Contacts of the helix formed by residues 254 - 269 (chain A) in PDB entry 4O5A
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 254 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.2 49.8 + - + +
252A TYR* 3.2 7.7 - - - +
253A ASP* 1.3 80.2 - - - +
255A ASP* 1.3 68.2 + - - +
256A VAL* 3.6 10.6 - - - +
257A MSE 2.9 29.8 + - - +
258A ALA* 3.3 13.9 + - - +
280A SER* 3.6 7.9 + - - -
281A TRP 3.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 1.3 75.7 + - - +
256A VAL* 1.3 81.7 + - - +
258A ALA* 3.2 4.2 + - - +
259A LEU* 3.0 23.4 + - - +
280A SER* 3.3 19.3 + - - +
281A TRP 4.6 1.2 + - - -
282A GLY 4.4 5.5 + - - +
283A ASP 4.7 1.5 - - - +
284A SER* 2.6 31.6 + - - +
286A MSE 3.4 22.4 - - - +
287A ASN* 3.9 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR 3.5 24.2 - - - +
230A PRO* 4.0 29.4 - - + -
254A ASN* 3.6 10.8 - - - +
255A ASP* 1.3 87.1 + - - +
257A MSE 1.3 63.1 + - + +
259A LEU* 3.5 6.8 + - + +
260A ALA* 2.9 26.2 + - - +
286A MSE 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.8 24.7 - - + +
195A ALA 4.1 2.2 - - - +
226A THR* 3.0 37.5 - - - +
228A TYR* 3.7 33.4 - - + +
229A THR 3.4 18.6 - - - +
230A PRO* 5.0 0.2 - - - -
233A GLY* 3.7 18.1 - - - -
252A TYR* 3.4 20.3 - - + -
253A ASP* 4.2 9.4 - - + +
254A ASN* 2.9 26.3 + - - +
256A VAL* 1.3 77.0 - - - +
258A ALA* 1.3 58.7 + - - +
260A ALA* 3.7 5.8 - - - +
261A GLY 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.5 28.7 - - + -
254A ASN 3.3 13.5 + - - +
255A ASP 3.2 9.0 + - - +
257A MSE 1.3 74.6 - - - +
259A LEU* 1.3 57.4 + - - +
261A GLY 3.4 0.9 + - - -
262A GLU* 2.8 30.1 + - - +
278A ILE* 4.0 14.7 - - + +
280A SER* 3.9 20.4 - - - -
294A ILE* 4.0 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP 3.0 16.0 + - - +
256A VAL* 3.7 8.7 - - + +
258A ALA* 1.3 77.0 - - - +
260A ALA* 1.3 62.1 + - - +
262A GLU* 3.2 20.5 + - - +
263A SER* 2.9 35.3 + - - +
286A MSE 3.9 29.4 - - + +
287A ASN* 5.8 0.2 - - - +
290A ALA* 3.9 20.6 - - + -
291A HIS 5.2 0.4 - - - +
294A ILE* 3.9 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 3.5 37.5 - - + +
234A ALA* 4.3 7.7 - - + +
256A VAL 2.9 17.9 + - - +
257A MSE 3.3 5.8 + - - +
259A LEU* 1.3 76.6 - - - +
261A GLY* 1.3 58.1 + - - +
263A SER* 3.4 8.0 + - - -
264A VAL* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY 4.9 0.6 + - - -
237A THR* 3.4 32.4 + - - +
252A TYR* 3.5 12.6 - - - -
257A MSE 2.8 14.0 + - - -
258A ALA 3.7 0.4 - - - -
260A ALA* 1.3 74.7 - - - +
262A GLU* 1.3 64.3 + - - +
264A VAL* 3.2 3.0 + - - +
265A ALA* 3.0 23.6 + - - +
276A LEU* 5.2 0.2 - - - +
278A ILE* 4.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA 2.8 19.9 + - - +
259A LEU* 3.2 12.4 + - - +
261A GLY* 1.3 72.0 - - - +
263A SER* 1.3 58.2 + - - +
265A ALA* 3.3 4.5 + - - +
266A SER* 3.0 33.6 + - - +
272A VAL* 4.1 14.4 - - + +
278A ILE* 3.6 21.5 - - + +
290A ALA* 3.5 9.2 - - - +
291A HIS 3.2 36.8 + - - +
292A PRO* 2.6 34.0 - - + +
294A ILE* 3.6 12.6 - - + +
336A SER* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 2.9 23.5 + - - +
260A ALA* 3.6 10.7 - - - -
262A GLU* 1.3 73.8 + - - +
264A VAL* 1.3 66.8 + - - +
266A SER* 3.3 6.8 + - - -
267A VAL* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 3.7 33.2 - - + +
237A THR* 3.8 19.5 - - + -
238A LYS* 3.8 35.2 - - + +
241A LEU* 4.4 4.7 - - + -
260A ALA 3.0 17.6 + - - +
261A GLY 3.2 7.8 + - - +
263A SER* 1.3 76.1 - - - +
265A ALA* 1.3 65.2 + - - +
267A VAL* 3.3 7.4 + - - +
268A LYS* 3.0 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 4.0 13.0 - - + -
261A GLY 3.0 13.1 + - - +
262A GLU 3.6 7.6 - - - +
264A VAL* 1.3 76.8 - - - +
266A SER* 1.3 62.6 + - - +
268A LYS* 3.1 2.7 + - - +
269A GLY 2.9 4.5 + - - -
270A VAL* 2.8 44.3 + - + +
272A VAL* 4.0 7.9 - - + -
276A LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 3.0 17.5 + - - +
263A SER* 3.7 10.0 - - - -
264A VAL 3.2 0.2 - - - -
265A ALA* 1.3 76.7 - - - +
267A VAL* 1.3 63.6 + - - +
269A GLY* 3.1 13.2 + - - -
270A VAL 4.3 5.1 + - - +
272A VAL* 5.4 3.8 + - - +
291A HIS* 4.6 15.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 3.0 24.4 + - - +
264A VAL* 3.8 7.0 - - - +
266A SER* 1.3 77.2 - - - +
268A LYS* 1.3 61.5 + - + +
269A GLY* 3.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LYS* 4.9 5.3 - - + +
241A LEU* 3.7 47.8 - - + -
242A SER* 3.6 17.7 + - - +
246A ARG* 5.9 0.9 - - - +
264A VAL* 3.0 23.4 + - + +
265A ALA* 3.1 5.8 + - - +
267A VAL* 1.3 78.9 - - - +
269A GLY* 1.3 59.0 + - - +
270A VAL* 3.3 14.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA 2.9 3.4 + - - -
266A SER 3.1 11.5 + - - -
267A VAL 3.2 1.2 + - - -
268A LYS* 1.3 78.3 - - - +
270A VAL* 1.3 64.2 + - - +
271A ARG* 3.4 9.8 + - - +
275A ASP* 3.9 6.1 - - - +
----------------------------------------------------------
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