Contacts of the helix formed by residues 250 - 267 (chain A) in PDB entry 2AXZ
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 ASN 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.4 18.2 + - - +
248A ASP* 3.5 11.2 - - + +
249A LYS* 1.3 76.1 - - - +
251A ILE* 1.3 72.4 + - - +
252A ASP* 3.1 31.8 + - - +
253A SER* 2.8 27.1 + - - +
265D LYS* 4.5 11.7 - - - +
273D HIS* 4.9 4.0 - - - -
277D VAL* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 4.2 14.1 - - + -
249A LYS 4.3 0.2 - - - -
250A ASN* 1.3 75.9 - - - +
252A ASP* 1.3 68.5 + - - +
254A TYR* 3.1 3.8 + - + +
255A LEU* 2.8 33.4 + - + +
258D VAL* 3.5 42.6 - - + +
261D ILE* 4.3 11.7 - - + -
262D ASN* 3.1 33.2 - - + +
265D LYS* 4.6 0.9 - - + -
273D HIS* 4.0 19.3 - - + +
277D VAL* 4.5 9.4 - - + +
280D LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASN* 2.8 20.2 + - - +
251A ILE* 1.3 93.5 - - - +
253A SER* 1.3 63.7 + - - +
255A LEU* 3.2 9.6 + - - +
256A ASN* 2.9 34.9 + - - +
262D ASN* 4.4 2.9 - - - +
265D LYS* 3.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN* 3.2 47.8 + - - +
244A GLN* 3.7 20.7 + - - +
245A PHE* 3.7 13.2 + - - -
248A ASP* 6.0 1.2 - - - +
250A ASN* 2.8 26.5 + - - +
252A ASP* 1.3 73.5 - - - +
254A TYR* 1.3 60.7 + - - -
256A ASN* 3.3 0.6 + - - -
257A ALA* 3.1 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.8 20.2 - - + -
245A PHE* 3.5 44.7 - + + +
250A ASN 3.6 1.8 + - - -
251A ILE* 3.1 9.5 + - - +
253A SER* 1.3 75.3 - - - +
255A LEU* 1.3 68.2 + - - +
257A ALA* 3.0 7.6 + - - +
258A VAL* 3.0 44.9 + - + +
280A LEU* 3.7 17.8 - - + +
283A ILE* 6.1 1.3 - - + -
284A SER* 2.7 29.7 + - - -
251D ILE* 4.2 1.7 - - - +
254D TYR* 3.4 23.7 - + - -
255D LEU* 3.6 15.3 - - + +
258D VAL* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 2.8 24.4 + - + +
252A ASP* 3.6 9.0 - - - +
254A TYR* 1.3 75.7 - - - +
256A ASN* 1.3 60.7 + - - +
258A VAL* 3.2 14.5 + - + +
259A ASN* 2.8 29.2 + - - +
255D LEU* 6.2 1.1 - - + -
258D VAL* 4.1 21.1 - - + -
259D ASN* 4.4 15.0 - - - +
262D ASN* 3.7 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN* 3.2 39.3 + - + +
252A ASP* 2.9 20.8 + - - +
253A SER 3.4 0.7 - - - +
255A LEU* 1.3 76.8 - - - +
257A ALA* 1.3 66.0 + - - +
259A ASN* 3.1 11.3 + - - +
260A ILE* 2.9 29.6 + - - +
262B ASN* 6.0 0.2 - - - +
266B ILE* 4.3 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.9 20.4 - - + +
241A GLN* 4.0 6.9 - - + +
242A ILE* 3.6 35.9 - - + -
253A SER 3.1 8.0 + - - +
254A TYR 3.0 10.4 + - - +
256A ASN* 1.3 80.1 - - - +
258A VAL* 1.3 61.2 + - - +
260A ILE* 3.3 2.4 + - - +
261A ILE* 3.0 29.6 + - - +
280A LEU* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.0 41.1 + - + +
255A LEU* 3.5 13.9 - - + +
257A ALA* 1.3 77.3 - - + +
259A ASN* 1.3 63.5 + - - +
261A ILE* 3.1 10.7 + - + +
262A ASN* 2.9 35.1 + - - +
280A LEU* 4.2 11.4 - - + -
255D LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU 2.8 16.6 + - - +
256A ASN* 3.4 13.3 - - - +
258A VAL* 1.3 77.5 - - - +
