Contacts of the helix formed by residues 217 - 234 (chain B) in PDB entry 1WR6
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 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 3.2 21.9 + - - +
216B HIS* 1.3 69.2 + - - +
218B LEU* 1.3 51.6 + - - +
219B GLU* 2.7 20.9 + - + +
220B GLU* 2.7 44.7 + - + +
221B VAL* 3.5 6.2 + - - +
9F THR* 5.7 5.6 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU 4.4 4.7 - - - +
216B HIS* 2.8 49.6 - - + +
217B THR* 1.3 77.6 - - - +
219B GLU* 1.3 56.0 + - - +
220B GLU 3.2 0.4 - - - -
221B VAL* 3.7 11.4 - - + +
222B ASN* 2.8 30.1 + - - +
262B LEU* 4.8 16.6 - - + -
265B LEU* 6.0 2.0 - - + -
278B ASP* 3.9 31.4 - - + +
279B ILE* 4.5 5.6 - - + +
282B ALA* 4.0 19.9 - - + +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B HIS 4.3 3.0 + - - +
217B THR* 2.7 7.6 + - + +
218B LEU* 1.3 79.5 - - - +
220B GLU* 1.3 58.2 + - - +
222B ASN* 3.3 10.4 + - - +
223B ASN* 2.8 70.4 + - - +
6F LYS* 5.6 2.1 + - - -
9F THR 4.5 3.8 - - - +
10F GLY* 4.2 19.9 - - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B THR* 2.7 27.1 + - + +
219B GLU* 1.3 79.8 - - - +
221B VAL* 1.3 66.7 + - + +
223B ASN* 3.2 1.6 + - - +
224B ASN* 2.9 31.0 + - - +
258B LYS* 3.3 32.7 - - - +
8F LEU* 3.0 27.4 - - + +
9F THR* 3.5 23.6 - - + +
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B THR* 4.1 10.3 - - - +
218B LEU* 3.3 14.1 + - + +
219B GLU 3.3 0.4 - - - -
220B GLU* 1.3 80.3 - - + +
222B ASN* 1.3 62.2 + - - +
224B ASN* 3.5 2.8 + - - +
225B VAL* 3.1 28.1 + - + +
258B LYS* 4.4 25.4 - - + -
262B LEU* 4.2 23.3 - - + -
282B ALA* 4.7 6.5 - - + -
286B LEU* 3.5 39.7 - - + -
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Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU 2.8 18.5 + - - +
219B GLU* 3.6 10.6 + - - +
221B VAL* 1.3 75.8 - - - +
223B ASN* 1.3 66.7 + - - +
225B VAL* 3.3 8.6 + - - +
226B ARG* 3.0 67.2 + - - +
285B ASN* 5.2 6.8 - - - +
268C GLU* 4.4 7.0 + - - +
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Residues in contact with ASN 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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219B GLU* 2.8 45.1 + - - +
220B GLU 3.2 5.4 + - - +
222B ASN* 1.3 82.2 - - - +
224B ASN* 1.3 65.5 + - - +
226B ARG* 3.3 14.6 + - - +
227B LEU* 3.0 25.3 + - - +
6F LYS* 5.4 7.7 - - - +
7F THR 3.7 4.4 - - - +
8F LEU* 3.5 26.8 - - + +
10F GLY* 3.2 26.7 + - - -
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Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLU* 2.9 20.4 + - - +
221B VAL* 3.8 7.9 - - - +
223B ASN* 1.3 74.6 - - - +
225B VAL* 1.3 64.1 + - - +
227B LEU* 3.3 3.2 + - - +
228B LEU* 3.0 26.0 + - - +
251B LEU* 4.1 16.6 + - + +
254B GLN* 3.8 22.2 - - - +
255B CYS* 4.2 15.6 - - - -
258B LYS* 2.8 34.9 + - + +
286B LEU* 5.6 0.4 - - + -
8F LEU* 3.6 35.6 - - - +
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Residues in contact with VAL 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 VAL* 3.1 18.8 + - + +
222B ASN* 3.6 10.3 - - - +
223B ASN 3.2 0.2 - - - -
224B ASN* 1.3 77.3 - - - +
226B ARG* 1.3 61.4 + - + +
228B LEU* 3.5 1.6 + - - +
229B SER* 2.7 42.4 + - - +
255B CYS* 4.7 0.7 - - - -
282B ALA 5.4 0.2 - - - +
285B ASN* 3.6 30.3 - - + +
286B LEU* 3.4 35.2 - - + +
289B VAL* 4.1 14.8 - - + +
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Residues in contact with ARG 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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222B ASN* 3.0 46.9 + - - +
223B ASN* 3.8 14.1 - - - +
224B ASN 3.3 0.4 - - - -
225B VAL* 1.3 77.7 - - + +
227B LEU* 1.3 62.5 + - - +
229B SER* 3.6 6.3 + - - -
230B GLU* 3.1 23.8 + - - +
268C GLU* 2.8 53.6 + - + +
269C THR* 3.7 1.6 - - - +
270C GLU* 3.7 38.6 + - - +
6F LYS* 6.0 1.8 - - - +
