Contacts of the strand formed by residues 520 - 523 (chain B) 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 THR 520 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518B PHE 5.2 1.1 - - - +
519B THR* 1.3 75.6 - - - +
521B GLY* 1.3 61.5 + - - +
522B LEU* 5.9 0.4 - - - -
563B GLN 4.9 1.0 + - - -
564B CYS* 2.9 29.7 - - - +
565B GLU 3.2 20.7 + - - -
657B LEU* 4.5 0.9 - - - -
658B LYS* 4.6 4.7 - - + -
659B ASN* 2.8 30.3 - - - +
856B VAL* 5.2 1.3 + - - +
859B LEU* 3.1 34.0 - - - +
860B LEU* 3.1 21.4 - - + +
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Residues in contact with GLY 521 (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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519B THR 3.9 1.6 + - - -
520B THR* 1.3 75.3 - - - +
522B LEU* 1.3 67.9 + - - +
565B GLU 3.4 9.6 - - - -
567B LEU* 5.2 0.4 - - - -
648B LEU* 4.2 6.3 - - - -
657B LEU* 4.0 22.5 - - - +
659B ASN 2.9 13.5 + - - -
660B GLY* 3.3 2.8 - - - -
661B PHE 3.0 23.6 + - - -
859B LEU* 5.3 0.3 - - - +
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Residues in contact with LEU 522 (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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520B THR* 5.4 0.7 - - - +
521B GLY* 1.3 82.4 - - - +
523B ILE* 1.3 64.0 + - - +
552B TRP* 3.9 30.0 - - + -
555B LEU* 4.3 11.0 - - + -
561B ARG* 4.2 19.1 - - + -
564B CYS* 3.5 35.0 - - + -
565B GLU 3.0 8.8 + - - +
566B CYS* 3.6 4.1 - - - +
567B LEU* 2.8 31.4 + - - +
648B LEU* 4.7 1.0 - - - +
661B PHE* 3.4 34.1 - - + +
663B VAL* 5.4 0.2 - - + -
856B VAL* 4.3 13.7 - - + -
859B LEU* 5.6 1.3 - - + -
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Residues in contact with ILE 523 (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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522B LEU* 1.3 75.0 - - - +
524B TYR* 1.3 69.9 + - - +
528B MET* 4.7 2.0 - - + -
552B TRP* 4.7 0.9 - - - -
567B LEU* 3.6 19.7 - - + +
568B ARG 4.7 1.3 - - - +
569B GLY* 3.3 37.0 - - - +
644B SER* 3.4 42.2 - - - +
647B ASP* 5.3 1.8 - - + -
648B LEU* 4.1 17.0 - - + +
661B PHE 3.1 7.1 + - - -
662B ALA* 3.9 11.4 - - + -
663B VAL* 2.9 29.3 + - - +
664B VAL* 3.7 16.6 - - + -
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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