Contacts of the helix formed by residues 228 - 242 (chain C) in PDB entry 5A31
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 TRP 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PHE* 3.4 39.9 - + + -
32C ILE* 3.9 41.0 - - + +
35C GLN* 3.5 20.1 + - + -
36C LEU* 3.9 23.3 - - + -
58C LEU* 4.6 8.1 - - + -
201C LEU* 3.1 32.7 - - + +
226C ASP 3.2 4.9 + - - -
227C THR* 1.3 79.3 - - + +
229C MET* 1.3 80.0 + - + -
230C LYS* 5.2 0.2 - - - -
231C GLU* 2.4 43.4 + - - +
232C PHE* 3.4 28.2 + + - -
259C PHE* 4.9 2.0 - + - -
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Residues in contact with MET 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TRP* 3.7 24.0 - - + -
200C PRO* 5.1 0.9 - - + -
201C LEU* 3.7 35.9 - - + +
203C TRP* 3.5 35.5 - - + -
206C TRP* 3.3 41.8 - - + +
227C THR* 2.9 9.8 + - - +
228C TRP* 1.3 100.7 - - + +
230C LYS* 1.3 61.5 + - - +
232C PHE* 3.2 9.1 + - - +
233C PHE* 3.0 24.2 + - - +
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C TRP* 4.0 17.3 - - + -
222C LEU 5.5 1.6 + - - -
224C LEU* 3.1 48.5 + - + +
225C PRO 3.0 21.7 - - - +
226C ASP* 4.8 7.3 + - - +
227C THR 2.7 20.6 + - - +
228C TRP 2.8 0.2 + - - -
229C MET* 1.3 71.9 - - - +
231C GLU* 1.3 57.5 + - - +
233C PHE* 3.4 2.7 - - + +
234C LEU* 2.8 48.7 + - + +
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 3.5 31.1 - - + -
228C TRP* 2.4 32.7 + - + +
230C LYS* 1.3 71.2 - - - +
232C PHE* 1.3 62.8 + - + +
234C LEU* 3.9 1.6 - - - +
235C ALA* 3.0 24.5 + - - +
250C LYS* 3.9 31.5 + - + +
253C ASN* 3.7 23.5 + - - -
254C LEU* 4.5 18.1 - - + +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 5.2 1.6 - + - -
54C TRP* 4.3 7.9 - + + -
58C LEU* 3.5 24.9 - - + -
203C TRP* 4.0 15.1 - - + -
228C TRP* 3.4 41.7 + + - -
229C MET* 3.2 10.8 + - - +
231C GLU* 1.3 79.7 - - + +
233C PHE* 1.3 59.2 + - - +
235C ALA* 3.5 6.2 - - - +
236C HIS* 2.9 29.8 + - - +
251C TYR* 4.6 3.7 + + - -
254C LEU* 3.3 36.6 - - + -
259C PHE* 3.8 13.9 - + - -
264C TYR* 4.2 18.2 + + - -
265C ILE* 3.8 25.8 - - + -
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TRP* 4.0 11.4 - - + -
206C TRP* 3.2 56.5 - + + -
209C LEU* 3.5 24.0 - - + -
210C CYS* 3.9 7.4 - - - -
213C ILE* 4.6 2.5 - - + -
219C LEU* 4.1 12.6 - - + -
224C LEU* 3.7 23.8 - - + -
229C MET 3.0 17.4 + - - +
230C LYS* 3.4 4.7 - - + +
232C PHE* 1.3 74.3 - - - +
234C LEU* 1.3 74.2 + - + +
236C HIS* 3.3 1.3 + - - +
237C ILE* 2.9 63.1 + - + +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C LEU* 4.1 24.0 - - + -
224C LEU* 5.2 0.9 - - + -
230C LYS* 2.8 39.9 + - + +
231C GLU* 3.9 0.4 - - - +
233C PHE* 1.3 91.8 - - + +
235C ALA* 1.3 59.0 + - - +
237C ILE* 3.3 3.5 + - - +
238C TYR* 2.9 69.3 + - + +
250C LYS* 3.5 20.9 - - - +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C GLU 3.0 16.5 + - - +
