Contacts of the helix formed by residues 276 - 289 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E GLY 3.8 0.8 + - - -
275E GLN* 1.3 75.1 - - - +
277E GLU* 1.3 67.4 + - - +
278E GLU* 3.0 5.9 + - - +
279E GLU* 3.0 32.8 + - - +
280E ALA* 2.9 21.0 + - - +
305E ALA* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E SER* 1.3 74.4 - - - +
278E GLU* 1.3 60.2 + - + +
280E ALA* 3.9 2.6 - - - +
281E SER* 2.9 14.4 + - - -
305E ALA* 3.5 24.4 - - - +
306E LEU 4.0 2.6 - - - +
308E ALA* 3.3 24.6 + - + +
309E SER* 2.8 50.5 + - - -
331E ARG* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E SER* 3.1 5.8 + - - +
277E GLU* 1.3 77.0 - - + +
279E GLU* 1.3 58.6 + - - +
280E ALA 3.1 2.0 - - - -
281E SER* 2.9 4.1 + - - -
282E PHE* 2.7 72.9 + - + -
331E ARG* 2.5 35.6 + - - -
343E TYR* 3.1 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E GLY 4.7 0.9 - - - +
275E GLN* 3.5 25.8 - - - +
276E SER* 3.0 35.8 + - - +
278E GLU* 1.3 76.2 - - - +
280E ALA* 1.3 56.9 + - - +
282E PHE* 3.9 5.0 - - - +
283E ASN* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E MET* 4.1 0.2 - - - +
272E SER* 4.4 2.5 - - - -
275E GLN* 3.6 19.4 + - + +
276E SER 2.9 16.1 + - - +
277E GLU 3.9 1.6 - - - +
279E GLU* 1.3 77.5 - - - +
281E SER* 1.3 57.5 + - - +
283E ASN* 3.8 1.0 - - - +
284E LEU* 2.8 26.9 + - - +
302E TYR* 3.1 40.8 + - + -
305E ALA* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E GLU 2.9 15.1 + - - -
278E GLU* 2.9 8.4 + - - -
280E ALA* 1.3 78.0 - - - +
282E PHE* 1.3 57.9 + - - +
285E ASN* 2.9 31.6 + - - +
331E ARG* 3.0 17.9 + - - -
334E VAL* 3.8 19.1 - - - -
335E ASN* 2.7 26.0 + - - -
338E ALA* 3.3 7.5 - - - +
343E TYR* 4.4 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E PRO* 4.5 15.6 - - + +
278E GLU* 2.7 55.1 + - + +
279E GLU* 3.9 5.8 - - - +
281E SER* 1.3 72.1 - - - +
283E ASN* 1.3 61.8 + - - +
285E ASN* 3.2 7.8 + - - +
286E ALA* 2.8 30.4 + - - +
343E TYR* 3.8 20.9 - + - -
344E GLU 6.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E MET* 3.7 20.2 - - - +
235E THR* 5.2 0.9 - - - +
246E PRO* 3.1 32.9 - - - +
249E ILE* 3.8 29.5 - - + +
250E ALA* 4.6 0.3 - - - +
275E GLN* 2.7 21.0 - - - +
279E GLU* 3.0 27.7 + - - +
280E ALA 3.9 0.7 - - - +
282E PHE* 1.3 77.6 - - - +
284E LEU* 1.3 64.1 + - - +
286E ALA* 3.2 5.9 + - - +
287E ILE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E MET* 4.1 5.1 - - + +
270E PHE* 4.2 13.5 - - + -
280E ALA 2.8 22.9 + - - +
281E SER 3.8 3.4 - - - +
283E ASN* 1.3 72.2 - - - +
285E ASN* 1.3 64.7 + - - +
287E ILE* 3.1 9.3 + - + +
288E ASN* 3.0 22.2 + - - +
298E LEU 3.3 26.2 - - - +
299E THR 3.8 11.4 - - - +
300E PHE* 3.7 41.5 - - + -
302E TYR* 3.5 9.6 - - + +
335E ASN* 4.0 14.1 - - - +
338E ALA* 3.7 12.1 - - + +
339E ALA* 4.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E SER 2.9 18.5 + - - +
282E PHE* 3.4 7.2 - - - +
284E LEU* 1.3 75.8 - - - +
286E ALA* 1.3 64.2 + - - +
288E ASN* 2.9 14.9 + - - +
289E ARG* 3.0 45.0 + - - +
338E ALA* 3.2 16.1 - - + +
341E GLY* 3.0 13.8 + - - -
343E TYR* 2.9 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E PRO* 3.2 38.6 - - + +
247E GLU* 4.1 14.1 - - - +
250E ALA* 3.5 8.2 - - + +
282E PHE 2.8 16.3 + - - +
283E ASN 3.5 7.6 - - - +
285E ASN* 1.3 75.3 - - - +
287E ILE* 1.3 57.5 + - - +
289E ARG* 2.9 25.1 + - - +
290E CYS* 3.0 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E MET* 4.0 24.5 - - + -
249E ILE* 5.3 1.1 - - + -
250E ALA* 3.4 26.0 - - - +
253E THR* 3.8 13.5 - - + -
254E VAL* 3.8 9.8 - - + +
270E PHE* 3.8 35.0 - - + -
283E ASN* 2.9 20.5 + - + +
284E LEU* 3.2 10.3 - - + +
286E ALA* 1.3 75.4 - - - +
288E ASN* 1.3 58.5 + - - +
290E CYS* 3.0 24.6 + - - +
294E ARG* 3.6 7.1 - - - -
298E LEU* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E LEU* 3.0 15.2 + - - +
285E ASN 2.9 4.7 + - - +
287E ILE* 1.3 72.6 - - - +
289E ARG* 1.3 59.8 + - - +
294E ARG* 2.8 35.3 + - - +
298E LEU* 2.8 39.1 + - - +
338E ALA 2.9 19.3 + - - +
339E ALA* 3.2 21.5 - - - +
340E GLN* 3.9 5.0 - - - +
341E GLY* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E GLU* 5.0 10.1 + - - -
285E ASN* 3.0 26.6 + - - +
286E ALA* 2.9 15.0 + - - +
288E ASN* 1.3 79.9 - - - +
290E CYS* 1.3 67.0 + - - +
291E PRO* 3.5 6.1 - - - +
294E ARG* 4.3 0.2 - - - -
341E GLY* 2.8 32.2 + - - +
344E GLU* 5.2 8.5 + - - -
----------------------------------------------------------
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