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Residues in contact with LEU 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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223B ASN 3.0 17.2 + - - +
224B ASN 3.8 3.4 - - - +
226B ARG* 1.3 75.0 - - - +
228B LEU* 1.3 65.5 + - - +
230B GLU* 3.1 14.7 + - + +
231B MSE 2.9 39.8 + - + +
247B LEU* 5.3 0.4 - - + -
251B LEU* 3.7 20.9 - - + -
8F LEU* 4.6 11.4 - - + -
44F ILE* 4.2 24.7 - - + -
47F GLY* 5.5 0.2 - - - -
68F HIS* 4.6 23.1 - - + +
70F VAL* 4.0 25.6 - - + -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ASN 3.0 17.0 + - - +
225B VAL* 4.7 0.4 - - - -
227B LEU* 1.3 76.6 - - - +
229B SER* 1.3 54.0 + - - +
231B MSE 3.4 2.1 + - - -
232B LEU* 2.8 61.8 + - + +
248B MSE 4.2 19.1 - - + +
251B LEU* 3.9 21.9 - - + +
252B PHE* 3.8 30.5 - - + +
255B CYS* 4.3 7.4 - - - -
289B VAL* 3.8 31.9 - - + +
293B TYR* 4.1 13.0 - - + -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 2.7 27.6 + - - +
226B ARG* 3.7 7.2 - - - -
228B LEU* 1.3 78.0 - - - +
230B GLU* 1.3 57.1 + - - +
232B LEU* 3.6 3.0 - - - +
233B LEU* 2.8 28.9 + - - +
289B VAL* 3.4 15.9 - - - +
215C LEU* 3.6 28.1 - - - +
265C LEU* 4.8 11.3 - - - +
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Residues in contact with GLU 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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226B ARG 3.1 17.9 + - - +
227B LEU* 3.1 13.8 + - + +
229B SER* 1.3 76.2 - - - +
231B MSE 1.3 64.9 + - - +
233B LEU* 3.1 6.4 + - + +
234B HIS* 3.1 31.2 + - + -
269C THR* 4.9 1.2 + - - -
270C GLU* 5.6 0.3 - - - -
273C ASP* 2.7 39.6 - - - +
275C SER* 3.3 21.4 - - - +
44F ILE* 5.9 0.2 - - - +
46F ALA* 4.1 3.6 + - - -
47F GLY* 3.7 23.1 + - - +
68F HIS* 4.7 12.3 + - - -
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Residues in contact with MSE 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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227B LEU* 2.9 37.2 + - + +
228B LEU 3.8 3.6 - - - +
230B GLU* 1.3 75.4 - - - +
232B LEU* 1.3 58.1 + - - +
234B HIS* 3.2 3.6 + - - +
235B TYR* 3.0 26.5 + - - +
244B ASP* 3.9 30.3 - - + +
247B LEU* 3.7 43.5 - - + -
248B MSE 4.0 25.5 - - + +
251B LEU* 4.2 12.3 - - - -
44F ILE* 4.1 9.6 - - + -
47F GLY* 3.5 30.9 - - - +
49F GLN 4.9 0.7 - - - +
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Residues in contact with LEU 232 (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 LEU* 2.8 40.6 + - + +
229B SER* 3.6 6.3 - - - +
231B MSE 1.3 78.0 - - - +
233B LEU* 1.3 62.2 + - - +
235B TYR* 3.0 13.9 + - + +
248B MSE 3.8 21.5 - - - -
289B VAL* 4.1 11.2 - - + +
292B SER* 4.0 11.7 - - - -
293B TYR* 4.0 25.1 - - + +
296B ILE* 4.2 19.5 - - + -
297B ILE* 4.0 19.3 - - + -
215C LEU* 4.4 8.3 - - + -
217C THR* 3.2 20.9 - - - +
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Residues in contact with LEU 233 (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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229B SER 2.8 19.3 + - - +
230B GLU* 3.3 9.6 - - - +
232B LEU* 1.3 75.6 - - - +
234B HIS* 1.3 68.5 + - + +
235B TYR 3.8 0.5 + - - +
215C LEU* 4.5 3.3 - - - +
216C HIS 3.6 20.2 - - - +
217C THR* 4.1 4.4 - - - +
218C LEU* 3.1 58.4 + - + +
262C LEU* 4.6 5.4 - - + -
265C LEU* 3.5 21.3 - - + -
275C SER* 3.5 24.9 - - - +
279C ILE* 3.6 25.1 - - + -
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 3.1 25.9 + - + +
231B MSE 3.2 5.1 + - - +
232B LEU 3.1 1.0 - - - -
233B LEU* 1.3 80.1 - - + +
235B TYR* 1.3 63.6 + - - +
236B SER* 4.6 1.0 - - - -
240B SER* 4.2 0.2 + - - -
218C LEU* 3.4 21.5 - - + +
275C SER* 3.1 32.7 + - - -
278C ASP* 3.0 30.9 + - + -
46F ALA* 3.3 33.1 + - + +
47F GLY* 4.3 4.7 - - - -
48F LYS* 3.1 37.5 + - - +
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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