Contacts of the helix formed by residues 321 - 342 (chain X) in PDB entry 1M6E
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 GLY 321 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317X LEU* 3.0 27.1 + - - -
318X ASP 4.8 0.2 - - - -
320X PHE* 1.3 82.5 - - - +
322X GLU* 1.3 64.8 + - - -
323X ALA* 3.4 3.6 + - - -
324X ILE* 3.6 7.8 + - - +
325X ILE* 3.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313X GLU* 5.5 2.1 - - - +
317X LEU* 3.0 29.4 - - + +
321X GLY* 1.3 69.5 - - - -
323X ALA* 1.3 66.2 + - - +
324X ILE 3.0 9.6 + - - +
325X ILE* 3.4 18.7 - - + +
326X GLU* 4.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242X ILE* 3.4 25.6 - - + -
321X GLY 3.4 1.4 + - - -
322X GLU* 1.3 76.5 - - - +
324X ILE* 1.3 62.3 + - - +
326X GLU* 3.6 19.4 - - - +
327X ASP* 4.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233X LEU* 5.0 3.1 - - + -
236X MET* 4.1 13.0 - - + -
241X LEU* 5.9 2.0 - - + -
242X ILE* 3.2 31.4 - - + +
243X GLU* 3.2 32.1 - - + +
316X LEU* 6.4 1.6 - - + -
320X PHE* 3.2 34.3 - - + -
321X GLY 3.6 6.9 + - - +
322X GLU 3.0 0.6 + - - -
323X ALA* 1.3 74.8 - - - +
325X ILE* 1.3 65.5 + - + +
326X GLU* 2.6 28.6 + - - +
327X ASP* 2.9 17.3 + - - +
328X VAL* 3.3 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309X ARG* 3.6 23.3 - - - +
313X GLU* 4.0 25.6 - - + +
316X LEU* 5.3 4.7 - - + -
317X LEU* 3.0 55.2 - - + +
320X PHE* 6.4 0.2 - - + -
321X GLY 3.6 8.7 - - - +
322X GLU* 3.4 17.5 - - + +
324X ILE* 1.3 77.9 - - + +
326X GLU* 1.3 70.7 + - - +
327X ASP 3.2 0.2 - - - -
328X VAL* 3.0 26.3 + - + +
329X PHE* 3.1 14.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309X ARG* 4.9 8.2 + - - +
322X GLU 4.3 6.8 + - - +
323X ALA* 3.6 13.8 - - - +
324X ILE 2.6 12.0 + - - +
325X ILE* 1.3 81.8 - - - +
327X ASP* 1.3 84.2 + - - +
329X PHE* 3.3 9.7 + - - +
330X HIS* 3.3 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 327 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236X MET* 4.4 14.1 - - - -
241X LEU* 5.8 3.4 - - + -
323X ALA 4.0 5.2 - - - +
324X ILE* 2.9 10.9 + - - +
326X GLU* 1.3 99.1 - - - +
328X VAL* 1.3 64.8 + - - +
329X PHE 3.1 2.3 + - - -
330X HIS* 3.3 11.2 + - - +
331X ARG* 3.1 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229X LEU* 3.4 30.3 - - + -
232X ALA* 4.3 4.8 - - + +
233X LEU* 3.7 16.4 - - + -
236X MET* 3.6 23.4 - - + -
316X LEU* 4.8 10.5 - - + -
324X ILE* 3.3 21.7 + - + -
325X ILE* 3.0 22.6 - - + +
327X ASP* 1.3 76.0 - - - +
329X PHE* 1.3 68.5 + - + +
331X ARG* 4.2 3.0 - - - +
332X TYR* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229X LEU* 5.0 4.3 - - + -
305X ALA* 4.5 9.0 - - + +
308X MET 3.8 9.2 - - - -
309X ARG* 3.4 72.0 - - + +
312X ALA* 5.0 0.9 - - + -
313X GLU* 4.3 15.7 - - + -
316X LEU* 3.6 32.1 - - + -
325X ILE* 3.1 23.9 + - + +
326X GLU 4.0 2.0 - - - +
327X ASP 3.1 0.8 - - - -
328X VAL* 1.3 81.7 - - + +
330X HIS* 1.3 61.9 + - - +
331X ARG 3.2 0.7 - - - -
332X TYR* 3.6 28.9 - + - +
333X LYS* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 330 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326X GLU 3.3 12.3 + - - +
327X ASP* 3.3 15.5 + - - +
329X PHE* 1.3 77.3 - - - +
331X ARG* 1.3 71.7 + - + +
333X LYS* 3.2 36.0 + - - +
334X LEU* 3.4 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232X ALA* 4.3 14.1 - - + -
235X GLN* 3.4 16.1 - - - +
236X MET* 3.4 31.6 - - - +
239X GLU* 2.6 46.9 + - - -
241X LEU* 3.9 11.8 - - - +
327X ASP* 3.1 25.9 + - - +
328X VAL 4.2 2.9 - - - +
330X HIS* 1.3 85.1 - - + +
332X TYR* 1.3 68.1 + - - +
