Contacts of the strand formed by residues 352 - 359 (chain A) in PDB entry 1ZY7
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A VAL* 4.1 12.3 - - + -
332A LEU* 3.8 43.7 - - + +
335A PHE* 3.6 36.8 - - + -
349A ARG* 3.9 23.9 - - - +
351A VAL* 1.3 75.8 - - - +
353A ALA* 1.3 62.3 + - - +
371A VAL* 3.9 11.2 - - + -
372A SER 3.5 15.0 - - - +
373A THR* 4.1 3.1 - - + -
445A TYR* 4.0 11.0 - - + -
446A ILE* 3.6 1.2 - - - -
447A SER* 2.8 34.8 + - - +
588A GLU* 5.6 0.9 - - - +
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Residues in contact with ALA 353 (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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331A VAL* 3.6 10.8 - - - +
352A LEU* 1.3 76.7 - - - +
354A GLY* 1.3 59.7 + - - +
371A VAL* 3.5 2.9 - - - -
372A SER* 2.9 42.1 + - - +
395A ALA* 3.6 21.5 - - + +
396A GLU* 3.7 11.2 - - + +
399A SER* 3.5 4.5 - - - +
444A LEU* 5.2 0.4 - - + -
445A TYR* 3.1 15.7 - - - +
446A ILE* 4.4 6.3 - - + -
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Residues in contact with GLY 354 (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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331A VAL* 3.9 17.8 - - - +
353A ALA* 1.3 77.2 - - - +
355A VAL* 1.3 64.2 + - - -
370A SER 3.1 13.5 - - - -
399A SER* 3.3 8.1 - - - -
444A LEU* 3.6 6.8 - - - +
445A TYR* 2.8 31.7 + - - +
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Residues in contact with VAL 355 (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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354A GLY* 1.3 78.4 - - - +
356A VAL* 1.3 61.8 + - - +
368A VAL* 3.7 1.0 - - - -
369A ILE* 2.8 39.1 + - + -
370A SER* 3.0 30.3 + - - +
399A SER* 4.0 17.0 - - - +
403A LEU* 4.3 10.5 - - + -
442A PHE* 4.0 27.6 - - + -
443A HIS 3.3 8.5 - - - +
444A LEU* 4.3 2.5 - - + -
542A PHE* 3.9 32.5 - - + -
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Residues in contact with VAL 356 (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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327A VAL* 3.8 35.4 - - + +
330A LEU* 4.2 7.2 - - + -
331A VAL* 3.7 24.9 - - + -
355A VAL* 1.3 80.3 - - - +
357A MET* 1.3 64.5 + - - +
358A THR* 4.7 0.2 - - + -
366A ALA* 3.8 27.6 - - + -
367A LYS 3.4 10.8 - - - +
368A VAL* 4.3 15.0 - - + -
442A PHE* 3.5 1.4 - - - -
443A HIS* 2.8 40.4 + - + +
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Residues in contact with MET 357 (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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356A VAL* 1.3 73.6 - - - +
358A THR* 1.3 71.1 + - - +
359A THR* 4.1 18.6 - - + -
365A ASP 4.4 0.7 - - - +
366A ALA* 3.3 4.5 - - - -
367A LYS* 2.8 51.7 + - + +
369A ILE* 3.6 22.1 - - + +
406A PHE* 3.9 14.8 - - + -
425A ILE* 3.9 21.8 - - + -
440A VAL* 3.7 17.7 - - + -
441A GLN 3.2 11.4 - - - +
442A PHE* 3.7 24.9 - - + -
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Residues in contact with THR 358 (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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318A HIS* 3.3 32.4 - - + +
323A LEU* 4.3 10.5 - - + -
356A VAL* 4.7 1.6 - - + -
357A MET* 1.3 78.6 - - - +
359A THR* 1.3 67.7 + - - +
360A GLY 4.7 0.2 + - - -
362A ASP 5.4 2.0 - - - -
363A VAL* 5.1 4.5 - - + -
366A ALA* 4.0 24.2 - - + +
439A ASN 3.5 1.0 - - - +
440A VAL* 3.4 3.3 - - - -
441A GLN* 2.9 38.6 + - - +
443A HIS* 2.8 34.5 + - + +
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Residues in contact with THR 359 (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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357A MET* 4.1 23.6 - - + +
358A THR* 1.3 81.7 - - - +
360A GLY* 1.3 65.4 + - - +
361A THR 3.8 0.7 + - - -
362A ASP* 4.3 12.5 + - - +
365A ASP* 4.1 26.3 + - - +
425A ILE* 5.7 1.6 - - + -
439A ASN 3.6 5.2 - - - -
440A VAL* 4.3 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