + - - +
564A CYS* 3.1 21.5 + - - +
566A CYS* 3.6 11.8 - - - -
694B GLN* 5.2 5.9 - - - +
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Residues in contact with SER 562 (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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556A GLN* 5.7 2.6 - - - +
559A GLY* 3.6 15.1 + - - -
561A ARG* 1.3 76.7 - - - +
563A GLN* 1.3 62.3 + - - +
564A CYS 3.2 6.1 + - - +
566A CYS* 5.6 0.9 - - - -
690B ARG* 5.3 0.4 - - - -
693B GLN* 3.4 45.5 + - - +
694B GLN* 3.9 19.6 - - - +
697B LYS* 3.5 19.8 + - - +
698B ALA 5.2 0.7 + - - -
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Residues in contact with GLN 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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519A THR* 3.3 24.3 - - - +
559A GLY 2.9 25.6 + - - +
560A LEU* 3.1 29.5 + - - +
562A SER* 1.3 79.6 - - - +
564A CYS* 1.3 59.2 + - - +
860A LEU* 3.9 22.8 - - + +
862A ASN* 5.5 3.5 + - - +
697B LYS* 3.5 18.8 - - - +
698B ALA* 4.0 29.8 - - + +
722B PRO* 6.2 2.2 - - - +
723B SER* 5.1 11.6 - - - -
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Residues in contact with CYS 564 (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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519A THR* 4.8 0.7 - - - -
520A THR* 3.0 33.9 - - - +
522A LEU* 3.6 33.0 - - + -
560A LEU 3.7 11.4 - - - -
561A ARG 3.1 16.6 + - - +
562A SER* 3.6 2.3 - - - +
563A GLN* 1.3 81.5 - - - +
565A GLU* 1.3 58.6 + - - +
566A CYS* 3.8 3.9 + - - -
856A VAL* 4.2 6.7 - - - -
860A LEU* 4.0 14.8 - - - -
697B LYS* 2.8 25.5 + - - -
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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