Contacts of the strand formed by residues 363 - 370 (chain A) in PDB entry 2OZO
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 GLN 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A LEU* 5.5 4.0 - - - +
356A VAL* 4.0 32.0 - - + +
357A TYR 3.4 6.5 - - - +
358A ARG* 4.2 16.2 - - + +
362A LYS* 1.3 79.8 - - - +
364A ILE* 1.3 61.8 + - - +
365A ASP* 4.4 4.5 - - - +
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Residues in contact with ILE 364 (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 PRO* 6.1 7.0 - - + -
322A PRO* 4.2 19.3 - - + -
356A VAL* 3.3 5.4 - - - +
357A TYR* 2.9 55.7 + - + +
359A MET* 3.4 33.9 - - + -
362A LYS* 3.6 20.4 - - + +
363A GLN* 1.3 75.5 - - - +
365A ASP* 1.3 67.7 + - - +
366A VAL* 4.0 22.0 - - + -
402A ILE* 4.4 12.1 - - + -
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Residues in contact with ASP 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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354A GLN* 5.2 7.6 + - + +
355A GLY 3.8 5.2 - - - +
356A VAL* 4.2 14.8 - - - +
363A GLN* 4.4 4.5 - - - +
364A ILE* 1.3 83.3 - - - +
366A VAL* 1.3 64.6 - - - +
415A GLU* 4.6 1.4 - - - -
416A MET* 3.6 33.2 + - + +
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Residues in contact with VAL 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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337A LEU* 4.1 4.5 - - + -
355A GLY 2.8 52.6 + - - +
356A VAL 3.9 11.2 - - - +
357A TYR* 3.9 16.4 - - + -
364A ILE* 4.0 14.4 - - + -
365A ASP* 1.3 77.7 - - - +
367A ALA* 1.3 60.6 - - - +
368A ILE* 3.6 15.3 - - + -
402A ILE* 4.3 6.5 - - + -
413A VAL* 3.6 25.8 - - + -
414A MET 3.4 12.6 - - - +
415A GLU* 5.4 0.4 - - - -
416A MET* 3.6 18.5 - - - +
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Residues in contact with ALA 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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344A LEU* 5.0 0.7 - - + -
352A VAL* 4.4 5.8 - - + -
353A ARG 3.5 6.5 - - - +
354A GLN* 4.6 0.9 - - - +
366A VAL* 1.3 77.2 - - - +
368A ILE* 1.3 62.9 + - - +
412A LEU 3.5 0.3 - - - +
413A VAL* 3.6 1.0 - - - -
414A MET* 2.9 39.8 + - + +
415A GLU 4.0 1.6 - - - +
416A MET* 4.5 4.7 - - + -
615A ANP 3.3 46.7 - - + +
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Residues in contact with ILE 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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337A LEU* 4.1 24.9 - - + -
339A ILE* 4.4 12.1 - - + -
352A VAL* 3.4 2.0 - - - -
353A ARG* 2.6 48.0 + - + +
354A GLN 4.0 2.7 - - - +
355A GLY* 3.9 15.9 - - - +
366A VAL* 3.6 28.3 - - + -
367A ALA* 1.3 74.4 - - - +
369A LYS* 1.3 59.8 + - - +
370A VAL* 3.1 18.4 + - + +
411A MET* 3.5 41.1 - - + -
412A LEU 3.3 5.6 - - - +
413A VAL* 4.3 6.7 - - + -
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Residues in contact with LYS 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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349A PHE* 4.5 17.0 - - + -
350A GLY 4.6 4.7 - - - +
351A SER 3.1 13.2 - - - +
352A VAL* 4.0 11.4 - - + +
367A ALA 3.8 1.6 + - - -
368A ILE* 1.3 72.5 - - - +
370A VAL* 1.3 71.5 + - - +
371A LEU 3.6 8.6 + - - +
372A LYS* 4.4 2.8 + - - -
411A MET* 4.0 0.2 - - - -
412A LEU* 2.8 43.3 + - + +
414A MET* 4.6 13.4 - - - +
479A ASP* 2.4 46.9 + - - -
482A LEU* 3.5 19.3 - - + +
615A ANP 3.2 29.2 + - - +
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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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339A ILE* 5.4 2.5 - - + -
350A GLY* 3.2 13.7 - - - -
351A SER* 2.8 17.4 + - - +
353A ARG* 3.4 50.9 - - + +
368A ILE* 3.9 18.8 - - + +
369A LYS* 1.3 75.1 - - - +
371A LEU* 1.3 82.6 + - + +
409A ALA* 4.4 12.1 - - + -
411A MET* 4.1 20.4 - - + -
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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