Contacts of the strand formed by residues 352 - 358 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B VAL* 4.1 8.7 - - + -
332B LEU* 3.7 46.2 - - + +
335B PHE* 3.7 33.2 - - + -
349B ARG* 3.8 24.4 - - - +
351B VAL* 1.3 76.6 - - - +
353B ALA* 1.3 61.5 + - - +
371B VAL* 3.8 15.3 - - + -
372B SER 3.4 15.3 - - - +
373B THR* 4.2 3.4 - - + -
445B TYR* 4.0 10.7 - - + -
446B ILE* 3.5 0.9 - - - -
447B SER* 2.7 40.0 + - - +
588B GLU* 5.6 0.9 - - - +
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Residues in contact with ALA 353 (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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331B VAL* 3.7 11.2 - - - +
352B LEU* 1.3 74.5 - - - +
354B GLY* 1.3 59.3 + - - +
371B VAL* 3.4 3.8 - - - +
372B SER* 2.8 35.4 + - - +
395B ALA* 3.7 26.9 - - + +
396B GLU* 3.8 9.9 - - + +
399B SER* 3.4 6.3 - - - +
444B LEU* 5.2 0.2 - - + -
445B TYR* 3.0 17.0 - - - +
446B ILE* 4.2 6.3 - - + -
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Residues in contact with GLY 354 (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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331B VAL* 4.0 16.9 - - - +
353B ALA* 1.3 77.4 - - - +
355B VAL* 1.3 63.4 + - - -
370B SER 3.1 14.1 - - - -
399B SER* 3.4 8.0 + - - -
444B LEU* 3.7 6.1 - - - +
445B TYR 2.8 34.1 + - - +
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Residues in contact with VAL 355 (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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331B VAL* 4.6 0.2 - - - +
354B GLY* 1.3 77.9 - - - +
356B VAL* 1.3 61.1 + - - +
368B VAL* 3.7 1.2 - - - +
369B ILE* 2.8 38.2 + - + -
370B SER* 3.0 28.9 + - - +
399B SER* 4.0 18.6 - - - +
403B LEU* 4.3 11.0 - - + -
442B PHE* 3.9 28.5 - - + -
443B HIS 3.3 7.9 - - - +
444B LEU* 4.3 3.1 - - + -
542B PHE* 3.9 31.6 - - + -
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Residues in contact with VAL 356 (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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327B VAL* 4.0 37.7 - - + +
330B LEU* 4.4 4.9 - - + -
331B VAL* 3.7 25.4 - - + -
355B VAL* 1.3 80.8 - - - +
357B MET* 1.3 64.5 + - - +
358B THR* 4.7 3.1 - - + -
366B ALA* 3.8 26.2 - - + -
367B LYS 3.4 10.3 - - - +
368B VAL* 4.2 14.8 - - + -
442B PHE* 3.5 1.6 - - - -
443B HIS* 2.8 38.6 + - + +
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Residues in contact with MET 357 (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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356B VAL* 1.3 74.3 - - - +
358B THR* 1.3 70.9 + - - +
359B THR* 4.2 16.8 - - + -
365B ASP 4.5 0.5 - - - +
366B ALA* 3.2 3.5 - - - -
367B LYS* 2.7 72.2 + - + +
369B ILE* 3.6 18.0 - - + +
406B PHE* 3.9 9.4 - - + -
425B ILE* 3.8 29.4 - - + -
440B VAL* 3.9 10.8 - - + -
441B GLN 3.3 12.3 - - - +
442B PHE* 3.7 22.2 - - + -
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Residues in contact with THR 358 (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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318B HIS* 3.5 29.9 + - + +
323B LEU* 4.3 9.2 - - + -
356B VAL* 4.7 1.3 - - + -
357B MET* 1.3 79.2 - - - +
359B THR* 1.3 69.8 + - - +
360B GLY 5.1 0.5 + - - -
362B ASP 5.4 0.9 - - - -
363B VAL* 5.1 3.1 - - - +
366B ALA* 4.0 24.7 - - + +
439B ASN 3.3 1.8 + - - +
440B VAL* 3.5 0.5 - - - -
441B GLN* 2.9 39.9 + - - +
443B HIS* 2.8 35.1 + - + +
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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