Contacts of the helix formed by residues 245 - 258 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244D TYR* 1.3 73.2 - - - +
246D PRO* 1.3 66.7 - - + +
247D GLU* 2.7 40.4 - - + +
248D GLU* 2.6 53.2 + - - +
249D ILE* 2.9 12.6 + - - +
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Residues in contact with PRO 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D TYR 4.1 4.0 - - - +
245D THR* 1.3 91.2 - - + +
247D GLU* 1.3 69.6 + - - +
249D ILE* 3.8 4.8 - - + +
250D ALA 2.9 21.5 + - - -
282D PHE* 4.5 17.7 - - + +
283D ASN* 3.1 34.6 + - - +
286D ALA* 3.2 25.2 - - + +
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D THR* 2.7 35.1 - - + +
246D PRO* 1.3 90.9 - - - +
248D GLU* 1.3 52.9 + - + +
250D ALA* 3.1 6.7 + - - +
251D MET* 2.8 37.5 + - - +
286D ALA* 4.1 15.2 - - - +
289D ARG* 5.0 10.2 + - - -
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 3.7 11.9 - - + +
243D LYS 4.0 3.6 - - - +
244D TYR* 3.0 31.4 - - + +
245D THR* 2.6 45.9 + - - +
247D GLU* 1.3 78.1 - - + +
249D ILE* 1.3 61.0 + - - +
251D MET* 3.3 8.4 + - - +
252D ALA* 3.1 18.0 + - - +
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Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 4.4 10.5 - - + -
233D MET* 4.7 5.8 - - + -
234D VAL 3.5 21.4 - - - +
235D THR* 3.9 21.5 - - + -
236D PRO* 4.8 3.6 - - + -
244D TYR* 4.3 21.3 - - + +
245D THR 2.9 14.1 + - - +
246D PRO* 3.8 8.5 - - + +
248D GLU* 1.3 73.1 - - - +
250D ALA* 1.3 63.2 + - - +
252D ALA* 3.3 2.3 + - - +
253D THR* 2.9 38.6 + - - +
279D GLU* 5.9 2.0 - - - +
283D ASN* 3.8 36.3 - - + +
287D ILE* 5.5 0.9 - - + -
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO 2.9 19.7 + - - +
247D GLU* 3.4 5.6 - - - +
249D ILE* 1.3 76.4 - - - +
251D MET* 1.3 58.3 + - - +
254D VAL* 2.9 37.1 + - - +
286D ALA* 3.5 8.7 - - + +
287D ILE* 3.4 45.8 - - + +
290D CYS* 4.5 6.7 - - + -
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Residues in contact with MET 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D GLU 2.8 17.0 + - - +
248D GLU* 3.5 10.3 - - - +
249D ILE 3.2 0.2 - - - -
250D ALA* 1.3 76.8 - - - +
252D ALA* 1.3 54.2 + - - +
254D VAL* 4.0 0.9 - - - +
255D THR* 2.7 40.2 + - - +
290D CYS* 3.9 5.3 - - - -
291D PRO* 3.8 33.2 - - + -
292D LEU* 3.6 28.7 - - + -
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 3.9 14.1 - - + -
203D GLN* 3.4 24.5 - - - +
234D VAL* 3.3 25.8 - - + -
248D GLU 3.1 16.1 + - - +
249D ILE 3.8 1.3 - - - +
251D MET* 1.3 73.8 - - - +
253D THR* 1.3 61.3 + - - +
255D THR* 3.3 2.0 + - - -
256D ALA* 2.9 31.5 + - - +
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Residues in contact with THR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ASN 5.2 0.4 - - - +
233D MET* 3.7 11.4 - - - +
234D VAL* 2.9 34.4 + - + +
249D ILE* 2.9 22.1 + - - +
250D ALA 3.8 2.7 - - - -
252D ALA* 1.3 78.2 - - - +
254D VAL* 1.3 63.7 + - + +
256D ALA* 3.4 1.9 + - - +
257D LEU* 3.0 26.5 + - + +
270D PHE* 3.3 39.5 - - + -
287D ILE* 3.8 13.7 - - + -
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Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ALA 2.9 21.0 + - - +
251D MET 4.2 0.4 - - - +
253D THR* 1.3 74.4 - - + +
255D THR* 1.3 66.3 + - - +
257D LEU* 3.3 7.0 + - + +
258D ARG* 2.9 43.3 + - + +
287D ILE* 3.8 29.4 - - + +
290D CYS* 4.0 20.4 - - + -
292D LEU* 3.8 15.3 - - + -
294D ARG* 3.8 23.8 - - + -
296D TRP* 6.0 0.9 - - + +
298D LEU* 4.3 7.9 - - + -
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 4.1 5.2 - - - +
203D GLN* 3.7 7.9 - - - +
251D MET* 2.7 27.0 + - - +
252D ALA* 3.3 5.3 + - - -
254D VAL* 1.3 79.5 - - - +
256D ALA* 1.3 66.7 + - - +
258D ARG* 3.2 12.1 + - + +
259D ARG* 3.2 60.9 + - + +
292D LEU* 3.6 13.4 - - + +
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLN* 3.9 10.0 - - + +
206D THR* 4.1 13.9 - - + -
207D GLU* 3.7 28.0 - - + -
210D LEU* 5.2 1.3 - - - -
234D VAL* 4.0 11.4 - - + -
252D ALA 2.9 17.7 + - - +
253D THR 3.6 4.0 - - - +
255D THR* 1.3 77.2 - - - +
257D LEU* 1.3 63.4 + - + +
259D ARG* 3.1 14.7 + - - +
260D THR* 3.2 17.2 + - - +
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Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D THR* 5.9 1.1 - - + -
210D LEU* 3.8 17.9 - - + -
229D LEU* 4.0 11.0 - - + -
231D PRO* 4.3 6.1 - - + -
253D THR* 3.0 20.2 + - + +
254D VAL* 3.8 6.5 - - + +
256D ALA* 1.3 79.6 - - + +
258D ARG* 1.3 59.8 + - - +
259D ARG 3.2 0.7 + - - -
260D THR* 4.0 2.7 - - - -
261D VAL* 2.8 48.7 + - + +
268D VAL* 3.8 16.4 - - + -
270D PHE* 3.5 34.1 - - + -
296D TRP* 3.4 17.3 - - + +
298D LEU* 3.9 14.6 - - + -
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Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLU* 5.5 4.4 + - - +
262A PRO* 3.7 0.3 - - - +
263A PRO* 3.3 37.1 + - + +
264A ALA* 2.6 53.7 + - + +
295A PRO* 4.9 6.9 + - - +
254D VAL* 2.9 44.3 + - + +
255D THR* 3.4 13.0 - - + +
257D LEU* 1.3 75.3 - - - +
259D ARG* 1.3 55.7 + - + +
260D THR 3.4 0.4 - - - -
292D LEU* 4.0 19.1 - - - +
293D PRO* 3.0 48.8 + - - +
294D ARG* 6.3 0.2 - - + -
296D TRP* 3.8 14.3 - - + -
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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