Contacts of the helix formed by residues 276 - 289 (chain B) 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 SER 276 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY 3.8 0.6 + - - -
275B GLN* 1.3 76.8 - - - +
277B GLU* 1.3 67.4 + - - +
278B GLU* 3.0 5.6 + - - +
279B GLU* 3.0 32.9 + - - +
280B ALA* 2.9 21.5 + - - +
305B ALA* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 1.3 74.6 - - - +
278B GLU* 1.3 60.5 + - + +
280B ALA* 3.8 3.1 + - - +
281B SER* 2.9 13.9 + - - -
305B ALA* 3.5 24.6 - - - +
306B LEU 4.0 2.8 - - - +
308B ALA* 3.3 24.8 + - + +
309B SER* 2.8 50.0 + - - -
331B ARG* 2.8 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B SER* 3.1 5.2 + - - +
277B GLU* 1.3 77.1 - - + +
279B GLU* 1.3 58.2 + - - +
280B ALA 3.1 1.8 - - - -
281B SER* 2.9 3.8 + - - -
282B PHE* 2.7 73.7 + - + -
331B ARG* 2.5 35.0 + - - -
343B TYR* 3.1 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 5.9 2.1 - - - +
274B GLY 4.7 1.0 - - - +
275B GLN* 3.5 26.5 - - + +
276B SER* 3.0 36.1 + - - +
278B GLU* 1.3 75.6 - - - +
280B ALA* 1.3 57.7 + - - +
282B PHE* 3.9 5.2 - - - +
283B ASN* 3.0 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B SER* 4.4 2.9 - - - -
275B GLN* 3.6 20.5 + - + +
276B SER 2.9 16.1 + - - +
277B GLU 3.9 2.2 - - - +
279B GLU* 1.3 76.7 - - - +
281B SER* 1.3 57.4 + - - +
283B ASN* 3.8 0.9 - - - +
284B LEU* 2.8 26.3 + - - +
302B TYR* 3.1 40.6 + - + -
305B ALA* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU 2.9 14.6 + - - -
278B GLU* 2.9 8.6 + - - -
280B ALA* 1.3 77.3 - - - +
282B PHE* 1.3 57.2 + - - +
284B LEU* 4.5 0.2 - - - -
285B ASN* 2.9 31.2 + - - +
331B ARG* 3.0 17.6 + - - -
334B VAL* 3.8 18.6 - - - -
335B ASN* 2.7 26.6 + - - -
338B ALA* 3.3 7.7 - - - +
343B TYR* 4.4 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 4.5 15.4 - - + +
278B GLU* 2.7 55.1 + - + +
279B GLU* 3.9 5.4 - - - +
281B SER* 1.3 72.2 - - - +
283B ASN* 1.3 63.7 + - - +
285B ASN* 3.2 7.8 + - - +
286B ALA* 2.8 30.1 + - - +
343B TYR* 3.8 22.0 - + - -
344B GLU 6.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B MET* 3.7 19.9 - - - +
235B THR* 5.2 1.4 - - - +
246B PRO* 3.1 33.3 - - - +
249B ILE* 3.8 28.8 - - + +
250B ALA* 4.6 0.2 - - - +
275B GLN* 2.7 21.0 - - - +
279B GLU* 3.0 27.3 + - - +
280B ALA 3.9 0.2 - - - +
282B PHE* 1.3 76.5 - - - +
284B LEU* 1.3 63.6 + - - +
286B ALA* 3.2 6.0 + - - +
287B ILE* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B MET* 4.1 5.5 - - + +
270B PHE* 4.2 13.7 - - + -
280B ALA 2.8 22.9 + - - +
281B SER* 3.8 3.6 - - - +
283B ASN* 1.3 72.6 - - - +
285B ASN* 1.3 64.6 + - - +
287B ILE* 3.1 9.6 + - + +
288B ASN* 3.0 21.5 + - - +
298B LEU 3.3 25.6 - - - +
299B THR 3.8 12.3 - - - +
300B PHE* 3.7 40.8 - - + -
302B TYR* 3.5 9.4 - - + +
335B ASN* 4.0 14.4 - - - +
338B ALA* 3.7 12.6 - - + +
339B ALA* 4.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER 2.9 19.0 + - - +
282B PHE* 3.4 6.7 - - - +
284B LEU* 1.3 74.7 - - - +
286B ALA* 1.3 65.3 - - - +
288B ASN* 2.9 14.2 + - - +
289B ARG* 3.0 45.4 + - - +
338B ALA* 3.2 15.6 - - + +
341B GLY* 3.0 15.1 + - - -
343B TYR* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 3.2 39.0 - - + +
247B GLU* 4.1 13.7 - - - +
250B ALA* 3.5 7.6 - - + +
282B PHE 2.8 17.4 + - - +
283B ASN 3.4 6.7 - - - +
285B ASN* 1.3 72.7 - - - +
287B ILE* 1.3 58.1 + - - +
289B ARG* 2.9 26.0 + - - +
290B CYS* 3.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B MET* 4.0 24.2 - - + -
249B ILE* 5.3 1.3 - - + -
250B ALA* 3.4 24.7 - - - -
253B THR* 3.8 14.1 - - + +
254B VAL* 3.8 9.7 - - + +
270B PHE* 3.8 35.4 - - + -
283B ASN* 2.9 20.4 + - + +
284B LEU* 3.2 9.9 - - + +
286B ALA* 1.3 75.7 - - - +
288B ASN* 1.3 58.8 + - - +
290B CYS* 3.0 25.1 + - - +
294B ARG* 3.6 6.9 - - - -
298B LEU* 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 3.0 14.1 + - - +
285B ASN 2.9 4.1 + - - +
287B ILE* 1.3 73.5 - - - +
289B ARG* 1.3 60.0 + - - +
294B ARG* 2.8 33.4 + - - +
298B LEU* 2.8 39.5 + - - +
338B ALA 2.9 20.1 + - - +
339B ALA* 3.2 22.0 - - - +
340B GLN* 3.9 4.7 - - - +
341B GLY* 3.4 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 5.0 9.5 + - - -
285B ASN* 3.0 27.4 + - - +
286B ALA* 2.9 15.7 + - - +
288B ASN* 1.3 80.1 - - - +
290B CYS* 1.3 66.8 + - - +
291B PRO* 3.5 5.5 - - - +
294B ARG* 4.3 0.4 - - - -
341B GLY* 2.8 32.0 + - - +
344B GLU* 5.2 7.9 + - - -
----------------------------------------------------------
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