Contacts of the helix formed by residues 261 - 278 (chain g) in PDB entry 5M32
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 ILE 261 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204f VAL* 3.0 48.5 - - + +
205f ASP 4.0 10.5 - - - +
206f LYS* 4.6 4.4 - - - +
248f SER* 4.5 7.0 - - - +
249f ALA* 3.7 35.2 - - + +
252f GLU* 5.0 11.7 - - + -
253f ILE* 5.0 0.9 - - + -
259g MET 4.3 2.7 - - - +
260g PHE* 1.3 80.7 - - - +
262g GLY* 1.3 63.3 + - - +
263g ASP 3.6 0.4 + - - -
264g GLY 4.4 2.1 + - - -
265g ALA* 4.4 9.5 + - - +
305g GLU* 3.4 16.4 - - - +
308g ARG* 3.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 262 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204f VAL 4.4 4.7 - - - -
205f ASP* 4.2 8.5 - - - -
206f LYS* 3.9 27.1 - - - +
261g ILE* 1.3 80.5 - - - +
263g ASP* 1.3 59.2 + - - +
264g GLY 3.5 0.2 - - - -
265g ALA* 3.5 3.6 + - - +
266g LYS* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206f LYS* 4.2 22.3 + - - +
169g ASP* 4.8 7.1 - - - +
171g ARG* 4.3 12.6 + - - -
258g GLN* 3.2 31.2 - - + +
260g PHE* 4.3 22.9 - - + +
261g ILE 3.6 1.2 - - - -
262g GLY* 1.3 73.5 - - - +
264g GLY* 1.3 61.3 + - - +
266g LYS* 4.1 20.6 + - - +
267g LEU* 2.7 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256g LEU 2.8 28.1 - - - +
258g GLN* 4.9 8.5 - - - +
260g PHE 4.9 1.6 + - - -
261g ILE 4.4 3.2 + - - -
262g GLY 3.5 0.4 - - - -
263g ASP* 1.3 78.0 - - - +
265g ALA* 1.3 59.4 + - - +
267g LEU* 2.3 26.3 - - - +
268g VAL* 3.6 9.5 - - - +
305g GLU* 4.7 6.1 + - - -
309g THR* 3.9 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201f SER* 3.9 29.4 - - - +
204f VAL* 5.5 5.2 - - + +
261g ILE 4.4 10.5 + - - +
262g GLY* 3.5 6.8 + - - +
263g ASP 3.3 0.2 - - - -
264g GLY* 1.3 73.5 - - - +
266g LYS* 1.3 65.0 + - - +
267g LEU 3.1 2.2 - - - -
268g VAL* 3.2 12.2 - - - +
269g ARG* 3.5 8.8 + - - +
308g ARG* 4.6 7.0 - - + +
309g THR* 4.2 6.3 + - - +
312g GLU* 3.2 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168g TYR* 4.9 4.5 - - + +
169g ASP* 3.5 41.6 + - - +
262g GLY 2.9 21.1 + - - +
263g ASP* 4.1 22.6 + - - +
264g GLY 3.4 0.2 - - - -
265g ALA* 1.3 77.3 - - - +
267g LEU* 1.3 61.4 + - - +
269g ARG* 3.8 22.3 + - - +
270g ASP* 3.1 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169g ASP* 4.8 11.2 - - - +
171g ARG* 5.2 10.3 - - + +
172g VAL* 3.7 28.0 - - + +
251g LEU* 5.8 1.8 - - + -
255g GLN* 3.5 24.0 - - + +
256g LEU* 3.8 24.5 - - + +
258g GLN* 5.3 6.5 - - - +
263g ASP* 2.7 19.5 - - - +
264g GLY* 2.3 42.0 - - - +
265g ALA 3.1 0.8 - - - -
266g LYS* 1.3 83.2 - - + +
268g VAL* 1.3 61.5 + - - +
270g ASP* 4.4 2.0 - - - +
271g ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251g LEU* 4.9 3.6 - - + -
256g LEU* 3.7 40.8 - - + -
264g GLY 3.6 11.4 - - - +
265g ALA* 3.2 20.9 - - - +
267g LEU* 1.3 77.9 - - - +
269g ARG* 1.3 57.8 + - - +
271g ALA* 3.1 6.7 + - - +
272g PHE* 2.9 35.3 + - + -
309g THR* 4.4 14.8 - - + +
312g GLU* 3.3 13.5 - - - +
313g LEU* 3.9 28.5 - - + +
316g GLN* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199f VAL* 6.0 0.9 - - - -
201f SER 4.7 1.2 + - - -
202f SER* 3.7 31.9 + - - +
205f ASP* 5.8 2.4 + - - -
265g ALA* 3.5 12.9 + - - +
