Contacts of the helix formed by residues 282 - 291 (chain B) in PDB entry 1WLZ
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 THR 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271B ARG* 3.4 1.8 - - - +
280B ILE 4.9 3.4 - - - +
281B LEU* 1.3 76.8 - - - +
283B ASP* 1.3 65.2 + - - +
284B GLU* 3.5 15.4 + - - +
285B GLN* 2.9 45.9 + - - +
286B PHE* 2.9 20.8 + - - +
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Residues in contact with ASP 283 (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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271B ARG* 2.8 41.5 + - - +
282B THR* 1.3 73.2 - - - +
284B GLU* 1.3 71.7 + - - +
286B PHE* 3.8 0.9 - - - +
287B ASP* 2.9 40.7 + - - +
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Residues in contact with GLU 284 (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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282B THR* 3.2 18.9 + - - +
283B ASP* 1.3 87.6 + - - +
285B GLN* 1.3 61.7 + - + +
287B ASP* 3.4 7.8 + - - +
288B ARG* 3.2 46.3 + - - +
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Residues in contact with GLN 285 (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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232B ASP* 4.0 11.6 + - - +
235B ILE* 3.8 28.3 - - + +
279B GLN* 4.5 7.8 + - - +
280B ILE 4.4 1.6 - - - +
281B LEU* 3.5 14.7 - - + +
282B THR* 2.9 44.9 + - - +
284B GLU* 1.3 76.8 - - + +
286B PHE* 1.3 58.2 + - - +
288B ARG* 3.3 25.1 + - - +
289B LEU* 2.9 28.5 + - - +
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Residues in contact with PHE 286 (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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267B ARG* 3.5 61.2 - - + -
268B GLU* 5.9 0.2 - - - -
270B PHE* 3.8 18.6 - + - -
271B ARG* 3.6 56.3 - - + +
274B CYS* 4.6 2.0 - - - -
281B LEU* 4.0 24.1 - - + +
282B THR 2.9 15.6 + - - +
283B ASP 3.8 2.7 - - - +
285B GLN* 1.3 75.1 - - - +
287B ASP* 1.3 67.4 + - - +
289B LEU* 3.1 5.1 + - + +
290B TRP* 2.8 41.2 + + + +
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Residues in contact with ASP 287 (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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267B ARG* 2.8 30.3 + - - +
271B ARG* 5.8 0.9 + - - -
283B ASP* 2.9 27.6 + - - +
284B GLU* 3.7 7.5 - - - +
285B GLN 3.3 0.2 - - - -
286B PHE* 1.3 77.8 - - - +
288B ARG* 1.3 63.2 + - + +
290B TRP* 3.4 3.8 + - - +
291B ASN* 3.2 26.8 + - - +
255D GLU* 4.3 18.2 - - - +
261D LYS* 4.5 12.2 + - - -
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Residues in contact with ARG 288 (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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228B MET* 4.3 7.1 - - + +
230B THR* 2.9 47.7 + - - +
231B ALA* 4.5 7.3 - - - +
232B ASP* 3.0 33.4 + - - +
284B GLU* 3.2 29.6 + - - +
285B GLN* 3.6 26.8 - - - +
286B PHE 3.2 0.4 - - - -
287B ASP* 1.3 78.9 - - + +
289B LEU* 1.3 65.3 + - - +
291B ASN* 3.2 28.5 + - - +
292B GLU* 3.6 10.3 - - - +
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Residues in contact with LEU 289 (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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235B ILE* 4.6 16.8 - - + -
236B LEU* 3.5 33.4 - - + -
239B LEU* 3.9 15.9 - - + -
270B PHE* 4.3 5.8 - - + -
274B CYS* 4.1 18.4 - - - -
278B VAL* 6.4 0.9 - - + -
281B LEU* 3.7 26.2 - - + -
285B GLN 2.9 16.9 + - - +
286B PHE* 3.6 7.9 - - + +
288B ARG* 1.3 75.7 - - - +
290B TRP* 1.3 59.2 + - - +
292B GLU* 2.9 27.3 + - - +
293B MET* 3.4 21.3 - - + +
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Residues in contact with TRP 290 (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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267B ARG* 3.1 57.5 - - + +
270B PHE* 3.6 32.8 - + - -
286B PHE* 2.8 26.8 + + + +
287B ASP 3.6 6.1 - - - +
289B LEU* 1.3 77.2 - - - +
291B ASN* 1.3 61.6 + - - +
292B GLU 3.0 0.2 - - - -
293B MET* 3.1 20.2 + - + +
295B VAL* 3.5 20.9 - - + +
299B GLY 3.4 20.6 - - - -
301B LEU* 3.7 33.7 - - + -
261D LYS* 2.8 28.7 + - + -
263D ASN* 3.0 27.0 + - - +
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Residues in contact with ASN 291 (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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227B HIS* 5.2 0.2 - - - +
228B MET* 3.6 40.4 - - + +
287B ASP* 3.2 18.5 + - - +
288B ARG* 3.2 21.3 + - - +
289B LEU 3.1 0.8 - - - -
290B TRP* 1.3 78.1 - - - +
292B GLU* 1.3 59.9 + - - +
293B MET 3.4 1.3 - - - +
263D ASN* 3.0 26.8 + - - +
303D TYR* 3.7 16.2 + - - -
304D PRO* 3.6 24.1 - - + +
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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