Contacts of the helix formed by residues 230 - 243 (chain B) in PDB entry 1W98
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLU* 2.8 27.7 + - - +
152B TYR* 3.5 16.6 - - - +
153B LEU* 3.6 45.5 - - + +
155B GLN* 5.6 0.2 - - - -
156B ASP* 5.1 0.9 - - + -
228B PRO* 3.5 9.3 + - + +
229B LEU* 1.3 75.7 - - - +
231B ILE* 1.3 65.4 + - - +
232B VAL* 3.6 4.0 - - - +
233B SER* 2.9 26.1 + - - -
234B TRP* 3.2 11.4 - - - -
281B TYR* 3.8 9.2 - - - -
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Residues in contact with ILE 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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152B TYR* 3.7 19.0 - - + -
155B GLN* 4.0 3.6 - - - +
230B THR* 1.3 76.1 - - - +
232B VAL* 1.3 63.0 + - - +
234B TRP* 3.3 7.6 + - - +
235B LEU* 3.4 8.7 + - - +
267B LEU* 3.7 39.0 - - + +
271B VAL* 3.6 28.3 - - + -
276B CYS* 5.1 1.1 - - - -
281B TYR* 3.6 42.8 - - + +
284B LEU* 3.5 30.7 - - + -
285B ALA* 3.5 10.5 - - + +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 4.0 19.5 - - + +
149B GLU* 3.5 34.5 - - + +
152B TYR* 3.6 30.6 - - + -
230B THR* 3.6 3.5 - - - +
231B ILE* 1.3 77.5 - - - +
233B SER* 1.3 63.6 + - - +
235B LEU* 3.1 11.8 + - + +
236B ASN* 2.9 32.0 + - - +
260B PHE* 3.9 23.8 - - + -
264B ALA* 5.0 4.7 - - + -
267B LEU* 5.3 2.2 - - + -
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 6.2 0.4 - - - -
154A VAL 4.5 0.2 - - - +
149B GLU* 3.9 13.5 - - - -
229B LEU* 3.7 21.3 - - - +
230B THR* 2.9 40.0 + - - -
232B VAL* 1.3 78.5 - - - +
234B TRP* 1.3 62.3 + - - +
236B ASN* 3.3 10.0 - - - +
237B VAL* 3.0 30.0 + - - +
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Residues in contact with TRP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.3 35.9 - + - -
105B MET* 3.9 22.2 - - + -
106B LEU* 4.1 17.5 - - + -
109B GLU* 3.9 22.6 + - + +
229B LEU* 3.5 44.5 + - + +
230B THR 3.2 21.3 + - - -
231B ILE 3.3 6.9 + - - +
232B VAL 3.1 0.6 - - - -
233B SER* 1.3 81.5 + - - +
235B LEU* 1.3 58.6 + - - +
237B VAL* 3.4 5.6 + - + +
238B TYR* 2.9 61.1 + + + -
281B TYR* 3.8 6.7 - - + +
282B GLY* 3.5 29.9 - - - +
285B ALA* 3.7 12.8 - - + -
304B TYR* 4.5 2.9 - - - -
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Residues in contact with LEU 235 (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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231B ILE 3.4 9.1 + - - +
232B VAL* 3.1 12.0 + - + +
234B TRP* 1.3 76.6 - - - +
236B ASN* 1.3 64.8 + - - +
238B TYR* 4.3 7.0 - - + -
239B MET* 3.0 43.4 + - + +
260B PHE* 3.8 33.0 - - + +
263B ILE* 3.9 27.4 - - + -
264B ALA* 3.9 32.1 - - + +
267B LEU* 4.1 14.6 - - + -
285B ALA* 4.0 6.9 - - + +
289B LEU* 4.6 12.6 - - + -
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Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL 3.3 14.0 - - - +
155A PRO* 3.7 19.4 + - + +
232B VAL* 2.9 24.4 + - - +
233B SER* 3.3 13.4 - - - +
234B TRP 3.3 0.2 - - - -
235B LEU* 1.3 78.0 - - - +
237B VAL* 1.3 63.3 + - - +
239B MET* 3.4 2.4 + - - +
240B GLN* 3.2 22.9 + - - +
255B TYR* 2.7 30.2 + - - -
260B PHE* 3.5 18.8 - - - -
344B ASN* 4.3 9.8 + - - +
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Residues in contact with VAL 237 (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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154A VAL* 3.0 32.2 + - + +
