Contacts of the strand formed by residues 332 - 336 (chain A) in PDB entry 1ZJK
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 TYR 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A ASN* 3.5 35.3 + - + +
328A CYS* 3.6 17.4 - - + +
329A GLU* 3.1 36.1 + - + +
330A THR 3.5 13.5 - - - -
331A GLY* 1.3 85.0 + - - +
333A GLU* 1.3 61.4 + - - +
361A CYS 3.6 16.8 - - - -
362A SER 3.5 4.9 - - - +
363A ILE* 3.4 51.6 - - + +
364A VAL* 4.3 2.7 - - - +
388A TYR* 5.2 4.5 - + - -
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Residues in contact with GLU 333 (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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328A CYS* 3.8 6.1 - - - -
332A TYR* 1.3 75.9 - - - +
334A LEU* 1.3 65.8 + - - +
335A LEU* 3.5 30.8 + - + +
340A PRO* 4.7 15.3 - - + +
360A ALA 3.5 1.2 - - - +
361A CYS* 3.6 0.2 - - - -
362A SER* 2.9 38.8 + - - +
363A ILE 4.8 2.4 - - - +
364A VAL* 4.1 27.1 - - + +
365A ASP 5.1 2.3 + - - -
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Residues in contact with LEU 334 (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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326A ILE* 3.6 46.0 - - + +
327A PHE* 5.1 5.6 - - + -
328A CYS* 3.7 15.0 - - - +
333A GLU* 1.3 73.3 - - - +
335A LEU* 1.3 59.4 + - - +
340A PRO* 3.2 9.5 - - - +
341A LEU* 3.1 40.4 + - + +
342A LYS 4.7 2.2 - - - +
343A SER* 3.9 27.6 - - - -
344A PHE* 4.0 8.5 - - + +
359A PRO* 4.0 18.6 - - + -
360A ALA 3.4 3.6 - - - +
361A CYS* 4.3 1.3 - - - -
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Residues in contact with LEU 335 (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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333A GLU* 3.5 19.7 + - + +
334A LEU* 1.3 75.0 - - - +
336A GLN* 1.3 59.4 + - - +
337A GLY 3.7 14.6 + - - +
338A HIS* 4.1 12.6 - - - +
339A LEU 3.4 4.7 - - - -
340A PRO* 3.5 37.2 - - + -
341A LEU* 4.6 0.2 - - - -
359A PRO* 3.5 5.8 - - - +
360A ALA* 2.8 46.1 + - + +
362A SER* 3.2 32.1 - - - +
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Residues in contact with GLN 336 (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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335A LEU* 1.3 70.8 - - - +
337A GLY* 1.3 62.1 + - - +
338A HIS 3.5 0.3 + - - -
339A LEU* 3.0 26.1 + - + +
341A LEU* 4.0 25.2 - - + +
344A PHE* 3.8 15.6 - - - -
356A ARG* 5.3 1.7 - - - +
357A PRO* 3.5 35.9 - - - +
358A MET 3.5 22.0 + - - -
359A PRO* 3.9 7.3 - - - +
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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