Contacts of the helix formed by residues 243 - 255 (chain P) in PDB entry 2X86
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 PHE 243 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169P ASN* 5.1 3.1 - - - -
184P VAL* 3.6 35.9 - - + -
188P LEU* 5.7 0.2 - - - +
200P LEU* 3.9 20.4 - - + +
204P SER* 4.2 10.3 + - - -
207P PHE* 3.4 30.2 + - + -
208P LYS* 4.8 0.2 - - - -
209P ARG* 3.7 37.0 - - + -
211P PHE* 3.8 22.4 - + - -
242P SER* 1.3 72.7 - - - +
244P GLN* 1.3 63.8 + - - +
246P VAL* 3.1 7.7 + - + +
247P ALA* 3.0 21.5 + - - +
272P TYR* 3.7 5.2 - - - -
401P ADP 3.6 42.2 - + - -
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Residues in contact with GLN 244 (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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200P LEU* 4.2 13.6 - - + +
204P SER 4.5 8.0 + - - +
205P GLU* 5.5 5.6 - - - -
242P SER* 3.1 13.3 + - - +
243P PHE* 1.3 78.7 - - - +
245P ALA* 1.3 55.7 + - - +
247P ALA* 3.3 6.4 + - - +
248P ASP* 2.8 66.5 + - - +
259P ILE* 4.2 13.0 - - - +
261P TYR* 3.9 17.8 + - - +
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Residues in contact with ALA 245 (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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241P GLU* 4.1 27.8 - - + +
242P SER* 2.9 22.9 + - - +
244P GLN* 1.3 73.2 - - - +
246P VAL* 1.3 64.2 + - - +
248P ASP* 3.2 14.0 + - - +
249P ALA* 3.0 22.9 + - - +
295P VAL* 4.0 8.2 - - + +
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Residues in contact with VAL 246 (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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171P TYR* 6.4 0.2 - - + -
184P VAL* 4.9 6.5 - - + -
185P ALA* 4.2 34.3 - - + +
188P LEU* 4.6 5.2 - - + -
211P PHE* 3.7 48.0 - - + -
242P SER 3.5 2.0 + - - +
243P PHE* 3.1 9.1 + - - +
245P ALA* 1.3 77.9 - - - +
247P ALA* 1.3 62.8 + - - +
249P ALA* 3.2 5.0 + - - +
250P THR* 3.0 27.0 + - - +
295P VAL* 3.8 19.9 - - + +
299P VAL* 4.2 9.3 - - + +
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Residues in contact with ALA 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188P LEU* 3.8 18.1 - - + +
200P LEU* 4.2 6.3 - - + -
243P PHE 3.0 13.5 + - - +
244P GLN* 3.4 11.9 - - - +
246P VAL* 1.3 76.0 - - - +
248P ASP* 1.3 52.9 + - - +
250P THR* 3.2 2.4 + - - -
251P LEU* 2.8 41.0 + - + +
259P ILE* 3.4 36.8 - - + -
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Residues in contact with ASP 248 (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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244P GLN* 2.8 52.1 + - - +
245P ALA* 3.2 13.0 + - - +
247P ALA* 1.3 72.2 - - - +
249P ALA* 1.3 62.8 + - - +
251P LEU* 3.5 5.1 + - - +
252P ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 249 (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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245P ALA 3.0 9.1 + - - +
246P VAL 3.2 7.8 + - - +
248P ASP* 1.3 79.5 - - - +
250P THR* 1.3 61.0 + - - +
252P ALA* 3.5 6.5 - - - +
253P TYR* 3.2 17.3 + - - +
295P VAL* 4.3 9.2 - - + +
296P ALA* 4.3 16.6 - - + +
299P VAL* 3.7 25.1 - - + +
300P THR* 3.8 15.4 - - + +
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Residues in contact with THR 250 (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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185P ALA* 4.6 0.7 - - - -
188P LEU* 4.1 21.5 - - + +
189P ASN 4.5 1.6 - - - +
192P LEU* 3.9 21.1 - - + -
246P VAL* 3.0 17.9 + - - +
247P ALA* 3.5 9.9 - - - -
249P ALA* 1.3 73.5 - - - +
251P LEU* 1.3 67.8 + - + +
252P ALA 3.1 1.1 - - - -
253P TYR* 3.1 4.0 + - - +
254P HIS* 3.1 25.1 + - + +
299P VAL* 3.4 17.8 - - - +
303P MET* 3.6 29.9 - - + +
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Residues in contact with LEU 251 (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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188P LEU* 5.5 1.3 - - + -
192P LEU* 3.8 22.4 - - + -
198P PRO* 3.9 18.8 - - + -
247P ALA* 2.8 29.2 + - + +
248P ASP* 4.2 4.5 - - - +
250P THR* 1.3 77.5 - - + +
252P ALA* 1.3 57.3 + - - +
254P HIS* 3.3 2.4 + - - +
255P LYS* 2.8 26.7 + - - -
256P LYS 3.5 18.8 + - - +
257P GLY 3.0 30.7 - - - +
258P GLN* 4.0 8.3 - - - +
259P ILE* 4.4 15.0 - - + +
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Residues in contact with ALA 252 (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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248P ASP 3.0 19.2 + - - +
249P ALA* 3.5 8.5 - - - +
251P LEU* 1.3 77.8 - - - +
253P TYR* 1.3 62.6 + - - +
255P LYS* 3.2 25.3 - - - +
300P THR* 5.6 2.7 - - + -
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Residues in contact with TYR 253 (chain P).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249P ALA 3.2 10.0 + - - +
250P THR 3.1 9.2 + - - +
252P ALA* 1.3 80.6 - - - +
254P HIS* 1.3 75.6 + + - +
255P LYS* 3.2 11.7 + - - +
300P THR* 4.3 18.8 - - + +
303P MET* 3.5 39.0 + - + -
304P ALA* 3.4 32.1 + - + +
307P ASN* 4.0 23.1 - - + +
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Residues in contact with HIS 254 (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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189P ASN* 2.8 32.3 + - - -
192P LEU* 3.8 37.0 - - + +
193P ASN* 3.4 23.2 + - - -
250P THR* 3.1 30.0 + - + +
251P LEU 4.0 2.9 - - - +
253P TYR* 1.3 87.3 - + - +
255P LYS* 1.3 68.6 + - - +
256P LYS* 3.0 29.1 + - + +
303P MET* 3.9 6.1 - - - -
307P ASN* 4.4 7.4 - - - -
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Residues in contact with LYS 255 (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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251P LEU 2.8 10.0 + - - -
252P ALA* 3.2 24.4 + - - +
253P TYR 3.2 11.1 - - - +
254P HIS* 1.3 77.4 - - - +
256P LYS* 1.3 59.4 + - - +
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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