Contacts of the helix formed by residues 246 - 265 (chain A) in PDB entry 4XZC
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 LYS 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLY 3.4 1.6 - - - -
245A HIS* 1.3 78.8 - - - +
247A ARG* 1.3 59.1 + - - +
248A LEU 3.4 0.7 - - - -
249A GLU* 3.4 29.3 + - - +
250A ASP* 3.1 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ARG 5.0 2.2 + - - -
206A ALA* 4.1 19.5 + - + +
207A ALA* 4.4 24.0 - - - +
239A VAL* 4.2 13.0 - - + +
240A ALA* 5.3 1.1 - - - -
243A ASP* 3.9 38.1 + - + +
244A GLY 3.5 15.7 + - - +
245A HIS 2.7 3.2 + - - -
246A LYS* 1.3 75.9 - - - +
248A LEU* 1.3 55.8 + - - +
249A GLU 3.0 5.4 - - - -
250A ASP* 3.0 53.4 + - - +
251A ILE* 3.2 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A MET* 3.7 28.0 - - + +
237A VAL* 5.3 0.2 - - - -
239A VAL* 6.1 0.4 - - + +
240A ALA* 3.8 24.9 - - + +
245A HIS* 3.2 24.8 + - + +
247A ARG* 1.3 77.6 - - - +
249A GLU* 1.3 59.9 + - + +
251A ILE* 3.5 13.8 - - + +
252A ARG* 3.3 16.3 + - - +
285A LEU* 3.5 28.9 - - + +
288A ALA* 4.0 15.9 - - + -
289A ILE* 3.7 38.2 - - + +
292A ALA* 4.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS* 4.6 4.4 + - - -
246A LYS* 3.4 22.6 + - - +
247A ARG 3.0 1.0 - - - -
248A LEU* 1.3 76.2 - - + +
250A ASP* 1.3 65.6 + - - +
251A ILE 3.1 1.1 - - - -
252A ARG* 3.1 32.9 + - - +
253A LYS* 3.1 25.8 + - - +
289A ILE* 5.6 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 3.4 19.5 - - - +
246A LYS* 3.1 21.1 - - - +
247A ARG* 3.0 38.3 + - - +
249A GLU* 1.3 78.3 - - - +
251A ILE* 1.3 56.1 + - - +
253A LYS* 3.3 15.3 + - - +
254A THR* 2.8 31.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
202A GLY 4.0 17.5 - - - +
205A LEU* 4.1 17.7 - - + -
206A ALA* 3.5 28.5 - - + +
236A MET* 3.6 45.8 - - + -
239A VAL* 5.4 5.6 - - + -
247A ARG 3.2 6.6 + - - +
248A LEU* 3.5 17.0 - - + +
249A GLU 3.1 0.4 - - - -
250A ASP* 1.3 76.8 - - - +
252A ARG* 1.3 58.6 + - - +
254A THR* 3.6 5.9 - - - -
255A LEU* 2.9 33.2 + - + +
285A LEU* 3.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU 3.3 6.4 + - - +
249A GLU* 3.1 41.7 + - - +
251A ILE* 1.3 72.8 - - - +
253A LYS* 1.3 65.4 + - - +
255A LEU* 3.4 6.6 + - + +
256A LEU* 3.1 30.2 + - + +
285A LEU* 3.5 19.3 - - + +
289A ILE* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU 3.1 15.4 + - - +
250A ASP* 3.6 17.7 - - - +
251A ILE 3.3 0.2 - - - -
252A ARG* 1.3 76.9 - - - +
254A THR* 1.3 60.2 + - - +
256A LEU* 3.3 18.1 - - + +
257A ASP* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.0 46.4 + - + +
206A ALA 3.8 2.3 + - - -
208A GLY* 3.4 28.6 + - - +
210A PHE* 3.7 15.0 - - + +
250A ASP 2.8 21.2 + - - -
251A ILE 3.6 5.6 - - - -
252A ARG 3.1 0.2 - - - -
253A LYS* 1.3 74.2 - - - +
255A LEU* 1.3 60.2 + - - +
256A LEU 3.0 1.3 - - - -
257A ASP* 2.9 10.2 + - - +
258A LEU* 2.9 25.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
205A LEU* 4.6 13.9 - - + -
