Contacts of the strand formed by residues 344 - 349 (chain A) in PDB entry 1WZ9
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 HIS 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ALA* 5.5 7.2 - - + -
266A ASN 3.8 19.7 + - - +
267A ALA* 3.4 7.3 - - + -
268A LYS* 2.8 33.0 + - - +
343A GLN* 1.3 80.3 - - - +
345A LYS* 1.3 56.7 + - - +
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Residues in contact with LYS 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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201A GLU* 5.6 5.2 - - - +
267A ALA* 4.7 0.7 - - - -
268A LYS* 3.5 15.7 - - + +
343A GLN 5.0 2.2 - - - +
344A HIS* 1.3 77.2 - - - +
346A ASP* 1.3 70.4 + - - +
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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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206A MET* 3.7 29.3 - - - +
208A ASN* 3.2 24.7 + - - +
215A LYS* 3.6 12.0 + - - -
267A ALA* 4.3 11.0 - - + +
268A LYS 3.1 9.5 + - - +
269A VAL* 3.1 6.6 - - + -
270A LYS* 3.0 24.1 + - - +
345A LYS* 1.3 79.3 - - - +
347A GLU* 1.3 81.7 + - - +
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Residues in contact with GLU 347 (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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206A MET* 3.6 4.7 - - - +
215A LYS* 2.7 38.6 + - - +
269A VAL* 4.3 0.4 - - - -
270A LYS* 3.7 20.6 - - + +
346A ASP* 1.3 83.4 + - - +
348A LEU* 1.3 65.9 + - - +
349A ASN* 3.8 21.2 - - + +
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Residues in contact with LEU 348 (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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206A MET* 3.9 9.9 - - + -
215A LYS* 3.7 34.5 - - + +
217A ILE* 3.8 28.5 - - + -
230A ILE* 4.8 5.4 - - + +
232A LEU* 3.8 27.8 - - + -
269A VAL* 3.8 16.8 - - + +
270A LYS 3.2 8.9 + - - +
271A LEU* 3.4 17.6 - - + -
272A SER 2.8 25.9 + - - +
273A ILE* 4.6 2.7 - - + -
347A GLU* 1.3 72.1 - - - +
349A ASN* 1.3 61.7 + - - +
350A ALA* 4.0 15.9 - - + +
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Residues in contact with ASN 349 (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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183A CME 6.4 0.2 - - - +
186A ARG* 3.4 7.6 + - - -
197A MET* 3.9 3.0 - - - +
215A LYS* 5.8 0.4 - - - +
232A LEU* 3.4 14.3 - - - +
270A LYS 5.6 0.2 - - - +
272A SER* 3.2 27.5 + - - +
347A GLU* 3.8 23.1 + - + +
348A LEU* 1.3 72.6 - - - +
350A ALA* 1.3 57.2 + - - +
351A ASP* 2.9 52.8 + - - +
352A HIS* 3.6 6.1 - - - -
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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
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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