Contacts of the helix formed by residues 216 - 231 (chain B) in PDB entry 1WKM
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 VAL 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B VAL* 3.4 1.9 - - - +
215B ARG* 1.3 82.8 - - + +
217B ALA* 1.3 57.1 + - - +
218B GLN* 4.1 13.5 - - + +
219B ALA* 3.1 18.3 + - + +
220B ARG* 2.8 36.5 + - - +
251B LEU* 6.1 7.2 - - + -
255B THR* 5.1 12.7 - - + +
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Residues in contact with ALA 217 (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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215B ARG 3.8 3.4 + - - -
216B VAL* 1.3 73.0 - - + +
218B GLN* 1.3 54.9 + - - +
220B ARG* 3.0 27.4 + - - +
221B PHE* 2.7 37.7 + - - +
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Residues in contact with GLN 218 (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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216B VAL* 3.4 10.9 - - + +
217B ALA* 1.3 79.1 - - - +
219B ALA* 1.3 58.3 + - - +
221B PHE* 3.4 10.4 + - + +
222B LEU* 3.0 27.4 + - - +
244B MET* 3.8 30.6 - - + +
248B GLN* 2.9 56.6 - - - +
252B ALA* 4.8 5.6 - - + -
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Residues in contact with ALA 219 (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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214B VAL* 4.9 3.4 - - + -
216B VAL* 3.1 24.0 + - + +
218B GLN* 1.3 77.8 - - - +
220B ARG* 1.3 65.0 + - - +
222B LEU* 3.4 2.1 + - - +
223B LEU 3.1 18.0 + - - -
252B ALA* 4.1 24.0 - - - +
255B THR* 4.0 23.8 - - + -
256B LEU* 3.3 21.4 - - + +
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Residues in contact with ARG 220 (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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214B VAL* 3.0 48.4 + - + +
215B ARG* 3.8 18.0 + - - +
216B VAL 2.8 10.6 + - - +
217B ALA* 3.3 29.3 - - - +
219B ALA* 1.3 75.7 - - - +
221B PHE* 1.3 63.7 - - - +
223B LEU* 3.3 5.4 + - + +
224B ALA* 3.2 21.8 + - - +
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Residues in contact with PHE 221 (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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217B ALA 2.7 19.8 + - - +
218B GLN* 3.6 10.8 - - + +
220B ARG* 1.3 74.8 - - - +
222B LEU* 1.3 67.5 + - - +
224B ALA* 3.3 9.4 + - + +
225B LYS* 3.0 45.4 + - + +
228B ARG* 5.5 8.0 + - - -
243B ASP* 5.7 6.5 - - + -
244B MET* 4.6 15.5 - - + -
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Residues in contact with LEU 222 (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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218B GLN 3.0 17.5 + - - +
219B ALA* 3.5 7.6 - - - +
221B PHE* 1.3 83.4 - - + +
223B LEU* 1.3 53.2 + - - +
225B LYS* 3.1 8.4 + - + +
226B ILE* 2.8 51.5 + - + +
240B LEU* 3.9 22.0 - - + -
243B ASP* 5.7 0.4 - - + +
244B MET* 4.0 14.4 - - + -
249B LEU* 3.9 13.0 - - + -
252B ALA* 3.6 22.2 - - + -
253B LEU* 3.5 29.2 - - + +
256B LEU* 4.1 5.6 - - + -
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Residues in contact with LEU 223 (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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208B TYR* 3.8 32.5 - - + -
211B ASP* 4.1 15.3 - - - +
212B VAL 3.6 26.7 - - - +
214B VAL* 4.4 5.6 - - + -
219B ALA 3.1 11.1 + - - +
220B ARG* 3.3 11.4 - - + +
222B LEU* 1.3 79.1 - - - +
224B ALA* 1.3 57.2 + - - +
226B ILE* 3.4 3.8 + - + +
227B LYS* 3.0 25.2 + - + +
256B LEU* 3.7 22.6 - - + +
261B ALA* 3.9 23.1 - - + -
262B ILE* 4.7 5.8 - - + -
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Residues in contact with ALA 224 (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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220B ARG 3.2 9.6 + - - +
221B PHE* 3.4 12.6 - - + +
223B LEU* 1.3 76.9 - - - +
225B LYS* 1.3 61.3 + - - +
227B LYS* 3.5 7.9 + - - +
228B ARG* 3.0 39.3 + - - +
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Residues in contact with LYS 225 (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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221B PHE* 3.0 32.8 + - + +
222B LEU* 3.4 13.5 - - + +
224B ALA* 1.3 73.9 - - - +
226B ILE* 1.3 56.5 + - - +
228B ARG* 3.4 27.0 - - - +
229B GLU* 2.8 68.5 + - - +
230B TYR* 4.1 5.8 + - + -
239B TRP 4.8 3.2 + - - -
240B LEU* 3.9 16.9 - - + +
243B ASP* 2.8 37.0 + - + +
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Residues in contact with ILE 226 (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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208B TYR* 3.8 20.6 - - + -
222B LEU* 2.8 42.6 + - + +
223B LEU* 3.5 4.9 - - - +
225B LYS* 1.3 74.7 - - - +
227B LYS* 1.3 60.1 + - - +
230B TYR* 2.7 49.7 + - + +
231B GLY 3.3 1.6 + - - -
235B PHE* 3.3 50.3 - - + -
240B LEU* 4.5 2.0 - - + -
253B LEU* 4.6 3.6 - - + -
256B LEU* 4.1 19.7 - - + -
262B ILE* 4.3 9.0 - - + -
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Residues in contact with LYS 227 (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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208B TYR* 3.8 42.8 - - + +
211B ASP* 2.7 33.5 + - - +
223B LEU* 3.0 18.5 + - + +
224B ALA* 3.7 7.9 - - - +
226B ILE* 1.3 76.1 - - - +
228B ARG* 1.3 62.5 + - - +
231B GLY* 3.3 21.7 + - - +
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Residues in contact with ARG 228 (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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221B PHE* 5.5 9.3 + - - -
224B ALA* 3.0 26.6 + - - +
225B LYS* 3.4 46.5 - - - +
227B LYS* 1.3 82.3 - - - +
229B GLU* 1.3 75.6 + - + +
231B GLY* 4.7 1.2 + - - -
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Residues in contact with GLU 229 (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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225B LYS* 2.8 58.9 + - - +
228B ARG* 1.3 96.0 + - + +
230B TYR* 1.3 85.7 + - + +
231B GLY 3.7 0.2 - - - -
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Residues in contact with TYR 230 (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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225B LYS* 4.1 2.3 + - - -
226B ILE* 2.7 30.5 + - + +
229B GLU* 1.3 104.3 + - + +
231B GLY* 1.3 67.8 + - - +
232B THR 3.2 0.3 + - - -
233B LEU* 3.1 36.5 + - + +
234B PRO 5.5 0.2 - - - +
235B PHE* 3.5 38.4 - + + -
239B TRP* 3.3 58.0 + + + +
240B LEU* 4.0 22.8 - - + +
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Residues in contact with GLY 231 (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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208B TYR* 3.2 31.1 + - - +
226B ILE 3.3 1.8 + - - -
227B LYS* 3.3 23.5 + - - -
228B ARG 4.6 1.0 + - - -
229B GLU 3.7 1.0 - - - -
230B TYR* 1.3 79.9 - - - +
232B THR* 1.3 62.6 + - - -
233B LEU 3.5 2.4 + - - +
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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