Contacts of the strand formed by residues 240 - 243 (chain B) in PDB entry 1WZ2
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 ASN 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B VAL* 3.7 6.1 - - - +
239B THR* 1.3 101.1 + - - +
241B MET* 1.3 71.3 + - - +
242B TRP* 3.9 5.5 - - - -
305B VAL* 3.7 14.7 - - - +
306B ILE* 3.5 17.0 - - + +
308B LEU* 3.3 32.7 - - + +
324B SER* 3.0 47.9 + - - +
326B PRO* 4.8 1.0 - - - +
336B LEU* 4.6 14.5 - - - +
350B ASP* 4.9 4.4 + - - -
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 3.5 33.4 - - + -
225B LEU* 3.5 45.3 - - + +
227B ALA* 4.1 7.9 - - + -
240B ASN* 1.3 78.1 - - - +
242B TRP* 1.3 67.5 + - - +
243B VAL* 5.8 0.4 - - + -
296B VAL* 3.4 21.1 - - + -
305B VAL* 3.9 7.0 - - + -
306B ILE 2.7 16.8 + - - +
307B ILE* 3.6 17.3 - - + -
308B LEU* 2.6 30.0 + - - +
321B VAL* 4.8 3.4 - - + -
322B VAL 4.1 4.7 - - - +
323B MET* 3.9 24.2 - - - -
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Residues in contact with TRP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ASN* 3.9 5.4 - - - -
241B MET* 1.3 82.7 - - - +
243B VAL* 1.3 68.1 + - - +
308B LEU* 3.2 25.9 - - + +
309B PRO 3.6 10.0 + - - -
310B ALA* 3.6 14.7 - - + +
312B PHE* 3.2 34.5 - + - -
313B VAL* 4.1 14.8 - - + -
320B GLY 3.9 0.9 - - - +
321B VAL* 3.4 1.9 - - - +
322B VAL* 2.9 46.4 + - + +
324B SER* 3.0 32.5 - - - -
332B ASP* 3.1 43.7 - - - -
333B HIS 3.6 5.6 - - - -
335B ALA* 4.3 3.4 - - - +
336B LEU* 4.2 31.4 - - + +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 4.8 3.1 - - + -
241B MET* 5.8 0.2 - - + -
242B TRP* 1.3 80.6 - - - +
244B ASN* 1.3 63.5 + - - +
249B TYR* 3.2 15.9 - - + +
288B GLY 4.0 12.3 - - - +
291B LEU* 3.9 18.2 - - + -
292B ILE* 3.4 33.4 - - + -
307B ILE* 3.8 14.6 - - + -
308B LEU 3.2 2.7 + - - +
309B PRO* 4.4 0.7 - - + -
310B ALA* 2.9 22.4 + - - +
313B VAL* 3.1 12.9 - - - +
320B GLY 4.6 0.2 - - - -
321B VAL* 3.7 26.0 - - + -
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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
------------------------------------------------------------
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