Contacts of the helix formed by residues 253 - 268 (chain A) in PDB entry 2PHA
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
----------------------------------------------------------
236A LEU* 3.8 4.0 - - - +
237A ASP* 5.5 0.2 - - - -
240A PHE* 4.0 18.2 - - + -
251A GLY 3.7 2.7 + - - -
252A LEU* 1.3 77.5 - - - +
254A TYR* 1.3 73.1 + - + +
255A ARG* 3.3 26.0 - - + +
256A GLU* 2.7 32.7 + - - +
257A GLY* 2.8 25.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
236A LEU* 5.5 2.9 - - - -
240A PHE* 3.5 39.1 - + + -
253A THR* 1.3 78.3 - - + +
255A ARG* 1.3 69.1 + - + +
257A GLY* 3.2 2.0 + - - -
258A LEU* 3.0 53.4 + - + +
294A ASN* 4.6 1.6 + - - +
295A THR* 3.3 46.0 - - + -
298A ALA* 3.1 27.4 - - + +
299A ILE* 5.5 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.3 16.0 - - + +
254A TYR* 1.3 88.0 - - + +
256A GLU* 1.3 58.3 + - + +
258A LEU* 3.2 1.9 + - - -
259A TYR* 2.8 27.4 + - - +
308A ARG* 3.3 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 4.4 4.0 - - - +
203A VAL* 3.3 27.1 - - - +
208A ILE* 3.7 29.3 + - + +
251A GLY 4.3 1.7 - - - +
252A LEU* 3.4 19.7 - - + +
253A THR* 2.7 45.6 + - - +
255A ARG* 1.3 77.2 - - + +
257A GLY* 1.3 57.8 + - - +
259A TYR* 3.6 3.6 - - - +
260A ILE* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 4.4 2.5 - - - -
236A LEU* 3.9 19.9 - - - +
252A LEU* 5.3 0.9 - - - -
253A THR 2.8 14.3 + - - -
254A TYR 3.2 3.6 + - - -
256A GLU* 1.3 76.4 - - - +
258A LEU* 1.3 60.3 + - - +
260A ILE* 3.5 9.8 - - - +
261A THR* 3.0 27.4 + - - +
299A ILE* 4.0 15.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
254A TYR* 3.0 43.9 + - + +
255A ARG 3.6 6.3 - - - +
257A GLY* 1.3 73.4 - - - +
259A TYR* 1.3 60.5 + - - +
261A THR* 3.3 3.3 + - - -
262A GLU* 2.9 38.0 + - + +
298A ALA* 3.8 37.5 - - + +
299A ILE* 4.1 11.2 - - + -
302A ALA* 4.4 7.4 - - + -
308A ARG* 3.7 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 3.3 38.8 - - + -
209A GLY* 3.7 31.0 + - - -
212A MET* 3.9 7.5 - - + +
255A ARG 2.8 18.0 + - - +
256A GLU 3.2 4.0 + - - +
258A LEU* 1.3 74.8 - - - +
260A ILE* 1.3 67.6 + - - +
262A GLU* 3.9 10.9 - - - +
263A GLU* 3.1 59.7 + - + +
308A ARG* 3.4 10.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
121A ILE* 5.2 2.9 - - + -
123A VAL* 4.1 23.6 - - + -
177A ILE* 4.1 23.3 - - + -
208A ILE* 3.1 28.5 - - + -
211A VAL* 5.4 0.4 - - + -
212A MET* 3.3 30.3 - - - +
229A LEU* 5.1 2.9 - - + -
231A PHE* 4.7 1.8 - - + -
252A LEU* 5.0 10.3 - - + -
256A GLU* 2.8 28.1 + - + +
257A GLY* 3.5 10.5 - - - +
259A TYR* 1.3 78.9 - - - +
261A THR* 1.3 67.8 + - + +
263A GLU 3.4 0.2 + - - -
264A ILE* 3.2 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 3.6 17.9 - - + -
231A PHE* 4.1 8.1 - - + -
257A GLY 3.0 15.7 + - - +
258A LEU* 3.3 8.0 + - - -
260A ILE* 1.3 77.8 - - + +
262A GLU* 1.3 58.6 + - - +
263A GLU 3.1 1.3 - - - -
264A ILE* 3.6 7.5 - - - +
265A TYR* 2.9 27.9 + - - +
299A ILE* 3.7 23.0 + - + +
302A ALA* 3.5 18.0 - - - +
303A CYS* 3.5 31.5 - - - -
----------------------------------------------------------
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 LEU* 2.9 26.0 + - - +
259A TYR* 3.9 11.0 - - + +
261A THR* 1.3 75.7 - - - +
263A GLU* 1.3 60.2 + - - +
265A TYR* 3.4 3.4 + - - +
266A LYS* 2.9 42.5 + - + +
302A ALA* 4.1 20.6 - - + +
306A LEU 4.1 6.8 - - - +
307A ALA* 3.9 7.8 - - + -
308A ARG* 3.1 64.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
212A MET* 3.9 17.4 - - + +
216A LEU* 4.2 13.9 - - + +
259A TYR* 3.1 53.4 + - + +
260A ILE 3.5 9.2 - - - +
261A THR 3.1 0.2 - - - -
262A GLU* 1.3 78.7 - - - +
264A ILE* 1.3 65.5 + - - +
266A LYS* 3.3 43.1 + - - +
267A THR* 3.3 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 4.3 24.9 - - + -
212A MET* 3.4 22.7 - - + -
216A LEU* 4.0 14.6 - - + -
227A ILE* 4.5 11.0 - - + -
229A LEU* 4.3 18.6 - - + -
260A ILE* 3.2 20.7 + - + +
261A THR* 3.6 10.1 - - - +
263A GLU* 1.3 75.1 - - - +
265A TYR* 1.3 64.3 + - - +
267A THR* 2.6 30.7 + - - +
268A GLY 3.8 0.5 + - - -
269A LEU 4.5 1.2 + - - -
270A LEU* 4.0 35.8 + - + -
303A CYS* 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 5.1 17.5 - - + -
44A GLU* 4.1 21.5 + - - -
261A THR 2.9 7.2 + - - +
262A GLU* 3.4 8.5 - - - +
264A ILE* 1.3 77.1 - - - +
266A LYS* 1.3 67.6 + - + +
268A GLY* 2.7 32.6 + - - -
270A LEU* 5.4 3.9 + - - +
302A ALA 3.3 19.1 - - - +
303A CYS 3.4 18.1 + - - +
304A PHE* 3.5 6.3 - + - -
305A GLY* 3.1 46.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 2.9 28.4 + - + +
263A GLU* 3.3 36.4 + - - +
265A TYR* 1.3 89.3 - - + +
267A THR* 1.3 59.1 + - - +
268A GLY* 3.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.7 34.1 - - + -
220A LEU* 4.2 15.3 - - + -
227A ILE* 3.9 6.5 - - + +
263A GLU 3.3 15.0 + - - +
264A ILE* 2.6 17.4 + - - +
265A TYR 2.9 0.8 + - - -
266A LYS* 1.3 76.8 - - - +
268A GLY* 1.3 61.0 + - - +
269A LEU* 2.9 33.0 + - - +
270A LEU 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 2.6 42.1 + - - -
265A TYR* 2.7 17.4 + - - -
266A LYS 3.1 1.9 - - - -
267A THR* 1.3 78.3 + - - +
269A LEU* 1.3 59.7 + - - +
270A LEU 3.5 2.9 - - - -
----------------------------------------------------------
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