Contacts of the strand formed by residues 342 - 346 (chain A) in PDB entry 4PBZ
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 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ALA* 4.0 16.4 - - + -
335A SER 3.4 11.4 - - - +
336A SER* 4.1 6.5 - - - -
341A ARG* 1.3 75.1 - - - +
343A ASN* 1.3 72.4 + - - +
344A VAL* 4.2 5.0 - - + +
368A PHE 3.9 0.7 - - - +
369A ILE* 3.7 0.3 - - - -
370A HIS* 2.8 47.4 + - + +
377A ILE* 3.7 10.8 - - + +
380A PHE* 3.5 40.6 - - + -
390A ILE* 4.5 3.1 - - + -
392A SER* 3.9 16.6 - - - +
402A TRP* 3.9 26.2 - - + -
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Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 3.8 15.3 + - - -
316A HIS* 3.1 43.3 + - - +
334A ALA* 3.1 4.9 - - - +
335A SER 2.9 33.2 + - - -
339A ASP* 5.1 0.2 + - - -
341A ARG* 4.1 6.7 + - - +
342A LEU* 1.3 74.7 - - - +
344A VAL* 1.3 64.4 + - - +
345A TRP* 3.8 23.9 + - + -
366A LEU* 4.0 11.7 - - + -
368A PHE 3.4 3.1 - - - -
369A ILE* 3.5 29.9 - - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.7 28.0 - - + -
333A LEU 3.4 5.4 - - - +
334A ALA* 4.3 5.6 - - + -
342A LEU* 4.2 16.2 - - + +
343A ASN* 1.3 77.9 - - - +
345A TRP* 1.3 63.3 + - - +
366A LEU* 3.8 3.5 - - - +
367A LEU* 2.9 33.7 + - + -
368A PHE* 2.9 24.6 + - + +
382A TRP* 4.1 6.5 - - + -
388A TRP* 4.4 0.4 - - + -
390A ILE* 4.8 5.2 - - + -
402A TRP* 4.4 11.2 - - + -
404A MET* 4.0 26.0 - - + -
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Residues in contact with TRP 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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298A VAL* 4.6 5.4 - - + +
313A PHE* 3.6 55.4 - + + -
314A GLU 3.9 15.3 - - - -
315A SER* 3.7 22.9 - - - -
316A HIS* 4.2 6.7 - + - -
331A THR 3.6 0.9 - - - +
332A ILE* 3.3 9.7 - - - +
333A LEU* 2.7 65.4 + - + +
334A ALA* 4.3 0.4 - - - -
335A SER* 2.9 24.8 + - - -
343A ASN* 3.8 26.6 + - + -
344A VAL* 1.3 76.2 - - - +
346A ASP* 1.3 60.2 + - - +
347A LEU* 4.1 0.9 - - + +
363A PRO* 4.2 7.2 - - + -
365A GLU* 3.2 11.2 - - + +
366A LEU* 3.9 31.2 - - + -
367A LEU* 4.6 1.3 - - - -
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Residues in contact with ASP 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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331A THR* 2.9 21.5 + - - -
332A ILE* 3.6 20.4 - - + +
345A TRP* 1.3 72.2 - - - +
347A LEU* 1.3 63.2 + - - +
348A SER* 2.8 27.5 + - - -
349A LYS* 3.0 38.8 + - + +
365A GLU* 2.8 25.9 + - - +
367A LEU* 4.4 13.2 - - + +
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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