90B LEU* 4.2 25.1 - - + -
102B TRP* 4.6 9.6 - - + -
105B MET* 3.9 29.2 - - + -
229B LEU* 6.2 0.9 - - + -
233B SER* 3.0 18.8 + - - +
234B TRP* 3.4 11.4 - - + +
236B ASN* 1.3 73.0 - - - +
238B TYR* 1.3 71.2 + - + +
240B GLN* 3.2 4.9 + - - +
241B VAL* 3.2 24.2 + - + +
301B VAL 5.2 0.9 - - - +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 4.7 3.6 - + - -
234B TRP* 2.9 48.6 + + + +
235B LEU* 3.8 7.2 - - + +
237B VAL* 1.3 76.3 - - + +
239B MET* 1.3 58.1 + - - +
241B VAL 3.3 1.0 + - - -
242B ALA* 3.0 25.3 + - - +
282B GLY* 2.7 28.5 + - - -
285B ALA* 3.7 19.3 - - + -
286B ALA* 3.5 28.0 - - - -
289B LEU* 4.6 14.6 - - + -
301B VAL* 3.3 40.2 - - + +
302B SER* 3.2 24.0 - - - -
304B TYR* 3.5 13.0 - - - -
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Residues in contact with MET 239 (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 LEU* 3.0 30.7 + - + +
236B ASN 3.9 0.9 - - - +
238B TYR* 1.3 74.3 - - - +
240B GLN* 1.3 64.0 + - - +
242B ALA* 3.4 5.1 - - - +
243B TYR* 3.3 53.1 + - + +
255B TYR* 3.6 24.3 - - + +
256B PRO 4.1 8.3 - - - +
259B ILE* 3.8 24.7 - - + -
260B PHE* 3.8 31.6 - - + +
263B ILE* 4.1 18.4 - - - -
289B LEU* 4.2 11.4 - - + -
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Residues in contact with GLN 240 (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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154A VAL* 4.8 1.6 - - + -
155A PRO* 3.1 41.1 - - + +
236B ASN 3.2 6.0 + - - +
237B VAL* 3.2 11.0 + - - +
239B MET* 1.3 74.2 - - - +
241B VAL* 1.3 65.9 + - - +
243B TYR* 3.3 5.7 + - - -
244B LEU* 3.2 21.9 + - - +
249B GLU 4.4 2.0 + - - -
250B VAL* 3.1 31.7 + - + +
252B LEU 3.0 23.4 + - - -
253B PRO* 3.3 3.1 - - - +
254B GLN* 2.8 29.0 + - - +
255B TYR* 3.0 19.7 + - - -
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Residues in contact with VAL 241 (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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89B PRO 3.5 22.9 - - - +
90B LEU* 4.1 25.6 - - + -
91B PRO* 4.6 1.3 - - + -
237B VAL* 3.2 14.8 + - + +
238B TYR 3.7 5.8 - - - +
240B GLN* 1.3 76.3 - - - +
242B ALA* 1.3 63.4 + - - +
244B LEU* 3.0 35.5 + - + +
250B VAL* 4.5 9.2 - - + -
300B LYS* 3.9 9.6 - - + +
301B VAL* 3.7 32.8 - - + +
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Residues in contact with ALA 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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238B TYR 3.0 15.0 + - - +
239B MET* 3.4 18.2 - - - +
240B GLN 3.3 0.2 - - - -
241B VAL* 1.3 77.2 - - - +
243B TYR* 1.3 73.6 + - + +
244B LEU 3.7 2.4 + - - +
289B LEU* 5.7 1.6 - - + -
297B LEU* 4.2 20.4 - - + +
301B VAL* 3.4 18.1 - - + +
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Residues in contact with TYR 243 (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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239B MET* 3.3 39.9 + - + +
240B GLN 3.5 5.1 - - - +
241B VAL 3.1 0.6 - - - -
242B ALA* 1.3 87.9 - - + +
244B LEU* 1.3 63.3 + - - +
245B ASN* 3.6 13.5 + - - +
254B GLN* 3.2 28.3 - - - +
255B TYR* 3.6 8.3 - - + -
256B PRO* 3.2 33.7 - - + +
259B ILE* 3.6 25.6 - - + +
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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