260A ILE* 1.3 63.0 + - - +
262A ASN* 3.2 7.9 + - - +
263A ILE* 3.1 20.8 + - - +
259B ASN* 2.9 33.8 + - - +
262B ASN* 3.7 14.3 - - - +
263B ILE* 3.0 23.7 - - - +
266B ILE* 4.9 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.3 37.2 - - + +
235A GLU* 5.2 0.2 - - - -
237A ASN* 3.9 17.3 - - + +
238A TYR* 3.7 33.0 - - + +
241A GLN* 4.4 4.0 - - + -
256A ASN 2.9 20.3 + - - +
257A ALA 3.6 4.3 - - - +
259A ASN* 1.3 74.2 - - + +
261A ILE* 1.3 66.8 + - - +
263A ILE* 3.1 17.2 + - - +
264A PHE* 3.5 11.7 + - + -
263B ILE* 4.5 16.2 - - + -
266B ILE* 4.3 22.7 - - + -
267B ILE* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.7 37.2 - - + -
257A ALA 3.0 13.6 + - - +
258A VAL* 3.1 7.6 + - + +
260A ILE* 1.3 75.7 - - + +
262A ASN* 1.3 64.2 + - - +
264A PHE* 3.3 17.0 - - - +
273A HIS* 3.0 24.2 - - + +
276A LEU* 3.6 34.1 - - + +
277A VAL* 4.1 21.5 - - + +
280A LEU* 3.9 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 2.9 27.4 + - - +
259A ASN* 3.5 13.0 - - - +
260A ILE 3.1 0.2 - - - -
261A ILE* 1.3 75.6 - - - +
263A ILE* 1.3 61.3 + - - +
264A PHE 3.0 2.2 - - - -
265A LYS* 2.8 32.3 + - - +
266A ILE* 3.1 24.1 + - + +
273A HIS* 4.2 13.1 + - - -
277A VAL* 6.1 0.2 - - - +
259B ASN* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 4.4 16.6 - - + -
259A ASN 3.1 8.1 + - - +
260A ILE 3.1 10.7 + - - +
262A ASN* 1.3 75.2 - - - +
264A PHE* 1.3 65.5 + - - +
266A ILE* 3.2 12.7 + - + +
267A ILE* 3.1 24.9 + - + +
234B LEU* 3.3 28.9 - - + -
259B ASN* 3.7 18.8 - - - +
260B ILE* 3.5 37.5 - - + -
263B ILE* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.7 43.3 - + + -
234A LEU* 3.7 29.4 - - + -
235A GLU* 4.1 13.5 - - + -
260A ILE* 3.5 16.0 + - + -
261A ILE* 3.3 12.0 + - - +
262A ASN 3.0 0.4 - - - -
263A ILE* 1.3 78.6 - - - +
265A LYS* 1.3 59.6 + - - +
267A ILE* 3.3 11.1 - - + +
269A LYS* 3.0 46.5 + - + +
272A ILE* 3.4 31.4 - - + -
273A HIS* 4.0 12.6 - - + -
276A LEU* 3.6 19.5 - - + -
302A TYR* 4.6 6.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 2.8 17.7 + - + +
264A PHE* 1.3 78.0 - - - +
266A ILE* 1.3 72.2 + - - +
267A ILE 3.1 1.3 + - - -
268A GLY* 3.2 11.3 + - - -
270A GLU* 3.1 39.6 - - - +
273A HIS* 3.1 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 3.1 22.4 + - + +
263A ILE* 3.2 17.7 + - + +
265A LYS* 1.3 85.4 - - + +
267A ILE* 1.3 57.2 + - + +
268A GLY 3.4 0.6 + - - -
237B ASN* 3.3 11.4 + - - -
241B GLN* 3.9 22.2 - - - +
256B ASN* 4.4 28.7 - - + +
259B ASN* 3.8 26.2 - - + +
260B ILE* 4.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 4.2 13.7 - - + -
234A LEU* 4.9 5.8 - - + -
263A ILE* 3.1 18.8 + - + +
264A PHE* 3.3 15.9 - - + +
266A ILE* 1.3 78.5 - - + +
268A GLY* 1.3 58.5 + - - +
269A LYS* 3.6 18.5 + - + +
221B LYS* 3.8 10.4 + - - -
230B GLY 5.5 0.2 - - - +
233B ASP* 3.5 29.6 - - + +
234B LEU* 3.6 35.2 - - + -
237B ASN* 3.1 35.9 + - + +
260B ILE* 4.8 5.6 - - + -
----------------------------------------------------------
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