Contacts of the helix formed by residues 243 - 255 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169K ASN* 5.2 2.9 - - - -
184K VAL* 3.6 35.4 - - + -
188K LEU* 5.7 0.2 - - - +
200K LEU* 3.9 19.6 - - + +
204K SER* 4.2 10.5 + - - -
207K PHE* 3.4 29.7 + - + -
208K LYS* 4.8 0.2 - - - -
209K ARG* 3.7 37.2 - - + -
211K PHE* 3.8 22.4 - + - -
242K SER* 1.3 72.3 - - - +
244K GLN* 1.3 63.7 + - - +
246K VAL* 3.1 8.1 + - + +
247K ALA* 3.0 21.7 + - - +
272K TYR* 3.7 3.8 - - - -
401K ADP 3.4 44.4 - + - -
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Residues in contact with GLN 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K LEU* 4.2 14.1 - - + +
204K SER 4.5 7.1 + - - +
205K GLU* 5.5 5.8 - - - +
242K SER* 3.1 13.8 - - - +
243K PHE* 1.3 78.0 - - - +
245K ALA* 1.3 56.7 + - - +
247K ALA* 3.3 7.2 + - - +
248K ASP* 2.8 65.5 + - - +
259K ILE* 4.2 12.9 - - - +
261K TYR* 3.9 17.6 + - - +
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Residues in contact with ALA 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K GLU* 4.1 27.8 - - + +
242K SER* 2.9 22.7 + - - +
244K GLN* 1.3 73.6 - - - +
246K VAL* 1.3 65.7 + - - +
248K ASP* 3.2 13.5 + - - +
249K ALA* 3.0 22.5 + - - +
295K VAL* 4.0 7.7 - - + +
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Residues in contact with VAL 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K VAL* 4.9 6.5 - - + -
185K ALA* 4.2 35.2 - - + +
188K LEU* 4.6 5.8 - - + -
211K PHE* 3.7 47.6 - - + -
242K SER 3.5 1.8 + - - +
243K PHE* 3.1 9.3 + - + +
245K ALA* 1.3 77.7 - - - +
247K ALA* 1.3 62.4 + - - +
249K ALA* 3.2 4.9 + - - +
250K THR* 3.0 26.0 + - - +
295K VAL* 3.8 19.7 - - + -
299K VAL* 4.2 8.9 - - + +
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Residues in contact with ALA 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K LEU* 3.8 17.0 - - + +
200K LEU* 4.3 5.8 - - + -
243K PHE 3.0 13.3 + - - +
244K GLN* 3.4 12.6 - - - +
246K VAL* 1.3 77.3 - - - +
248K ASP* 1.3 52.4 + - - +
250K THR* 3.2 1.9 + - - -
251K LEU* 2.8 41.0 + - + +
259K ILE* 3.4 37.0 - - + -
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Residues in contact with ASP 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244K GLN* 2.8 51.8 + - - +
245K ALA* 3.2 12.8 + - - +
247K ALA* 1.3 72.9 - - - +
249K ALA* 1.3 63.0 + - - +
251K LEU* 3.9 4.6 - - - +
252K ALA* 2.9 27.3 + - - +
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Residues in contact with ALA 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245K ALA 3.0 9.3 + - - +
246K VAL 3.2 7.6 + - - +
248K ASP* 1.3 79.7 - - - +
250K THR* 1.3 60.6 + - - +
252K ALA* 3.5 6.7 - - - +
253K TYR* 3.2 17.3 + - - +
295K VAL* 4.3 10.3 - - + +
296K ALA* 4.3 15.9 - - + +
299K VAL* 3.7 25.1 - - + +
300K THR* 3.7 15.7 - - + +
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Residues in contact with THR 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K ALA* 4.6 0.7 - - - -
188K LEU* 4.1 21.6 - - + +
189K ASN 4.5 1.8 - - - +
192K LEU* 3.9 21.5 - - + -
246K VAL* 3.0 17.3 + - - +
247K ALA* 3.5 9.6 - - - -
249K ALA* 1.3 73.3 - - - +
251K LEU* 1.3 65.4 + - + +
252K ALA 3.1 1.6 - - - -
253K TYR* 3.1 4.2 + - - +
254K HIS* 3.1 24.4 + - + +
299K VAL* 3.4 17.1 - - - +
303K MET* 3.6 30.8 - - + +
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Residues in contact with LEU 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K LEU* 5.5 1.1 - - + -
192K LEU* 3.8 22.9 - - + -
198K PRO* 3.9 19.3 - - + -
247K ALA* 2.8 29.7 + - + +
248K ASP* 4.2 4.0 - - - +
250K THR* 1.3 76.2 - - + +
252K ALA* 1.3 57.6 + - - +
254K HIS* 3.3 2.6 + - - +
255K LYS* 2.8 26.5 + - - -
256K LYS 3.5 17.9 + - - +
257K GLY 3.1 30.3 - - - +
258K GLN* 4.0 8.3 - - - +
259K ILE* 4.4 14.4 - - + +
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Residues in contact with ALA 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K ASP 2.9 19.4 + - - +
249K ALA* 3.5 8.7 - - - +
250K THR 3.1 0.2 - - - -
251K LEU* 1.3 77.8 - - - +
253K TYR* 1.3 62.2 + - - +
255K LYS* 3.2 25.8 - - - +
300K THR* 5.6 2.9 - - + -
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Residues in contact with TYR 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K ALA 3.2 10.6 + - - +
250K THR 3.1 9.4 + - - +
252K ALA* 1.3 80.7 - - - +
254K HIS* 1.3 75.2 + + - +
255K LYS* 3.2 11.6 + - - +
300K THR* 4.3 18.7 - - + +
303K MET* 3.5 39.4 + - + -
304K ALA* 3.4 31.8 + - + +
307K ASN* 4.0 22.6 - - + +
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Residues in contact with HIS 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K ASN* 2.8 32.7 + - - -
192K LEU* 3.8 37.5 - - + +
193K ASN* 3.4 23.2 + - - -
250K THR* 3.1 30.2 + - + +
251K LEU 3.3 3.1 + - - +
253K TYR* 1.3 88.3 - + - +
255K LYS* 1.3 68.7 + - - +
256K LYS* 3.0 28.7 + - + +
303K MET* 3.9 6.5 - - - -
307K ASN* 4.4 7.2 - - - -
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Residues in contact with LYS 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K LEU 2.8 10.4 + - - -
252K ALA* 3.2 24.4 + - - +
253K TYR 3.2 11.1 - - - +
254K HIS* 1.3 77.3 - - - +
256K LYS* 1.3 59.6 + - - +
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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