Contacts of the helix formed by residues 245 - 258 (chain K) in PDB entry 1XFB
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 245 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244K TYR* 1.3 73.8 - - - +
246K PRO* 1.3 66.4 - - + +
247K GLU* 2.7 40.2 - - + +
248K GLU* 2.6 51.1 + - - +
249K ILE* 2.9 12.4 + - - +
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Residues in contact with PRO 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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244K TYR 3.8 4.0 - - - +
245K THR* 1.3 88.9 - - + +
247K GLU* 1.3 68.3 + - - +
249K ILE* 3.8 4.7 - - + +
250K ALA 2.9 22.5 + - - -
282K PHE* 4.5 18.6 - - + +
283K ASN* 3.1 33.0 + - - +
286K ALA* 3.2 25.0 - - + +
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Residues in contact with GLU 247 (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 THR* 2.7 35.2 - - + +
246K PRO* 1.3 91.2 - - - +
248K GLU* 1.3 53.0 + - + +
250K ALA* 3.1 7.0 + - - +
251K MET* 2.8 37.9 + - - +
286K ALA* 4.1 15.3 - - - +
289K ARG* 5.0 10.4 + - - -
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Residues in contact with GLU 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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199K LEU* 3.7 12.5 - - + +
243K LYS 4.0 3.1 - - - +
244K TYR* 3.0 31.5 - - + +
245K THR* 2.6 44.4 + - - +
247K GLU* 1.3 78.3 - - + +
249K ILE* 1.3 61.0 + - - +
251K MET* 3.3 8.8 + - - +
252K ALA* 3.1 18.5 + - - +
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Residues in contact with ILE 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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199K LEU* 4.4 10.5 - - + -
233K MET* 4.7 5.6 - - + -
234K VAL 3.5 20.5 - - - +
235K THR* 3.9 21.5 - - + -
236K PRO* 4.8 4.0 - - + -
244K TYR* 4.3 20.6 - - + +
245K THR 2.9 14.3 + - - +
246K PRO* 3.8 8.5 - - + +
248K GLU* 1.3 72.4 - - - +
250K ALA* 1.3 63.1 + - - +
252K ALA* 3.3 1.9 + - - +
253K THR* 2.9 39.4 + - - +
279K GLU* 5.9 2.0 - - - +
283K ASN* 3.8 37.5 - - + +
287K ILE* 5.5 1.1 - - + -
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Residues in contact with ALA 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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246K PRO 2.9 19.2 + - - +
247K GLU* 3.4 5.6 - - - +
249K ILE* 1.3 76.8 - - - +
251K MET* 1.3 57.7 + - - +
253K THR* 3.8 0.4 - - - -
254K VAL* 2.9 37.1 + - - +
286K ALA* 3.5 8.7 - - + +
287K ILE* 3.4 46.2 - - + +
290K CYS* 4.5 6.1 - - + -
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Residues in contact with MET 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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247K GLU 2.8 17.9 + - - +
248K GLU* 3.5 10.3 - - - +
250K ALA* 1.3 77.9 - - - +
252K ALA* 1.3 54.1 + - - +
254K VAL* 4.0 0.9 - - - +
255K THR* 2.7 40.4 + - - +
290K CYS* 3.9 5.4 - - - -
291K PRO* 3.8 33.2 - - + -
292K LEU* 3.6 30.0 - - + +
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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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199K LEU* 3.9 14.6 - - + -
203K GLN* 3.4 25.1 - - - +
234K VAL* 3.3 25.6 - - + -
248K GLU 3.1 15.6 + - - +
249K ILE 3.8 1.3 - - - +
251K MET* 1.3 73.8 - - - +
253K THR* 1.3 61.5 + - - +
255K THR* 3.3 2.0 + - - -
256K ALA* 2.9 31.7 + - - +
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Residues in contact with THR 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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232K ASN 5.2 0.4 - - - +
233K MET* 3.7 10.9 - - - +
234K VAL* 2.9 34.0 + - + +
249K ILE* 2.9 21.8 + - - +
250K ALA 3.8 2.7 - - - -
252K ALA* 1.3 78.4 - - - +
254K VAL* 1.3 64.4 + - + +
256K ALA* 3.4 1.7 + - - +
257K LEU* 3.0 26.0 + - + +
270K PHE* 3.3 40.2 - - + -
287K ILE* 3.8 13.7 - - + -
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Residues in contact with VAL 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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250K ALA 2.9 21.4 + - - +
251K MET 4.2 0.2 - - - +
253K THR* 1.3 73.3 - - + +
255K THR* 1.3 66.3 + - - +
257K LEU* 3.3 6.7 + - + +
258K ARG* 2.9 44.9 + - + +
287K ILE* 3.8 28.5 - - + +
290K CYS* 4.0 20.4 - - + -
292K LEU* 3.8 14.6 - - + -
294K ARG* 3.8 23.1 - - + -
296K TRP* 6.0 1.3 - - - +
298K LEU* 4.3 8.3 - - + -
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Residues in contact with THR 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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225J GLU* 4.1 5.2 - - - +
203K GLN* 3.7 7.4 - - - +
251K MET* 2.7 27.9 + - - +
252K ALA* 3.6 5.6 - - - -
254K VAL* 1.3 79.7 - - - +
256K ALA* 1.3 65.8 + - - +
258K ARG* 3.2 11.0 + - + +
259K ARG* 3.2 61.1 + - - +
292K LEU* 3.6 13.7 - - + +
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Residues in contact with ALA 256 (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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203K GLN* 3.9 10.3 - - + +
206K THR* 4.1 13.2 - - + -
207K GLU* 3.7 28.7 - - + -
210K LEU* 5.2 1.1 - - - -
234K VAL* 4.0 11.2 - - + -
252K ALA 2.9 17.3 + - - +
253K THR 3.6 4.5 - - - +
255K THR* 1.3 76.2 - - - +
257K LEU* 1.3 64.0 + - + +
259K ARG* 3.1 14.4 + - - +
260K THR* 3.2 17.2 + - - +
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Residues in contact with LEU 257 (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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206K THR* 5.9 1.1 - - + -
210K LEU* 3.8 17.9 - - + -
229K LEU* 4.0 10.8 - - + -
231K PRO* 4.3 5.8 - - + -
253K THR* 3.0 18.1 + - + +
254K VAL* 3.8 6.7 - - + +
256K ALA* 1.3 80.0 - - + +
258K ARG* 1.3 57.5 + - - +
259K ARG 3.2 0.7 + - - -
260K THR* 4.0 2.7 - - - -
261K VAL* 2.8 50.0 + - + +
268K VAL* 3.8 15.9 - - + -
270K PHE* 3.5 34.8 - - + -
296K TRP* 3.4 16.6 - - + +
298K LEU* 3.9 14.4 - - + -
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Residues in contact with ARG 258 (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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225J GLU* 5.4 5.8 + - - +
263J PRO* 3.5 36.5 + - + +
264J ALA* 2.5 56.6 + - + +
295J PRO* 5.1 6.1 + - - +
254K VAL* 2.9 42.7 + - + +
255K THR* 3.2 13.9 + - + +
257K LEU* 1.3 76.6 - - - +
259K ARG* 1.3 51.4 + - + +
260K THR 3.4 0.4 - - - -
292K LEU* 4.0 19.6 - - - +
293K PRO* 3.0 48.6 + - - +
294K ARG* 6.3 0.4 - - + -
295K PRO* 5.7 0.2 - - - +
296K TRP* 3.8 13.7 - - + -
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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