236A MET* 6.2 0.4 - - - -
251A ILE* 2.9 33.3 + - + +
252A ARG* 3.7 7.0 - - + +
254A THR* 1.3 76.4 - - - +
256A LEU* 1.3 57.1 + - - +
258A LEU* 3.3 10.7 + - + +
259A LYS* 2.9 28.8 + - - +
278A VAL* 5.1 6.5 - - + +
281A LEU* 3.7 38.1 - - + +
282A THR* 3.7 38.1 - - + +
285A LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 3.1 23.1 + - + +
253A LYS* 3.3 22.7 - - + +
254A THR 3.0 1.0 - - - -
255A LEU* 1.3 77.9 - - - +
257A ASP* 1.3 57.6 + - - +
259A LYS* 3.2 21.5 + - + +
260A LYS* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY* 5.4 1.8 - - - +
210A PHE* 4.0 22.2 - - + -
253A LYS* 3.0 24.5 + - - +
254A THR* 2.9 11.3 + - - +
256A LEU* 1.3 75.0 - - - +
258A LEU* 1.3 60.7 + - - +
260A LYS* 3.5 7.9 + - - +
261A TRP* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.4 35.7 - - + -
213A VAL* 3.7 12.6 - - + -
214A PHE* 4.1 19.5 - - + -
254A THR 2.9 12.4 + - - +
255A LEU* 3.4 14.6 - - + +
257A ASP* 1.3 77.2 - - - +
259A LYS* 1.3 56.8 + - - +
261A TRP* 2.9 18.4 + - + +
262A ILE* 2.9 31.2 + - + +
277A LEU* 4.3 5.6 - - + -
278A VAL* 4.2 15.7 - - + -
281A LEU* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU 2.9 14.0 + - - +
256A LEU* 3.2 24.1 + - + +
258A LEU* 1.3 75.1 - - - +
260A LYS* 1.3 59.2 + - - +
262A ILE* 3.3 3.8 + - - +
263A GLU* 3.0 38.2 + - + +
278A VAL* 4.1 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU 3.0 15.7 + - - +
257A ASP* 3.8 8.5 - - - +
259A LYS* 1.3 76.5 - - - +
261A TRP* 1.3 56.9 + - - +
263A GLU* 3.5 27.8 - - - +
264A ASP* 3.0 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.7 32.5 - + + -
214A PHE* 4.6 16.9 - + - -
257A ASP 3.0 13.5 + - - +
258A LEU* 2.9 11.5 + - + +
260A LYS* 1.3 76.4 - - - +
262A ILE* 1.3 76.2 + - + +
264A ASP* 3.1 11.2 + - + -
265A ASN* 3.1 44.2 + - + +
269A LEU* 5.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 5.4 2.0 - - + -
258A LEU* 2.9 34.9 + - + +
259A LYS* 3.9 3.8 - - - +
261A TRP* 1.3 80.5 - - + +
263A GLU* 1.3 57.2 + - - +
265A ASN 4.5 0.2 - - - +
266A LYS* 2.7 44.5 + - + +
269A LEU* 4.3 29.2 - - + -
273A LYS 5.4 0.7 - - - +
274A GLY* 3.6 30.1 - - - +
275A ASP* 4.8 7.9 - - - +
277A LEU* 4.9 5.4 - - + -
278A VAL* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 3.0 22.2 + - + +
260A LYS* 3.5 31.5 + - - +
262A ILE* 1.3 79.6 - - - +
264A ASP* 1.3 74.4 + - - +
265A ASN 3.4 0.9 + - - -
266A LYS* 4.2 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LYS* 3.0 54.6 + - - +
261A TRP* 3.1 5.1 + - + +
263A GLU* 1.3 88.1 - - - +
265A ASN* 1.3 73.2 + - - +
266A LYS 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TRP* 3.1 60.3 + - + +
262A ILE* 3.1 5.6 + - - -
264A ASP* 1.3 92.0 - - - +
266A LYS* 1.3 54.7 + - - +
267A ASP* 2.8 20.1 + - - +
268A GLU* 2.9 32.4 + - + +
269A LEU* 4.0 7.5 - - + +
----------------------------------------------------------
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