Contacts of the helix formed by residues 228 - 241 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE* 4.0 36.8 - + + -
32P ILE* 3.9 44.8 - - + +
35P GLN* 3.5 20.0 + - - -
36P LEU* 3.9 23.3 - - + -
58P LEU* 4.6 7.9 - - + -
201P LEU* 3.1 33.3 - - + +
226P ASP 3.3 4.3 + - - -
227P THR* 1.3 80.1 - - + +
229P MET* 1.3 80.2 + - + -
231P GLU* 2.4 44.5 + - - +
232P PHE* 3.4 27.5 + + + -
259P PHE* 4.9 2.5 - + - -
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Residues in contact with MET 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 5.6 0.2 - - - -
54P TRP* 3.7 23.8 - - + -
200P PRO* 5.1 0.9 - - + -
201P LEU* 3.8 34.5 - - + +
203P TRP* 3.5 36.6 - - + -
206P TRP* 3.3 41.5 - - + +
227P THR* 3.2 7.8 - - - +
228P TRP* 1.3 105.0 - - + +
230P LYS* 1.3 61.4 + - - +
232P PHE* 3.2 8.7 + - - +
233P PHE* 2.9 23.1 + - - +
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Residues in contact with LYS 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206P TRP* 4.0 17.8 - - + -
222P LEU 5.5 1.0 + - - -
224P LEU* 3.1 48.2 + - + +
225P PRO 2.9 21.3 - - - +
226P ASP* 4.8 7.1 + - - +
227P THR 2.7 20.4 + - - +
228P TRP 2.8 0.4 + - - -
229P MET* 1.3 71.9 - - - +
231P GLU* 1.3 52.2 + - - +
233P PHE* 3.4 3.9 - - + +
234P LEU* 2.8 58.5 + - + +
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Residues in contact with GLU 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PHE* 3.1 33.4 - - + -
228P TRP* 2.4 33.8 + - + +
230P LYS* 1.3 71.0 - - - +
232P PHE* 1.3 63.5 + - + +
234P LEU* 3.9 1.4 - - - +
235P ALA* 3.0 25.2 + - - +
250P LYS* 3.9 30.9 + - + +
253P ASN* 3.1 32.0 + - - +
254P LEU* 4.5 13.9 - - + +
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Residues in contact with PHE 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE* 5.6 2.2 - + - -
54P TRP* 4.2 7.9 - + + -
58P LEU* 3.5 29.2 - - + -
203P TRP* 4.0 14.7 - - + -
228P TRP* 3.9 38.1 - + + -
229P MET* 3.2 10.1 + - - +
231P GLU* 1.3 79.8 - - + +
233P PHE* 1.3 58.3 + - - +
235P ALA* 3.5 6.3 - - - +
236P HIS* 2.8 29.5 + - - +
251P TYR* 4.5 3.6 + + - -
254P LEU* 3.3 43.1 - - + -
259P PHE* 4.0 14.4 - + - -
264P TYR* 4.1 19.8 + + - -
265P ILE* 4.1 15.7 - - + -
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Residues in contact with PHE 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203P TRP* 4.0 12.3 - + + -
206P TRP* 3.2 56.8 - + + -
209P LEU* 3.6 26.5 - - + -
210P CYS* 4.0 7.9 - - - -
213P ILE* 4.6 0.7 - - + -
219P LEU* 4.1 11.2 - - + -
224P LEU* 3.7 24.5 - - + -
229P MET 2.9 16.9 + - - +
230P LYS* 3.4 6.7 - - + +
232P PHE* 1.3 74.7 - - - +
234P LEU* 1.3 70.2 + - + +
236P HIS* 3.7 1.1 - - - +
237P ILE* 2.7 64.8 + - + +
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Residues in contact with LEU 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P LEU* 4.4 16.8 - - + -
224P LEU* 6.2 0.7 - - + -
230P LYS* 2.8 49.5 + - + +
233P PHE* 1.3 82.5 - - + +
235P ALA* 1.3 58.6 + - - +
237P ILE* 3.3 3.8 + - - +
238P TYR* 2.8 86.5 + - + +
250P LYS* 3.5 17.9 - - - +
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Residues in contact with ALA 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P GLU 3.0 17.8 + - - +