232C PHE* 3.5 7.0 - - - +
234C LEU* 1.3 77.0 - - - +
236C HIS* 1.3 63.0 + - - +
238C TYR* 3.2 8.1 + - - +
239C THR* 3.1 20.4 + - - -
247C ALA* 3.8 6.9 - - - +
250C LYS* 3.8 28.4 - - + +
251C TYR* 3.8 28.9 + - + +
254C LEU* 4.9 2.0 - - + -
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Residues in contact with HIS 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TRP* 4.1 12.6 - + + -
207C LEU* 4.0 19.3 - - + +
210C CYS* 3.4 29.4 - - + +
211C ASN* 5.5 0.6 + - - -
232C PHE 2.9 20.2 + - - +
233C PHE 3.7 4.0 - - - +
235C ALA* 1.3 72.8 - - - +
237C ILE* 1.3 63.3 + - - +
239C THR* 3.3 21.8 - - + +
240C GLU* 3.4 19.7 + - - +
251C TYR* 3.3 15.1 + - - +
264C TYR* 3.1 23.5 + + - +
268C GLN* 4.5 15.3 - - - -
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C CYS* 3.7 30.1 - - + +
213C ILE* 3.9 20.0 - - + -
219C LEU* 4.1 21.5 - - + -
233C PHE* 2.9 61.6 + - + +
234C LEU* 3.9 4.0 - - - +
236C HIS* 1.3 73.1 - - - +
238C TYR* 1.3 68.6 + - + +
240C GLU* 3.0 8.3 + - + +
241C LEU* 2.9 42.4 + - + +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LYS* 6.2 1.1 - - + -
219C LEU* 4.7 14.1 - - + +
234C LEU* 2.9 57.3 + - + +
235C ALA* 3.5 2.2 - - - +
237C ILE* 1.3 79.9 - - + +
239C THR* 1.3 63.4 + - - +
241C LEU* 3.2 3.1 + - + +
242C GLN 2.9 19.6 + - - -
243C LEU* 3.0 47.6 + - + +
246C GLU* 3.8 33.3 + - + +
247C ALA* 3.3 27.1 - - + -
250C LYS* 4.5 7.9 - - + -
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C ALA 3.1 11.7 + - - -
236C HIS* 3.3 20.4 - - + +
237C ILE 3.1 0.2 - - - -
238C TYR* 1.3 78.0 - - - +
240C GLU* 1.3 67.4 + - + +
242C GLN* 3.0 23.4 + - - +
244C ILE* 4.1 7.0 - - - +
247C ALA* 3.8 7.6 - - - +
251C TYR* 4.3 10.4 - - - -
268C GLN* 4.1 18.3 + - - +
271C VAL* 5.3 6.5 - - + +
272C ALA* 3.9 27.2 + - - +
275C ASN* 3.8 13.1 + - - +
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C CYS* 3.0 30.0 - - - +
211C ASN* 3.6 17.4 - - - +
213C ILE 5.3 0.3 - - - +
236C HIS* 3.4 25.2 + - - +
237C ILE* 3.0 10.7 + - - +
239C THR* 1.3 83.5 - - + +
241C LEU* 1.3 72.0 + - + +
242C GLN* 3.1 23.2 + - - +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C CYS 5.9 0.2 - - - +
213C ILE* 4.2 20.4 - - + +
214C THR* 4.3 11.7 - - - +
215C ASP* 3.8 10.5 - - - +
216C LYS* 3.8 36.6 - - + +
219C LEU* 5.4 3.4 - - + -
237C ILE* 2.9 34.7 + - + +
238C TYR* 3.9 0.9 - - + +
240C GLU* 1.3 84.8 - - + +
242C GLN* 1.3 71.0 + - - +
243C LEU* 3.3 30.4 - - + +
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C TYR 2.9 4.9 + - - -
239C THR 3.0 15.1 + - - +
240C GLU* 3.1 17.9 + - - +
241C LEU* 1.3 81.8 - - - +
243C LEU* 1.3 54.8 + - - +
244C ILE* 2.6 34.6 + - + +
275C ASN* 3.4 22.4 + - - +
429C ARG* 5.5 11.2 - - - +
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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