Contacts of the helix formed by residues 245 - 258 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H TYR* 1.3 72.9 - - - +
246H PRO* 1.3 65.8 - - + +
247H GLU* 2.7 40.4 - - + +
248H GLU* 2.6 52.2 + - - +
249H ILE* 2.9 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H TYR 3.8 4.5 - - - +
245H THR* 1.3 88.8 - - + +
247H GLU* 1.3 69.8 + - - +
249H ILE* 3.8 4.6 - - + +
250H ALA* 2.9 22.0 + - - +
282H PHE* 4.5 17.9 - - + +
283H ASN* 3.1 34.1 + - - +
286H ALA* 3.2 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ARG* 5.8 9.9 - - - +
245H THR* 2.7 35.7 - - + +
246H PRO* 1.3 89.8 - - - +
248H GLU* 1.3 52.8 + - + +
250H ALA* 3.1 7.7 + - - +
251H MET* 2.8 37.9 + - - +
286H ALA* 4.1 14.9 - - - +
289H ARG* 5.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H LEU* 3.7 12.4 - - + +
243H LYS 4.0 3.3 - - - +
244H TYR* 3.0 31.7 - - + +
245H THR* 2.6 45.7 + - - +
247H GLU* 1.3 77.9 - - + +
249H ILE* 1.3 60.4 + - - +
251H MET* 3.3 8.5 + - - +
252H ALA* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H LEU* 4.4 9.9 - - + -
233H MET* 4.7 5.6 - - + -
234H VAL 3.5 21.0 - - - +
235H THR* 3.9 21.3 - - + -
236H PRO* 4.8 4.0 - - + -
244H TYR* 4.3 20.2 - - + +
245H THR 2.9 13.7 + - - +
246H PRO* 3.8 8.3 - - + +
248H GLU* 1.3 72.9 - - - +
250H ALA* 1.3 63.4 + - - +
252H ALA* 3.3 2.6 + - - +
253H THR* 2.9 38.6 + - - +
279H GLU* 5.9 2.2 - - - +
283H ASN* 3.8 36.6 - - + +
287H ILE* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H PRO 2.9 19.5 + - - +
247H GLU* 3.4 5.4 - - - +
249H ILE* 1.3 75.9 - - - +
251H MET* 1.3 58.7 + - - +
253H THR* 4.4 0.2 - - - -
254H VAL* 2.9 36.7 + - - +
283H ASN 5.2 0.2 - - - -
286H ALA* 3.5 8.5 - - + +
287H ILE* 3.4 45.5 - - + +
290H CYS* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ARG* 5.0 6.7 - - - +
247H GLU 2.8 17.2 + - - +
248H GLU* 3.5 11.0 - - - +
250H ALA* 1.3 75.8 - - - +
252H ALA* 1.3 53.7 + - - +
254H VAL* 4.0 1.0 - - - +
255H THR* 2.7 39.6 + - - +
290H CYS* 3.9 6.7 - - - -
291H PRO* 3.8 33.4 - - + -
292H LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H LEU* 3.9 15.7 - - + -
203H GLN* 3.4 24.8 - - - +
234H VAL* 3.3 24.7 - - + -
248H GLU 3.1 15.8 + - - +
249H ILE 3.8 1.6 - - - +
251H MET* 1.3 74.2 - - - +
253H THR* 1.3 61.6 + - - +
255H THR* 3.3 2.3 + - - -
256H ALA* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H ASN 5.2 0.4 - - - +
233H MET* 3.7 11.6 - - - +
234H VAL* 2.9 33.8 + - + +
249H ILE* 2.9 20.6 + - - +
250H ALA 3.8 2.7 - - - -
252H ALA* 1.3 77.6 - - - +
254H VAL* 1.3 64.0 + - + +
256H ALA* 3.4 2.4 + - - +
257H LEU* 3.1 25.4 + - + +
270H PHE* 3.3 40.4 - - + -
287H ILE* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H ALA 2.9 21.4 + - - +
251H MET 4.2 0.2 - - - +
253H THR* 1.3 73.3 - - + +
255H THR* 1.3 67.2 + - - +
257H LEU* 3.8 7.0 - - + +
258H ARG* 2.9 44.2 + - + +
287H ILE* 3.8 29.6 - - + +
290H CYS* 4.0 19.7 - - + -
292H LEU* 3.8 14.4 - - + -
294H ARG* 3.8 23.3 - - + -
296H TRP* 6.0 1.1 - - - +
298H LEU* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E GLU* 4.6 3.8 - - - +
203H GLN* 3.7 7.2 - - - +
251H MET* 2.7 28.6 + - - +
252H ALA* 3.6 4.3 - - - -
254H VAL* 1.3 78.9 - - - +
256H ALA* 1.3 66.2 + - - +
258H ARG* 3.2 12.6 + - + +
259H ARG* 3.2 62.2 + - + +
292H LEU* 3.6 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H GLN* 3.9 10.0 - - + +
206H THR* 4.1 13.9 - - + -
207H GLU* 3.7 28.9 - - + -
210H LEU* 5.2 1.3 - - - -
234H VAL* 4.0 11.7 - - + -
252H ALA 2.9 17.3 + - - +
253H THR 3.6 4.0 - - - +
255H THR* 1.3 77.7 - - - +
257H LEU* 1.3 63.6 + - + +
259H ARG* 3.1 14.6 + - - +
260H THR* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H THR* 5.9 0.9 - - + -
210H LEU* 3.8 17.7 - - + -
229H LEU* 4.0 11.2 - - + -
231H PRO* 4.3 6.3 - - + -
253H THR* 3.1 19.7 + - + +
254H VAL* 3.8 7.4 - - + +
256H ALA* 1.3 77.7 - - + +
258H ARG* 1.3 57.8 + - - +
259H ARG 3.2 0.5 + - - -
260H THR* 4.0 2.7 - - - -
261H VAL* 2.8 49.3 + - + +
268H VAL* 3.8 15.9 - - + -
270H PHE* 3.5 34.8 - - + -
296H TRP* 3.4 17.1 - - + +
298H LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E GLU* 5.2 7.1 + - - +
262E PRO* 3.8 0.5 - - - +
263E PRO* 3.7 38.9 + - + +
264E ALA* 2.9 44.2 + - + +
295E PRO* 5.4 3.6 + - - +
254H VAL* 2.9 43.1 + - + +
255H THR* 3.4 13.2 - - + +
257H LEU* 1.3 75.7 - - - +
259H ARG* 1.3 58.5 + - + +
260H THR 3.4 0.2 - - - -
292H LEU* 4.0 19.2 - - - +
293H PRO* 3.0 48.4 + - - +
296H TRP* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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