333X LYS 3.0 1.1 - - - -
334X LEU* 3.1 9.0 + - - +
335X LEU* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 332 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225X ILE* 2.5 52.7 + - + +
228X LEU* 3.7 14.4 - - + -
229X LEU* 3.4 36.3 - - + -
232X ALA* 3.9 10.9 - - + +
305X ALA* 4.9 3.4 - - + -
308X MET* 3.5 30.6 - - + +
328X VAL 3.0 19.3 + - - +
329X PHE* 3.6 29.2 - + - -
331X ARG* 1.3 79.3 - - - +
333X LYS* 1.3 64.4 - - - +
335X LEU* 3.3 3.0 + - - +
336X ILE* 2.9 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297X VAL 6.1 0.2 - - - +
301X GLY* 4.5 1.5 - - - -
302X TYR* 3.7 50.2 - - + +
305X ALA* 4.1 15.7 - - + -
329X PHE* 2.9 15.1 + - - +
330X HIS* 3.2 34.7 + - - +
331X ARG 3.0 0.2 - - - -
332X TYR* 1.3 78.5 - - - +
334X LEU* 1.3 74.7 + - + +
336X ILE* 3.3 5.2 + - - +
337X ILE* 3.0 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330X HIS* 3.4 38.8 + - + +
331X ARG* 3.1 9.7 + - - +
333X LYS* 1.3 96.5 - - + +
335X LEU* 1.3 73.5 + - + +
337X ILE* 3.2 16.7 + - + +
338X GLU* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228X LEU* 3.3 32.9 - - + +
231X MET* 4.4 26.7 - - + -
232X ALA* 5.0 6.3 - - + +
331X ARG* 3.0 24.4 + - + +
332X TYR* 3.3 9.2 + - - +
334X LEU* 1.3 81.8 - - + +
336X ILE* 1.3 58.3 + - - +
338X GLU* 3.9 7.4 - - - +
339X ARG* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225X ILE* 4.5 4.0 - - + -
228X LEU* 3.7 18.1 - - + +
284X TRP* 3.2 35.4 - - + -
300X GLU* 3.3 19.3 - - + +
304X VAL* 4.1 9.9 - - + -
305X ALA* 3.9 37.9 - - + +
332X TYR* 2.9 39.3 - - + +
333X LYS 3.4 7.0 - - - +
335X LEU* 1.3 72.9 - - - +
337X ILE* 1.3 56.4 + - - +
339X ARG* 3.4 2.4 - - + -
340X MET* 2.6 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X SER* 3.6 29.3 - - - +
297X VAL* 4.0 20.4 - - + +
300X GLU* 4.6 0.6 - - - +
301X GLY* 3.0 37.2 - - - +
333X LYS* 3.0 24.4 + - + +
334X LEU* 3.5 26.9 - - + +
336X ILE* 1.3 74.0 - - - +
338X GLU* 1.3 67.5 + - - +
340X MET* 2.8 24.4 - - - +
341X SER* 3.6 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 338 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334X LEU 2.9 19.3 + - - +
335X LEU* 3.9 6.8 - - - +
337X ILE* 1.3 74.8 - - - +
339X ARG* 1.3 68.1 + - - +
340X MET 2.6 12.3 + - - -
341X SER* 2.7 29.2 + - - +
342X LYS* 3.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X THR* 3.2 27.3 + - - +
224X LEU* 3.4 40.7 - - + +
228X LEU* 3.9 17.7 - - + -
231X MET* 5.5 5.0 - - + +
335X LEU 2.8 22.5 + - - +
336X ILE* 3.4 4.9 - - - +
338X GLU* 1.3 80.9 + - - +
340X MET* 1.3 60.9 + - - +
341X SER* 3.2 0.8 + - - -
342X LYS* 3.8 28.9 - - - +
343X GLU* 2.4 53.6 + - - +
345X THR* 4.1 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 340 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295X GLY 3.1 22.9 - - - +
296X SER* 2.5 41.7 - - - -
299X GLU* 3.1 29.6 - - + +
300X GLU* 2.8 48.8 - - + +
336X ILE 2.6 13.1 + - - +
337X ILE 2.8 12.6 - - - +
338X GLU 2.6 4.8 + - - -
339X ARG* 1.3 73.3 - - - +
341X SER* 1.3 54.4 + - - +
343X GLU 2.2 27.3 - - - +
345X THR* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296X SER* 4.7 8.7 + - - -
337X ILE* 3.7 7.1 + - - +
338X GLU* 2.7 16.5 + - - -
340X MET* 1.3 76.1 - - - +
342X LYS* 1.3 55.5 + - - -
343X GLU* 2.6 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338X GLU* 3.9 20.9 + - - +
339X ARG* 3.8 39.8 - - - +
341X SER* 1.3 76.2 - - - +
343X GLU* 1.3 91.9 + - - +
----------------------------------------------------------
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