266g LYS* 4.0 25.8 + - - +
267g LEU 3.4 0.2 - - - -
268g VAL* 1.3 80.0 - - - +
270g ASP* 1.3 66.4 + - - +
272g PHE* 3.5 2.8 + - - +
273g ALA* 2.9 25.3 + - + +
312g GLU* 3.4 39.9 + - - +
316g GLN* 4.1 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167g GLU 4.9 1.5 - - - +
168g TYR* 3.7 36.7 - - + +
172g VAL* 4.0 6.6 - - + +
266g LYS* 3.1 41.5 + - + +
267g LEU* 3.8 5.2 - - - +
269g ARG* 1.3 86.4 + - - +
271g ALA* 1.3 59.4 + - - +
273g ALA* 3.6 11.8 - - - +
274g LEU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172g VAL* 3.7 16.6 - - + -
249g LEU* 4.3 14.6 - - + +
251g LEU* 4.7 20.0 - - + -
267g LEU 2.9 21.4 + - - +
268g VAL* 3.1 10.3 + - - +
270g ASP* 1.3 77.9 - - - +
272g PHE* 1.3 65.5 + - + +
274g LEU* 3.2 5.1 + - - +
275g ALA* 3.0 26.3 + - - +
283g ILE* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251g LEU* 5.9 2.9 - - + -
268g VAL* 2.9 17.5 + - + +
269g ARG 4.0 0.4 - - - +
271g ALA* 1.3 79.0 - - + +
273g ALA* 1.3 60.5 + - - +
275g ALA* 3.7 5.5 - - + +
276g LYS* 2.9 34.0 + - - +
283g ILE* 3.6 36.3 - - + -
285g ILE* 5.3 4.9 - - + -
313g LEU* 3.6 44.0 - - + -
316g GLN* 3.3 50.9 - - + +
317g LEU* 4.2 14.6 - - + -
326g VAL* 5.0 6.7 - - + +
328g VAL* 4.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168g TYR* 6.0 1.6 - - + -
269g ARG 2.9 18.6 + - - +
270g ASP* 3.7 17.5 - - + +
271g ALA 3.2 0.2 - - - -
272g PHE* 1.3 76.5 - - - +
274g LEU* 1.3 52.9 - - - +
276g LYS* 3.3 7.3 + - - +
277g GLU* 2.2 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168g TYR* 3.2 24.0 - - + +
172g VAL* 3.6 32.8 - - + +
173g LYS* 4.6 3.8 - - + -
176g GLU* 3.2 28.0 - - - +
247g THR* 5.7 3.8 - - + +
249g LEU* 4.2 17.9 - - + -
270g ASP 2.9 14.5 + - - +
271g ALA 3.4 8.3 - - - +
273g ALA* 1.3 76.0 - - - +
275g ALA* 1.3 58.5 + - - +
277g GLU* 3.3 12.3 + - - +
278g LYS* 2.9 58.3 + - + +
281g SER* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249g LEU* 4.5 4.3 - - + -
271g ALA 3.0 16.3 + - - +
272g PHE* 3.9 4.7 - - - +
273g ALA 3.3 0.2 - - - -
274g LEU* 1.3 80.3 - - - +
276g LYS* 1.3 57.5 + - - +
278g LYS* 5.1 0.2 - - - -
279g ALA* 2.8 31.0 + - - +
281g SER* 3.2 17.1 + - - +
283g ILE* 3.6 26.9 - - + -
326g VAL* 3.4 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272g PHE* 2.9 26.1 + - - +
273g ALA* 3.7 7.8 - - - +
274g LEU 3.2 0.2 - - - -
275g ALA* 1.3 76.6 - - - +
277g GLU* 1.3 65.3 + - - +
279g ALA* 3.4 16.4 + - - +
316g GLN* 4.5 13.9 + - - -
322g PRO* 3.9 33.0 + - - +
325g GLN* 4.4 22.7 + - + +
326g VAL* 4.1 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166g THR* 4.1 19.2 + - - +
168g TYR* 3.9 20.8 + - - -
273g ALA* 2.2 43.5 + - - +
274g LEU* 3.4 15.1 - - - +
276g LYS* 1.3 76.4 - - - +
278g LYS* 1.3 67.1 + - + +
279g ALA 3.3 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168g TYR* 5.0 5.0 + - - -
173g LYS* 6.3 2.1 - - - +
176g GLU* 4.7 12.3 - - - +
247g THR* 3.4 31.6 - - + +
274g LEU* 2.9 42.3 + - + +
275g ALA 3.7 1.3 - - - -
277g GLU* 1.3 86.0 + - + +
279g ALA* 1.3 66.6 + - - +
280g PRO* 3.4 2.9 - - - +
281g SER* 4.1 3.1 - - - +
----------------------------------------------------------
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