Contacts of the strand formed by residues 265 - 274 (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 ALA 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A CME 4.1 3.4 - - - -
206A MET* 2.8 36.5 + - - +
263A THR 4.2 0.6 + - - +
264A MET* 1.3 75.0 - - - +
266A ASN* 1.3 68.0 + - - +
267A ALA* 3.4 2.9 + - + +
344A HIS* 5.5 7.2 - - + -
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Residues in contact with ASN 266 (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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203A THR* 3.8 27.6 + - - +
204A PHE* 3.7 14.7 + - - -
205A CME 3.5 25.7 + - - +
265A ALA* 1.3 74.8 - - - +
267A ALA* 1.3 60.8 + - - +
343A GLN* 5.1 2.3 + - - -
344A HIS* 3.8 19.9 + - - +
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Residues in contact with ALA 267 (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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203A THR* 3.2 7.8 - - - -
204A PHE 3.0 35.0 + - - +
206A MET* 4.5 9.9 - - + -
265A ALA* 4.3 5.6 - - + +
266A ASN* 1.3 76.0 - - - +
268A LYS* 1.3 62.2 + - - +
269A VAL* 3.5 3.9 + - + +
344A HIS* 3.4 19.5 - - + +
346A ASP* 4.3 23.3 - - + +
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Residues in contact with LYS 268 (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* 4.9 15.1 - - + +
202A ALA 3.8 6.1 - - - +
203A THR* 4.4 12.7 - - + +
267A ALA* 1.3 69.2 - - - +
269A VAL* 1.3 59.8 + - - +
270A LYS 4.1 0.2 + - - -
344A HIS 2.8 15.4 + - - +
345A LYS* 3.5 13.5 - - + +
346A ASP 3.1 21.7 + - - +
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Residues in contact with VAL 269 (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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200A MET 3.7 0.2 - - - +
201A GLU* 3.4 6.2 - - - +
202A ALA 2.9 40.2 + - - +
204A PHE* 3.5 28.9 - - + +
206A MET* 4.3 11.7 - - - -
217A ILE* 3.9 20.2 - - + -
267A ALA* 3.7 13.2 - - + +
268A LYS* 1.3 71.3 - - - +
270A LYS* 1.3 65.9 + - - +
271A LEU* 3.3 13.3 + - + +
346A ASP* 3.1 10.5 - - + +
348A LEU* 3.8 26.9 - - + +
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Residues in contact with LYS 270 (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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200A MET 3.9 5.2 - - - +
201A GLU* 4.2 22.7 - - + +
268A LYS 4.1 0.8 + - - -
269A VAL* 1.3 68.4 - - - +
271A LEU* 1.3 59.4 + - - +
272A SER* 5.0 1.9 + - - -
346A ASP 3.0 13.1 + - - +
347A GLU* 3.7 15.5 - - + +
348A LEU 3.2 22.7 + - - +
349A ASN* 5.6 0.2 - - - +
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Residues in contact with LEU 271 (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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175A PHE* 3.5 31.4 - - + -
198A MET 3.7 0.2 - - - +
199A ASN* 3.3 6.9 + - - +
200A MET* 2.9 42.1 + - + +
204A PHE* 3.6 27.8 - - + -
217A ILE* 4.1 15.7 - - + -
219A LEU* 3.7 16.6 - - + -
269A VAL* 3.3 11.9 + - + +
270A LYS* 1.3 71.8 - - - +
272A SER* 1.3 64.7 + - - +
273A ILE* 3.6 24.9 - - + -
348A LEU* 3.4 20.0 - - + +
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Residues in contact with SER 272 (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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197A MET* 3.6 10.1 - - - -
198A MET 3.2 6.1 - - - -
199A ASN* 2.6 27.0 + - - -
270A LYS 5.0 1.6 + - - -
271A LEU* 1.3 72.3 - - - +
273A ILE* 1.3 65.4 + - - +
348A LEU 2.8 9.9 + - - +
349A ASN* 3.2 30.9 + - - +
350A ALA 2.8 29.8 + - - -
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Residues in contact with ILE 273 (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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171A TRP* 3.8 24.5 - - + -
175A PHE* 3.7 15.7 - - + -
197A MET* 3.7 6.0 - - - +
198A MET* 2.7 61.0 + - + +
219A LEU* 4.1 10.5 - - + -
228A MET* 5.4 2.5 - - - -
230A ILE* 3.8 25.6 - - + -
271A LEU* 3.6 22.6 - - + +
272A SER* 1.3 80.0 - - - +
274A PRO* 1.3 76.8 - - + +
276A PHE* 5.7 2.0 - - + -
326A ILE* 4.2 3.8 - - + -
348A LEU* 4.6 0.9 - - + -
350A ALA* 4.3 4.3 - - + -
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Residues in contact with PRO 274 (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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185A PHE* 4.5 2.2 - - + -
195A VAL* 3.7 22.4 - - + -
196A GLN 3.4 6.5 - - - +
197A MET* 3.8 7.4 - - - -
198A MET* 3.7 10.2 - - - +
273A ILE* 1.3 91.5 - - + +
275A LYS* 1.3 61.6 - - - +
276A PHE* 3.4 19.0 + - + -
326A ILE* 4.0 3.6 - - - +
350A ALA 3.6 21.3 - - - +
354A PHE* 3.9 20.2 - - + -
372A PHE* 3.9 30.3 - - + -
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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