Contacts of the helix formed by residues 252 - 273 (chain A) in PDB entry 3PMM
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 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.6 25.3 - - + +
249A PRO* 3.1 27.8 + - + +
250A GLU 3.3 1.8 + - - -
251A GLY* 1.3 77.4 - - - +
253A ALA* 1.3 61.2 + - - +
254A VAL* 2.9 32.6 + - - +
255A ARG* 3.0 15.2 + - + +
256A ARG* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLY 3.2 5.7 + - - +
252A ASN* 1.3 74.1 + - - +
254A VAL* 1.3 60.2 + - + +
256A ARG* 3.8 8.0 - - - +
257A TYR* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 3.8 30.5 - - + -
197A LEU* 4.9 20.6 - - + -
242A PHE* 5.6 1.1 - - + -
248A LEU* 4.3 13.5 - - + -
252A ASN* 2.9 11.4 + - - +
253A ALA* 1.3 76.9 - - + +
255A ARG* 1.3 66.4 + - - +
257A TYR* 3.8 3.9 - - - +
258A LEU* 3.0 41.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
243A LEU* 4.0 20.6 - - + +
248A LEU* 3.2 40.5 + - + +
249A PRO 3.3 21.3 - - - -
250A GLU* 3.8 32.1 + - - +
251A GLY 4.7 2.6 - - - +
252A ASN* 3.0 14.1 + - + +
254A VAL* 1.3 76.7 - - - +
256A ARG* 1.3 65.0 + - - +
258A LEU 3.4 0.5 + - - -
259A ILE* 3.0 55.0 + - + +
308A LYS 5.3 2.0 + - - -
309A ARG 5.8 1.0 + - - -
310A TYR* 3.8 24.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLY* 4.8 20.3 + - - +
252A ASN 2.9 16.9 + - - +
253A ALA* 3.8 7.4 - - - +
255A ARG* 1.3 81.5 - - - +
257A TYR* 1.3 57.6 + - - +
259A ILE* 3.4 8.7 + - - +
260A THR* 2.9 31.4 + - - +
381A FMT 3.0 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.1 26.2 - - + -
200A VAL* 3.5 29.0 - - + +
204A MSE 4.3 7.3 - - - +
253A ALA 2.8 20.1 + - - +
254A VAL* 3.9 4.9 - - - +
256A ARG* 1.3 76.2 - - - +
258A LEU* 1.3 69.6 + - + +
260A THR* 3.1 17.6 + - + -
261A VAL* 2.9 44.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
193A THR* 5.7 0.4 - - + -
196A PHE* 4.3 30.1 - - + -
197A LEU* 4.7 7.2 - - + -
200A VAL* 4.6 15.3 - - + -
239A ILE* 3.8 16.8 - - + +
242A PHE* 3.9 33.7 - - + -
243A LEU* 4.2 17.0 - - + -
246A VAL* 6.2 0.2 - - + -
248A LEU* 6.3 0.2 - - + -
254A VAL* 3.0 32.7 + - + +
255A ARG 4.0 2.7 - - - +
257A TYR* 1.3 88.2 - - + +
259A ILE* 1.3 59.0 + - - +
261A VAL* 3.4 6.5 + - + +
262A LEU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.5 21.1 - - + -
255A ARG* 3.0 59.6 + - + +
256A ARG* 3.7 6.7 - - + +
258A LEU* 1.3 75.6 - - - +
260A THR* 1.3 60.7 + - - +
262A LEU* 3.2 6.1 + - - +
263A ASP* 2.8 32.7 + - + +
310A TYR* 3.3 45.1 - - + +
311A VAL* 5.1 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 2.9 17.3 + - - +
257A TYR* 3.1 25.0 + - + +
259A ILE* 1.3 78.5 - - - +
261A VAL* 1.3 58.5 + - + +
263A ASP* 3.4 6.2 + - - +
264A ALA* 3.0 30.3 + - + +
381A FMT 3.9 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 4.2 15.7 - - + -
204A MSE 4.5 13.5 - - + -
209A GLY 4.9 1.0 - - - +
211A TRP* 3.8 34.3 - - + +
239A ILE* 4.4 9.4 - - + -
257A TYR* 2.9 53.4 + - + +
258A LEU* 3.6 10.5 - - + +
260A THR* 1.3 77.9 - - + +
262A LEU* 1.3 63.2 + - - +
264A ALA* 3.4 7.3 + - - +
265A GLN* 3.1 21.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
236A THR* 4.1 28.5 - - + +
239A ILE* 4.0 24.9 - - + +
240A PRO* 3.9 17.5 - - + -
243A LEU* 4.7 2.2 - - + -
258A LEU 2.9 17.2 + - - +
259A ILE* 3.6 4.9 - - - +
261A VAL* 1.3 76.6 - - - +
263A ASP* 1.3 58.5 + - - +
265A GLN* 3.2 8.1 + - - +
266A ILE* 2.9 48.7 + - + +
305A ALA* 3.8 24.7 - - + -
310A TYR* 4.5 13.7 - - + -
