Contacts of the helix formed by residues 253 - 264 (chain A) in PDB entry 3N4E
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 THR 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MSE 6.3 2.9 - - + -
87A PRO* 5.1 10.1 - - + -
88A GLU* 4.6 21.1 - - + +
92A THR* 4.8 7.2 - - + -
251A THR* 4.0 1.6 - - - +
252A TYR* 1.3 86.5 - - + +
254A LEU* 1.3 65.0 + - - +
255A GLN* 3.6 13.9 + - - +
256A ALA* 3.1 26.5 + - + +
257A LEU* 3.0 22.0 + - - +
275A MSE 3.6 9.3 - - - +
229B TYR* 5.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 1.3 73.2 - - - +
255A GLN* 1.3 75.8 + - - +
257A LEU* 3.2 8.5 + - - +
258A LYS* 3.0 22.9 + - - +
275A MSE 3.9 6.5 - - + +
280A GLY 6.0 0.2 - - - +
283A GLN* 3.8 54.5 - - + +
284A CYS* 3.9 13.0 - - - +
287A LEU* 3.6 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MSE 6.0 1.4 - - - +
253A THR* 3.7 17.0 + - - +
254A LEU* 1.3 92.9 + - + +
256A ALA* 1.3 61.6 + - - +
258A LYS* 3.2 18.1 + - + +
259A ASP* 2.9 31.3 + - - +
229B TYR* 3.1 57.0 - - + +
230B HIS* 3.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 6.0 2.9 - - + +
251A THR* 3.6 19.4 - - + +
252A TYR 4.9 2.0 - - - +
253A THR* 3.1 22.7 + - + +
255A GLN* 1.3 74.5 - - - +
257A LEU* 1.3 58.7 + - - +
259A ASP* 3.3 12.3 + - - +
260A LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY* 4.9 1.1 - - - -
251A THR* 3.5 19.4 - - + +
253A THR 3.0 14.8 + - - +
254A LEU* 3.2 11.4 - - - +
256A ALA* 1.3 76.1 - - - +
258A LYS* 1.3 61.5 + - - +
260A LEU* 3.2 11.6 + - + +
261A ILE* 3.0 32.4 + - + +
268A VAL* 3.9 34.3 - - + -
270A PRO* 4.1 17.9 - - + -
275A MSE 5.7 0.9 - - + -
284A CYS* 3.7 41.7 - - + +
287A LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 3.0 9.9 + - - +
255A GLN* 3.2 16.5 + - + +
257A LEU* 1.3 76.4 - - - +
259A ASP* 1.3 80.4 + - - +
261A ILE* 3.2 7.8 + - - +
262A LEU* 2.9 55.8 + - + +
287A LEU* 3.6 29.3 - - + +
291A HIS* 5.0 4.9 - - + +
229B TYR 5.7 0.4 + - - -
230B HIS* 5.6 3.8 - - - +
231B VAL 5.3 2.4 - - - +
232B GLY* 4.3 21.4 - - - +
233B ALA 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 4.3 8.8 - - + +
255A GLN 2.9 19.6 + - - +
256A ALA* 3.3 11.8 + - - +
258A LYS* 1.3 102.0 + - - +
260A LEU* 1.3 58.1 + - - +
262A LEU* 3.3 8.1 + - - +
263A SER* 2.9 30.5 + - - -
229B TYR 5.0 3.1 - - - +
231B VAL* 4.5 19.9 + - - +
232B GLY* 5.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 4.3 19.7 - - + +
234A MSE 4.3 8.7 - - + -
247A ALA* 3.7 22.0 - - + +
248A GLY* 3.7 30.5 - - - +
251A THR* 3.9 11.2 - - - +
256A ALA 2.9 14.2 + - - +
257A LEU* 3.4 13.5 - - + +
259A ASP* 1.3 74.1 - - - +
261A ILE* 1.3 62.2 + - - +
263A SER* 2.5 26.1 + - - +
265A VAL* 3.5 33.9 + - + -
268A VAL* 4.0 15.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
257A LEU* 3.0 24.8 + - + +
258A LYS* 3.6 6.7 - - - +
260A LEU* 1.3 73.4 - - - +
262A LEU* 1.3 67.9 + - + +
264A GLY 3.1 4.0 + - - -
265A VAL* 3.8 6.3 - - - +
266A ARG* 2.7 31.0 + - - +
268A VAL* 3.9 22.7 - - + -
287A LEU* 4.0 32.5 - - + +
288A ALA* 4.8 2.0 - - - -
291A HIS* 3.8 34.8 - - + +
293A VAL* 3.9 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 2.9 49.4 + - + +
259A ASP* 3.3 8.3 + - - +
261A ILE* 1.3 76.6 - - + +
263A SER* 1.3 62.1 + - - +
264A GLY* 3.2 2.1 + - - -
266A ARG* 5.0 2.9 + - - +
291A HIS* 4.0 28.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
231A VAL* 3.5 33.8 + - - +
232A GLY* 4.7 6.3 - - - +
235A GLY* 3.3 23.5 + - - -
236A GLU 4.0 1.4 + - - -
239A GLN* 4.7 2.3 - - - +
259A ASP 2.9 14.8 + - - -
260A LEU* 2.5 24.4 + - - +
262A LEU* 1.3 76.8 - - - +
264A GLY* 1.3 55.3 + - - +
265A VAL* 3.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLY 3.9 1.3 - - - -
238A ALA* 3.6 14.8 - - - +
239A GLN* 2.8 37.7 + - - -
261A ILE 3.1 4.8 + - - -
262A LEU 3.2 0.9 - - - -
263A SER* 1.3 81.0 + - - +
265A VAL* 1.3 64.9 + - - +
266A ARG* 3.3 18.5 + - - +
----------------------------------------------------------
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