Contacts of the strand formed by residues 369 - 376 (chain B) in PDB entry 1Z3S
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 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ARG* 4.5 3.8 - - - +
283B ASP* 2.5 37.6 + - + +
323B THR* 5.7 0.4 - - - -
363B LEU* 3.3 40.7 - - + +
364B THR* 3.9 15.0 - - + -
366B GLN* 5.2 0.6 + - + -
367B GLN* 3.4 36.4 + - + -
368B ARG* 1.3 77.0 - - - +
370B VAL* 1.3 65.9 + - - +
388B GLU 3.7 1.3 - - - +
389B HIS* 3.5 6.9 + - - -
390B PHE* 2.8 43.3 + - + +
491B ILE* 3.9 17.9 - - + -
492B ARG* 3.4 25.1 - - - -
493B PRO* 3.4 12.3 - - + -
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B TRP* 4.5 9.7 - - + -
368B ARG 5.7 0.2 - - - +
369B TYR* 1.3 75.9 - - - +
371B LEU* 1.3 63.0 + - - +
372B LYS 4.1 0.4 + - - -
386B LEU* 3.3 31.6 - - + -
387B TYR 3.1 14.4 - - - +
388B GLU* 3.2 21.1 - - - +
390B PHE* 4.6 0.7 - - - -
490B MET 4.0 0.3 - - - +
491B ILE* 3.3 8.7 - - - +
492B ARG* 2.7 38.3 + - + +
493B PRO 4.6 10.3 - - - +
494B ALA* 5.2 4.7 - - + +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 4.6 9.0 - - + -
370B VAL* 1.3 72.3 - - - +
372B LYS* 1.3 70.5 + - - +
373B ILE* 4.2 20.6 - - + -
385B SER 3.9 0.2 - - - +
386B LEU* 3.3 5.0 - - - +
387B TYR* 2.9 51.7 + - + -
390B PHE* 3.5 47.0 - - + +
401B ILE* 4.9 2.9 - - + -
403B LEU* 4.2 11.0 - - + -
416B ILE* 5.3 1.3 - - + -
489B MET* 4.5 11.2 - - + -
490B MET 3.3 16.6 - - - +
491B ILE* 3.9 13.2 - - + -
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 5.7 4.6 - - - +
318B GLY* 5.5 9.3 - - - +
322B TRP* 3.8 40.8 - - + +
370B VAL 4.1 0.8 + - - -
371B LEU* 1.3 74.2 - - - +
373B ILE* 1.3 66.9 + - - +
374B HIS* 4.1 15.2 - - + +
384B TYR* 4.0 31.2 - - + -
385B SER 3.5 6.7 - - - +
386B LEU* 3.5 19.3 - - + -
488B THR 3.6 0.2 - - - +
489B MET* 3.6 1.7 - - - -
490B MET* 2.9 49.8 + - + +
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Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 4.2 17.9 - - + -
372B LYS* 1.3 77.5 - - - +
374B HIS* 1.3 61.1 + - - +
375B LEU* 3.6 28.3 + - + +
384B TYR* 3.0 7.3 - - - -
385B SER* 2.9 43.6 + - - +
387B TYR* 4.0 16.6 - - + -
416B ILE* 4.4 9.0 - - + -
455B LEU* 3.7 15.9 - - + -
474B TRP* 3.5 33.2 - - + -
488B THR 3.5 7.4 - - - +
489B MET* 4.2 16.2 - - + -
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Residues in contact with HIS 374 (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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372B LYS* 4.1 15.0 - - + -
373B ILE* 1.3 71.2 - - - +
375B LEU* 1.3 74.4 + - - +
376B LYS* 4.3 11.5 + - + +
382B GLU* 2.8 48.6 + - + +
383B ALA* 3.5 11.5 + - - -
384B TYR* 4.3 11.0 - - + -
486B ALA 4.0 0.2 - - - +
487B THR* 3.4 2.6 - - - -
488B THR* 2.9 49.3 + - + +
490B MET* 4.7 7.0 - - + -
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ILE* 3.6 23.8 - - + +
374B HIS* 1.3 86.2 + - - +
376B LYS* 1.3 63.9 + - - +
382B GLU* 3.1 8.3 - - - +
383B ALA 2.7 38.2 + - - +
410B ALA* 4.3 9.4 - - + -
455B LEU* 4.4 5.4 - - + -
474B TRP* 3.4 46.4 - - + +
477B TRP* 3.6 25.1 - - + -
484B LEU* 4.2 8.1 - - + -
486B ALA 3.6 1.8 - - - -
487B THR* 3.5 24.7 - - + -
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 4.3 9.9 + - - +
375B LEU* 1.3 76.6 - - - +
377B ASP* 1.3 64.6 + - - +
381B ASN 3.5 7.9 - - - +
382B GLU* 3.0 36.3 - - + +
477B TRP* 4.1 0.9 - - - -
484B LEU* 3.4 11.0 - - - +
485B LYS* 3.0 30.3 + - + +
486B ALA* 3.0 38.6 + - + +
487B THR 6.3 0.2 - - - -
488B THR* 5.3 8.1 - - - +
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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
------------------------------------------------------------
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