Contacts of the strand formed by residues 337 - 346 (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 LEU 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A LEU* 5.4 2.0 - - + -
333A LYS 3.7 6.3 + - - +
334A ARG* 2.7 39.0 + - - +
335A ASP 3.2 2.6 - - - -
336A ASN* 1.3 80.2 - - - +
338A LEU* 1.3 64.1 + - - +
339A ILE* 3.4 33.9 - - + -
356A VAL 3.6 10.8 - - - +
357A TYR* 4.2 13.7 - - + -
366A VAL* 4.1 20.4 - - + -
368A ILE* 4.1 11.2 - - + -
405A CYS* 4.6 8.1 - - + -
411A MET* 4.5 13.2 - - + -
413A VAL* 4.1 25.6 - - + -
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Residues in contact with LEU 338 (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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335A ASP 6.1 0.4 - - - +
336A ASN 4.1 1.0 + - - +
337A LEU* 1.3 77.4 - - - +
339A ILE* 1.3 63.9 + - - +
355A GLY* 2.9 25.8 - - - -
356A VAL* 2.8 39.9 + - + +
363A GLN* 5.5 4.3 - - - +
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Residues in contact with ILE 339 (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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334A ARG* 3.6 28.8 + - - +
337A LEU* 3.4 34.9 + - + -
338A LEU* 1.3 81.5 - - - +
340A ALA* 1.3 75.5 + - - +
341A ASP* 4.2 5.9 + - - +
353A ARG* 4.3 21.3 - - + +
354A GLN 4.1 5.8 - - - +
368A ILE* 4.4 13.0 - - + -
370A VAL* 5.4 1.1 - - + -
408A GLU* 4.4 2.2 - - - +
411A MET* 3.4 25.4 - - - -
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Residues in contact with ALA 340 (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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338A LEU 4.2 0.2 + - - -
339A ILE* 1.3 89.0 - - - +
341A ASP* 1.3 61.8 + - - +
342A ILE* 3.1 27.1 + - + +
353A ARG* 3.4 13.7 - - - +
354A GLN* 3.1 29.3 + - + +
355A GLY* 4.6 1.3 - - - -
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Residues in contact with ASP 341 (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* 4.8 5.0 - - - +
340A ALA* 1.3 75.1 - - - +
342A ILE* 1.3 71.9 + - + +
343A GLU* 4.1 3.3 + - - +
353A ARG* 4.6 18.5 + - - +
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Residues in contact with ILE 342 (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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340A ALA* 3.1 17.4 - - + +
341A ASP* 1.3 100.9 - - + +
343A GLU* 1.3 72.0 + - - +
344A LEU* 4.7 2.5 - - + +
353A ARG* 4.0 16.6 - - - +
354A GLN* 4.0 7.1 + - - +
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Residues in contact with GLU 343 (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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341A ASP 4.1 2.9 + - - +
342A ILE* 1.3 86.7 - - - +
344A LEU* 1.3 65.7 + - - +
345A GLY* 3.3 18.3 - - - +
346A CYS* 3.6 16.4 - - - +
351A SER* 2.8 35.0 - - - +
352A VAL 3.4 6.9 + - - +
353A ARG* 4.6 9.0 - - + +
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Residues in contact with LEU 344 (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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342A ILE* 4.7 2.0 - - + +
343A GLU* 1.3 81.0 - - - +
345A GLY* 1.3 57.3 + - - +
352A VAL* 2.8 22.3 + - + +
353A ARG 4.1 3.6 - - - +
354A GLN* 3.8 44.6 - - + +
367A ALA* 5.0 1.3 - - + -
416A MET* 4.0 16.8 - - + -
418A GLY* 6.1 0.9 - - - -
615A ANP 3.4 47.1 + - + +
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Residues in contact with GLY 345 (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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343A GLU* 3.3 15.6 - - - +
344A LEU* 1.3 80.8 - - - +
346A CYS* 1.3 63.1 + - - -
352A VAL* 3.1 23.4 + - - +
424A LYS* 6.4 0.4 - - - -
615A ANP 4.3 10.1 - - - -
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Residues in contact with CYS 346 (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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343A GLU* 3.6 24.0 - - - +
345A GLY* 1.3 76.4 - - - +
347A GLY* 1.3 61.0 + - - +
350A GLY 3.9 4.0 - - - +
351A SER* 3.8 14.6 - - - +
615A ANP 3.6 24.5 + - - +
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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