Contacts of the strand formed by residues 362 - 371 (chain A) in PDB entry 1OZ2
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 VAL 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A GLU* 4.0 20.6 - - + +
353A ALA 3.4 9.9 - - - +
354A VAL* 4.2 17.7 - - + -
359A PRO 5.6 1.1 - - - +
360A SER 4.0 1.2 + - - -
361A LEU* 1.3 75.8 - - - +
363A CYS* 1.3 63.3 + - - +
398A HIS* 4.5 4.7 - - + +
402A TRP* 4.1 21.1 - - + -
403A CYS* 3.4 26.7 - - - -
408A LYS* 3.5 23.2 - - - +
409A PRO 3.9 4.8 + - - +
410A LEU* 3.6 7.3 - - - -
411A THR* 2.9 23.8 + - - -
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Residues in contact with CYS 363 (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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352A GLU* 3.3 4.9 - - - -
353A ALA* 2.8 34.4 + - - +
355A ASP* 4.2 8.5 - - - -
361A LEU* 3.7 29.8 - - - -
362A VAL* 1.3 82.1 - - - +
364A VAL* 1.3 64.9 + - - +
365A ALA* 3.4 1.4 + - - +
379A PHE* 3.6 26.9 - - + -
382A TRP* 6.0 3.6 - - - +
410A LEU* 3.9 6.5 - - - -
411A THR* 3.4 23.6 - - + +
412A PRO 5.8 0.4 - - - +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU 4.0 3.8 - - - -
363A CYS* 1.3 72.0 - - - +
365A ALA* 1.3 62.9 + - - +
379A PHE* 3.8 8.0 - - - +
380A ASP* 3.4 27.4 + - - +
382A TRP* 5.7 0.7 - - - -
410A LEU* 4.0 9.2 - - + -
411A THR 3.0 16.2 + - - +
412A PRO* 4.1 1.7 - - + -
413A PRO* 3.9 20.8 - - + +
422A PHE* 3.6 30.1 - - + -
424A TRP* 3.6 26.5 - - + -
427A TYR* 3.7 26.2 - - + -
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Residues in contact with ALA 365 (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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350A LYS* 3.3 9.5 - - - +
351A LEU* 2.9 38.6 + - + +
353A ALA* 4.1 10.3 - - + -
363A CYS 4.0 6.1 - - - +
364A VAL* 1.3 77.4 - - - +
366A SER* 1.3 65.0 + - - +
377A VAL* 4.0 21.8 - - + -
378A HIS 3.2 16.2 - - - +
379A PHE* 4.2 4.3 - - + -
380A ASP* 3.5 3.4 - - - -
424A TRP* 4.4 0.2 - - - -
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Residues in contact with SER 366 (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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348A GLY* 5.2 3.4 - - - -
349A MET 3.3 10.8 - - - -
350A LYS* 2.7 25.5 + - - +
351A LEU* 3.9 6.7 - - - -
365A ALA* 1.3 74.0 + - - +
367A VAL* 1.3 67.0 - - - +
368A THR* 3.6 10.4 + - - -
376A LEU 3.6 1.0 - - - +
377A VAL* 3.6 1.6 - - - -
378A HIS* 2.8 34.8 + - - +
380A ASP* 2.6 22.8 + - - -
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Residues in contact with VAL 367 (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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345A PHE* 4.1 23.6 - - + -
346A GLN 3.5 31.2 - - - +
347A VAL* 3.5 4.5 - - - +
348A GLY* 2.9 28.2 + - - -
349A MET 2.9 15.0 + - - +
351A LEU* 4.0 15.3 - - + -
366A SER* 1.3 74.0 - - - +
368A THR* 1.3 63.1 + - - +
369A ASP 3.8 17.5 - - - +
370A VAL* 3.9 7.6 - - + -
375A PHE* 4.1 16.2 - - + -
376A LEU 3.3 4.9 - - - +
377A VAL* 5.0 0.2 - - - +
436A VAL* 4.2 6.3 - - + -
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Residues in contact with THR 368 (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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253A SER* 5.8 0.2 - - - -
347A VAL* 3.9 17.9 - - - +
366A SER* 4.2 7.9 - - - +
367A VAL* 1.3 77.4 - - - +
369A ASP* 1.3 63.3 + - - +
376A LEU* 3.0 27.5 + - - +
378A HIS* 3.5 42.4 - - + +
387A ASP* 4.5 1.0 + - - -
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Residues in contact with ASP 369 (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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253A SER 4.9 2.6 - - - +
255A TYR* 2.9 25.1 + - - -
301A HIS* 2.6 33.2 + - - -
347A VAL* 3.7 6.4 - - - +
367A VAL* 3.7 1.6 - - - +
368A THR* 1.3 80.4 + - - +
370A VAL* 1.3 78.6 + - - +
371A VAL* 3.8 0.9 - - - +
375A PHE* 3.3 4.3 - - - +
376A LEU* 2.9 47.1 + - + +
389A TRP* 3.6 13.6 - - + -
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Residues in contact with VAL 370 (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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301A HIS* 4.6 3.8 + - - -
341A PRO* 4.4 9.6 - - + -
342A PRO* 3.3 32.8 - - + -
345A PHE 3.8 19.1 - - - +
346A GLN* 4.5 0.7 - - - -
347A VAL* 4.0 17.2 - - + +
367A VAL* 3.9 15.9 - - + -
369A ASP* 1.3 84.5 + - - +
371A VAL* 1.3 69.7 + - - +
372A ASP 4.4 2.2 - - - +
374A ARG 3.5 5.8 - - - +
375A PHE* 4.0 5.4 - - + +
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Residues in contact with VAL 371 (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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255A TYR* 3.8 6.1 - - - +
288A PRO 5.4 1.3 - - - +
291A HIS* 3.9 7.2 - - + +
295A TRP* 3.7 34.3 - - + -
301A HIS* 3.8 4.7 - - + -
335A SER* 3.8 20.2 - - - +
337A SER* 4.4 5.2 - - - +
369A ASP* 3.8 13.9 - - - +
370A VAL* 1.3 79.9 - - - +
372A ASP* 1.3 76.3 + - - +
373A SER 3.1 0.7 + - - -
374A ARG* 2.9 28.3 + - - +
389A TRP* 3.8 20.9 - - + -
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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