Contacts of the helix formed by residues 245 - 258 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244L TYR* 1.3 73.6 - - - +
246L PRO* 1.3 67.0 - - + +
247L GLU* 2.7 40.6 - - + +
248L GLU* 2.6 52.1 + - - +
249L ILE* 2.9 12.2 + - - +
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Residues in contact with PRO 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L TYR 3.8 4.2 - - - +
245L THR* 1.3 90.0 - - + +
247L GLU* 1.3 69.2 + - - +
249L ILE* 3.8 4.8 - - + +
250L ALA 2.9 22.0 + - - -
282L PHE* 4.5 18.2 - - + +
283L ASN* 3.1 33.4 + - - +
286L ALA* 3.2 25.4 - - + +
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Residues in contact with GLU 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245L THR* 2.7 34.9 - - + +
246L PRO* 1.3 90.3 - - - +
248L GLU* 1.3 53.2 + - + +
250L ALA* 3.1 7.1 + - - +
251L MET* 2.8 37.7 + - - +
286L ALA* 4.1 15.6 - - - +
289L ARG* 5.0 10.4 + - - -
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Residues in contact with GLU 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L LEU* 3.7 12.5 - - + +
243L LYS 4.0 3.3 - - - +
244L TYR* 3.0 30.2 - - + +
245L THR* 2.6 45.2 + - - +
247L GLU* 1.3 78.9 - - + +
249L ILE* 1.3 60.8 + - - +
251L MET* 3.3 8.3 + - - +
252L ALA* 3.1 18.5 + - - +
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Residues in contact with ILE 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L LEU* 4.4 10.5 - - + -
233L MET* 4.7 5.8 - - + -
234L VAL 3.5 20.8 - - - +
235L THR* 3.9 20.9 - - + -
236L PRO* 4.8 4.5 - - + -
244L TYR* 4.3 20.2 - - + +
245L THR 2.9 13.3 + - - +
246L PRO* 3.8 8.7 - - + +
248L GLU* 1.3 73.4 - - - +
250L ALA* 1.3 63.2 + - - +
252L ALA* 3.3 2.3 + - - +
253L THR* 2.9 39.6 + - - +
279L GLU* 5.9 2.2 - - - +
283L ASN* 3.8 36.1 - - + +
287L ILE* 5.5 1.3 - - + -
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Residues in contact with ALA 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L PRO 2.9 19.0 + - - +
247L GLU* 3.4 5.4 - - - +
249L ILE* 1.3 76.6 - - - +
251L MET* 1.3 58.0 + - - +
253L THR* 4.4 0.2 - - - -
254L VAL* 2.9 37.6 + - - +
283L ASN 5.5 0.2 + - - -
286L ALA* 3.5 8.5 - - + +
287L ILE* 3.4 46.4 - - + +
290L CYS* 4.5 6.1 - - + -
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Residues in contact with MET 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L GLU 2.8 17.5 + - - +
248L GLU* 3.5 9.6 - - - +
250L ALA* 1.3 77.9 - - - +
252L ALA* 1.3 53.7 + - - +
254L VAL* 4.2 0.9 - - - +
255L THR* 2.7 40.7 + - - +
290L CYS* 3.9 5.8 - - - -
291L PRO* 3.8 32.8 - - + -
292L LEU* 3.6 28.7 - - + -
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Residues in contact with ALA 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199L LEU* 3.9 15.0 - - + -
203L GLN* 3.4 24.3 - - - +
234L VAL* 3.3 25.4 - - + -
248L GLU 3.1 16.5 + - - +
249L ILE 3.8 1.3 - - - +
251L MET* 1.3 74.2 - - - +
253L THR* 1.3 61.0 + - - +
255L THR* 3.3 1.9 + - - -
256L ALA* 2.9 32.1 + - - +
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Residues in contact with THR 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L ASN 5.2 0.4 - - - +
233L MET* 3.7 10.8 - - - +
234L VAL* 2.9 34.1 + - + +
249L ILE* 2.9 20.7 + - - +
250L ALA 3.8 2.9 - - - -
252L ALA* 1.3 79.1 - - - +
254L VAL* 1.3 63.9 + - + +
256L ALA* 3.4 1.7 + - - +
257L LEU* 3.0 26.1 + - + +
270L PHE* 3.3 40.4 - - + -
287L ILE* 3.8 13.2 - - + -
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Residues in contact with VAL 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L ALA 2.9 22.0 + - - +
251L MET 4.2 0.4 - - - +
253L THR* 1.3 73.1 - - + +
255L THR* 1.3 66.6 + - - +
257L LEU* 3.3 7.1 + - + +
258L ARG* 2.9 44.5 + - + +
287L ILE* 3.8 29.2 - - + +
290L CYS* 4.0 20.2 - - + -
292L LEU* 3.8 14.1 - - + -
294L ARG* 3.8 22.7 - - + -
296L TRP* 6.0 0.9 - - - +
298L LEU* 4.3 8.1 - - + -
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Residues in contact with THR 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I GLU* 4.2 4.0 - - - +
203L GLN* 3.7 7.4 - - - +
251L MET* 2.7 27.4 + - - +
252L ALA* 3.6 5.1 - - - -
254L VAL* 1.3 80.5 - - - +
256L ALA* 1.3 65.5 + - - +
258L ARG* 3.2 11.7 + - + +
259L ARG* 3.2 61.4 + - + +
292L LEU* 3.6 13.2 - - - +
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Residues in contact with ALA 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203L GLN* 3.9 10.5 - - + +
206L THR* 4.1 13.0 - - + -
207L GLU* 3.7 28.9 - - + -
210L LEU* 5.2 1.1 - - - -
234L VAL* 4.0 11.4 - - + -
252L ALA 2.9 18.1 + - - +
253L THR 3.6 4.3 - - - +
255L THR* 1.3 76.6 - - - +
257L LEU* 1.3 64.1 + - + +
259L ARG* 3.1 14.9 + - - +
260L THR* 3.2 17.1 + - - +
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Residues in contact with LEU 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L THR* 5.9 0.4 - - + -
210L LEU* 3.8 17.7 - - + -
229L LEU* 4.0 11.0 - - + -
231L PRO* 4.3 6.1 - - + -
253L THR* 3.0 18.9 + - + +
254L VAL* 3.8 7.2 - - + +
256L ALA* 1.3 79.4 - - + +
258L ARG* 1.3 57.7 + - - +
259L ARG 3.1 0.7 + - - -
260L THR* 4.0 2.2 - - - -
261L VAL* 2.8 49.4 + - + +
268L VAL* 3.8 15.7 - - + -
270L PHE* 3.5 34.5 - - + -
296L TRP* 3.4 17.5 - - + +
298L LEU* 3.9 14.6 - - + -
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Residues in contact with ARG 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I GLU* 5.5 4.4 + - - +
262I PRO* 3.6 0.3 - - - +
263I PRO* 3.3 38.2 + - + +
264I ALA* 2.7 51.9 + - + +
295I PRO* 5.1 5.7 + - - +
254L VAL* 2.9 41.8 + - + +
255L THR* 3.4 13.5 - - + +
257L LEU* 1.3 76.6 - - - +
259L ARG* 1.3 57.3 + - + +
260L THR 3.4 0.2 - - - -
292L LEU* 4.0 20.4 - - - +
293L PRO* 3.0 48.2 + - - +
294L ARG* 6.3 0.4 - - + -
295L PRO* 5.7 0.2 - - - +
296L TRP* 3.8 13.5 - - + -
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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