Contacts of the helix formed by residues 245 - 258 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C TYR* 1.3 72.9 - - - +
246C PRO* 1.3 67.4 - - + +
247C GLU* 2.7 40.4 - - + +
248C GLU* 2.6 50.6 + - - +
249C ILE* 2.9 12.9 + - - +
342L LYS* 5.4 8.9 - - - +
344L GLU* 4.9 5.0 + - - +
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Residues in contact with PRO 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR 3.8 4.0 - - - +
245C THR* 1.3 88.1 - - + +
247C GLU* 1.3 69.0 + - - +
249C ILE* 3.8 4.9 - - + +
250C ALA* 2.9 21.8 + - - +
282C PHE* 4.5 17.5 - - + +
283C ASN* 3.1 34.5 + - - +
286C ALA* 3.2 24.8 - - + +
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Residues in contact with GLU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C THR* 2.7 34.9 - - + +
246C PRO* 1.3 89.7 - - - +
248C GLU* 1.3 52.3 + - + +
250C ALA* 3.1 7.7 + - - +
251C MET* 2.8 38.1 + - - +
286C ALA* 4.1 15.5 - - - +
289C ARG* 5.0 10.2 + - - -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LEU* 3.6 13.3 - - + +
243C LYS 4.0 3.3 - - - +
244C TYR* 3.0 31.2 - - + +
245C THR* 2.6 45.8 + - - +
247C GLU* 1.3 78.9 - - + +
249C ILE* 1.3 60.5 + - - +
251C MET* 3.3 8.2 + - - +
252C ALA* 3.1 18.4 + - - +
289L ARG* 4.7 10.9 + - - -
342L LYS* 6.0 0.9 - - - +
344L GLU* 3.4 22.7 - - - +
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LEU* 4.4 9.6 - - + -
233C MET* 4.7 5.6 - - + -
234C VAL 3.5 20.4 - - - +
235C THR* 3.9 21.8 - - + -
236C PRO* 4.8 3.8 - - + -
244C TYR* 4.3 20.9 - - + +
245C THR 2.9 13.5 + - - +
246C PRO* 3.8 8.7 - - + +
248C GLU* 1.3 72.7 - - - +
250C ALA* 1.3 63.1 + - - +
252C ALA* 3.3 2.3 + - - +
253C THR* 2.9 39.8 + - - +
279C GLU* 5.9 2.0 - - - +
283C ASN* 3.8 37.0 - - + +
287C ILE* 5.5 0.9 - - + -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C PRO 2.9 19.4 + - - +
247C GLU* 3.4 5.2 - - - +
249C ILE* 1.3 76.8 - - - +
251C MET* 1.3 57.9 + - - +
253C THR* 4.4 0.2 - - - -
254C VAL* 2.9 37.6 + - - +
283C ASN 5.5 0.2 + - - -
286C ALA* 3.5 8.7 - - + +
287C ILE* 3.4 46.4 - - + +
290C CYS* 4.5 5.8 - - + -
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Residues in contact with MET 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C GLU 2.8 17.7 + - - +
248C GLU* 3.5 10.3 - - - +
249C ILE 3.2 0.2 - - - -
250C ALA* 1.3 75.8 - - - +
252C ALA* 1.3 53.7 + - - +
254C VAL* 4.2 0.9 - - - +
255C THR* 2.7 41.1 + - - +
290C CYS* 3.9 5.6 - - - -
291C PRO* 3.8 33.2 - - + -
292C LEU* 3.6 29.4 - - + -
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Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LEU* 3.9 13.7 - - + -
203C GLN* 3.4 24.3 - - - +
234C VAL* 3.3 25.6 - - + -
248C GLU 3.1 15.6 + - - +
249C ILE 3.8 1.6 - - - +
251C MET* 1.3 73.8 - - - +
253C THR* 1.3 60.2 + - - +
255C THR* 3.3 2.1 + - - -
256C ALA* 2.9 32.2 + - - +
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C ASN 5.2 0.4 - - - +
233C MET* 3.7 11.3 - - - +
234C VAL* 2.9 34.6 + - + +
249C ILE* 2.9 21.5 + - - +
250C ALA 3.8 2.7 - - - -
252C ALA* 1.3 77.1 - - - +
254C VAL* 1.3 63.8 + - + +
256C ALA* 3.4 1.6 + - - +
257C LEU* 3.0 27.3 + - + +
270C PHE* 3.3 39.7 - - + -
287C ILE* 3.8 14.4 - - + -
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA 2.9 21.2 + - - +
251C MET 4.2 0.2 - - - +
253C THR* 1.3 73.9 - - + +
255C THR* 1.3 68.0 + - - +
257C LEU* 3.3 7.0 + - + +
258C ARG* 2.9 43.4 + - + +
287C ILE* 3.8 30.1 - - + +
290C CYS* 4.0 20.0 - - + -
292C LEU* 3.8 15.0 - - + -
294C ARG* 3.8 23.1 - - + -
296C TRP* 6.0 1.1 - - + +
298C LEU* 4.3 8.1 - - + -
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLU* 4.4 4.5 - - - +
203C GLN* 3.7 7.6 - - - +
251C MET* 2.7 27.0 + - - +
252C ALA* 3.6 4.9 - - - -
254C VAL* 1.3 78.9 - - - +
256C ALA* 1.3 65.1 - - - +
258C ARG* 3.2 11.6 + - + +
259C ARG* 3.2 61.0 + - + +
292C LEU* 3.6 14.0 - - + +
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLN* 3.9 9.8 - - + +
206C THR* 4.1 13.7 - - + -
207C GLU* 3.7 28.7 - - + -
210C LEU* 5.2 1.1 - - - -
234C VAL* 4.0 11.4 - - + -
252C ALA 2.9 17.5 + - - +
253C THR 3.6 4.3 - - - +
255C THR* 1.3 76.6 - - - +
257C LEU* 1.3 64.5 + - + +
259C ARG* 3.1 14.0 + - - +
260C THR* 3.2 17.9 + - - +
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Residues in contact with LEU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C THR* 5.9 0.9 - - + -
210C LEU* 3.8 17.3 - - + -
229C LEU* 4.0 11.0 - - + -
231C PRO* 4.3 6.3 - - + -
253C THR* 3.0 19.1 + - + +
254C VAL* 3.8 7.0 - - - +
256C ALA* 1.3 78.3 - - + +
258C ARG* 1.3 58.8 + - - +
259C ARG 3.2 0.3 + - - -
260C THR* 4.0 2.9 - - - -
261C VAL* 2.8 50.3 + - + +
268C VAL* 3.8 15.7 - - + -
270C PHE* 3.5 34.5 - - + -
296C TRP* 3.4 16.4 - - + +
298C LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLU* 5.2 6.4 + - - +
262B PRO* 3.8 0.3 - - - +
263B PRO* 3.6 38.6 + - + +
264B ALA* 2.8 51.0 + - + +
295B PRO* 5.3 4.9 + - - +
254C VAL* 2.9 42.2 + - + +
255C THR* 3.4 12.8 - - + +
257C LEU* 1.3 76.0 - - - +
259C ARG* 1.3 58.3 + - + +
260C THR 3.4 0.7 - - - -
292C LEU* 4.0 20.2 - - - +
293C PRO* 3.0 47.8 + - - +
294C ARG* 6.3 0.2 - - + -
296C 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