311A VAL* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 2.8 24.7 + - + +
260A THR* 3.7 7.0 - - - +
262A LEU* 1.3 73.0 - - - +
264A ALA* 1.3 58.0 + - - +
266A ILE* 3.8 2.3 - - - +
267A ALA* 2.8 31.0 + - - +
310A TYR 4.7 1.4 - - - +
311A VAL* 3.5 34.0 - - + +
312A GLY 4.6 1.4 + - - -
315A TYR* 4.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MSE 6.1 4.3 - - + -
208A THR 4.5 0.3 - - - +
209A GLY* 4.1 18.5 - - - +
260A THR* 3.0 19.0 + - + +
261A VAL* 3.7 7.2 - - - +
263A ASP* 1.3 77.8 - - - +
265A GLN* 1.3 62.2 + - - +
267A ALA* 3.6 6.3 + - - +
268A ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY 3.3 21.2 + - - +
210A LEU* 4.1 11.9 - - + -
211A TRP* 4.2 10.4 - - + +
232A ASN* 3.0 49.7 + - - +
235A LEU* 4.2 10.0 - - - +
236A THR* 2.7 36.3 + - - +
239A ILE* 5.8 1.4 - - + +
261A VAL* 3.1 12.8 + - + +
262A LEU* 3.2 11.7 + - - +
264A ALA* 1.3 76.2 - - - +
266A ILE* 1.3 58.8 + - - +
268A ALA* 3.1 3.5 + - - +
269A LEU* 2.9 38.8 + - + +
298A PHE* 4.5 1.0 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
236A THR* 4.2 13.0 - - + -
262A LEU* 2.9 42.0 + - + +
263A ASP* 3.9 4.0 - - - +
265A GLN* 1.3 77.1 - - - +
267A ALA* 1.3 57.2 + - - +
269A LEU* 3.2 6.5 + - + +
270A ALA* 2.8 29.2 + - + +
302A ILE* 3.9 38.8 - - + -
305A ALA* 4.2 17.7 - - + -
311A VAL* 4.2 10.3 - - + -
315A TYR* 3.6 35.7 - - + -
318A VAL* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 2.8 21.4 + - - +
264A ALA* 3.8 8.1 - - - +
266A ILE* 1.3 78.8 - - - +
268A ALA* 1.3 61.9 + - - +
270A ALA* 3.4 3.6 + - - +
271A GLU* 3.3 21.4 + - - +
315A TYR* 3.4 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A THR* 3.3 26.9 - - - +
209A GLY 4.6 0.2 - - - -
210A LEU* 3.6 20.9 - - + -
264A ALA 3.1 9.9 + - - +
265A GLN* 3.1 9.4 + - - +
267A ALA* 1.3 76.7 - - - +
269A LEU* 1.3 62.9 + - - +
271A GLU* 3.1 21.8 + - - +
272A CYS* 3.2 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.1 7.0 - - + -
236A THR* 4.0 15.3 - - + +
265A GLN* 2.9 30.7 + - + +
266A ILE* 3.2 9.2 + - - +
268A ALA* 1.3 73.6 - - - +
270A ALA* 1.3 66.6 + - - +
272A CYS* 3.1 3.5 + - - -
273A GLN* 3.1 11.3 + - - +
279A TRP* 2.8 46.3 + - + +
283A LEU* 4.0 17.7 - - + -
298A PHE* 3.4 52.5 - - + -
302A ILE* 4.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE 2.8 16.9 + - - +
267A ALA* 3.7 7.0 - - - +
269A LEU* 1.3 76.2 - - - +
271A GLU* 1.3 60.2 + - - +
273A GLN* 3.8 13.0 + - - +
279A TRP* 4.9 0.2 - - - -
315A TYR* 4.0 13.9 - - + -
318A VAL* 3.7 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA 3.3 9.2 + - - +
268A ALA* 3.1 14.9 + - - +
269A LEU 3.1 0.6 - - - -
270A ALA* 1.3 82.2 - - - +
272A CYS* 1.3 59.2 + - + +
273A GLN 4.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.7 7.4 - - - -
268A ALA 3.2 17.4 + - - +
269A LEU* 3.1 9.9 + - - -
271A GLU* 1.3 77.0 - - + +
273A GLN* 1.3 64.3 + - - +
274A ASP* 3.5 2.4 + - - -
279A TRP* 3.8 21.9 - - - -
280A HIS* 4.3 15.4 - - - -
283A LEU* 3.7 36.4 - - - +
284A ASP* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU 3.1 8.6 + - - +
270A ALA 3.8 9.0 + - - +
271A GLU 3.5 4.1 - - - +
272A CYS* 1.3 77.6 - - - +
274A ASP* 1.3 73.6 + - - +
275A ASP* 3.9 2.6 + - - +
277A GLY* 3.1 30.3 + - - +
278A LEU 4.0 0.4 - - - +
279A TRP* 3.5 35.8 - - + +
318A VAL* 3.1 44.0 + - - +
321A LYS* 3.7 14.6 - - - +
322A ALA 3.6 6.7 - - - +
----------------------------------------------------------
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