232P PHE* 3.5 6.5 - - - +
234P LEU* 1.3 77.3 - - - +
236P HIS* 1.3 62.5 + - - +
238P TYR* 3.3 8.8 + - - +
239P THR* 3.1 21.8 + - - -
247P ALA* 3.8 5.5 - - - +
250P LYS* 3.8 28.8 - - + +
251P TYR* 3.8 29.5 + - + +
254P LEU* 5.0 1.8 - - + -
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Residues in contact with HIS 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P TRP* 4.1 12.2 - + + -
207P LEU* 4.0 20.2 - - + +
210P CYS* 3.4 29.6 - - + +
211P ASN* 5.5 0.6 + - - -
232P PHE 2.8 21.1 + - - +
233P PHE* 3.7 4.0 - - - +
235P ALA* 1.3 73.6 - - - +
237P ILE* 1.3 62.2 + - - +
239P THR* 3.3 21.8 - - + +
240P GLU* 3.4 18.9 + - - +
251P TYR* 3.3 12.5 + - - +
264P TYR* 3.2 22.8 + + - +
268P GLN* 4.0 20.6 - - - -
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Residues in contact with ILE 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P CYS* 3.8 27.8 - - - +
213P ILE* 4.1 18.8 - - + -
219P LEU* 4.1 21.8 - - + -
233P PHE* 2.7 65.9 + - + +
234P LEU* 3.9 4.3 - - - +
236P HIS* 1.3 75.0 - - - +
238P TYR* 1.3 68.3 + - + +
240P GLU* 3.0 7.8 + - + +
241P LEU* 2.9 41.7 + - + +
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Residues in contact with TYR 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216P LYS* 6.3 2.7 - - + -
219P LEU* 4.7 12.9 - - + +
234P LEU* 2.8 54.5 + - + +
235P ALA* 3.5 2.7 - - - +
237P ILE* 1.3 78.0 - - + +
239P THR* 1.3 56.7 + - - +
241P LEU* 2.9 30.7 + - + +
242P GLN 3.2 18.5 - - - +
243P LEU* 4.0 22.4 - - + +
244P ILE* 4.1 2.9 - - - +
246P GLU* 3.8 32.2 + - + +
247P ALA* 3.4 26.7 - - + -
250P LYS* 4.5 9.0 - - + -
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Residues in contact with THR 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235P ALA 3.1 12.3 + - - -
236P HIS* 3.3 17.9 - - + +
237P ILE 3.1 0.2 - - - -
238P TYR* 1.3 75.6 - - - +
240P GLU* 1.3 66.4 + - + +
241P LEU 3.3 7.4 - - - +
244P ILE* 3.9 7.8 - - - +
247P ALA* 3.9 6.2 - - - +
251P TYR* 4.2 8.9 - - - -
268P GLN* 4.1 19.1 + - - +
271P VAL* 4.4 10.3 - - + -
272P ALA* 3.2 33.6 + - - +
275P ASN* 2.5 32.7 + - - +
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Residues in contact with GLU 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P CYS* 3.0 30.5 - - - +
211P ASN* 3.7 16.5 - - - +
213P ILE 5.3 0.3 - - - +
236P HIS* 3.4 26.2 + - - +
237P ILE* 3.0 10.9 + - + +
239P THR* 1.3 86.8 - - + +
241P LEU* 1.3 68.8 + - + +
242P GLN* 5.0 0.9 - - - +
275P ASN* 4.2 5.6 + - - +
365P LEU* 5.6 6.4 - - - +
397P ARG* 4.0 20.3 + - + +
428P LEU* 5.8 0.3 - - - +
429P ARG* 5.2 7.4 + - - -
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Residues in contact with LEU 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P CYS 5.9 0.2 - - - +
213P ILE* 4.2 17.3 - - + +
214P THR 4.3 3.1 - - - +
215P ASP* 3.9 10.8 - - - +
216P LYS* 3.8 38.6 - - + +
219P LEU* 5.4 3.4 - - + -
237P ILE* 2.9 34.6 + - + +
238P TYR* 2.9 16.9 + - + +
239P THR 3.3 6.1 - - - +
240P GLU* 1.3 86.7 - - + +
242P GLN* 1.3 80.6 + - - +
244P ILE* 3.8 5.5 - - - +
275P ASN* 5.5 0.3 - - - +
397P ARG* 3.6 34.8 - - - +
429P ARG* 5.4 0.5 + - - -
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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