Contacts of the helix formed by residues 293 - 307 (chain M) in PDB entry 6CET
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 LYS 293 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M VAL* 1.3 80.8 - - + +
294M ASN* 1.3 77.9 + - - +
296M GLN* 3.1 25.3 + - - +
297M GLN* 2.9 37.0 + - - +
468M ALA* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M VAL 3.5 1.6 - - - +
293M LYS* 1.3 94.8 - - - +
295M LEU* 1.3 57.8 + - - +
297M GLN* 3.4 19.8 - - - +
298M LEU* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M VAL* 3.2 37.4 - - + +
294M ASN* 1.3 76.4 - - - +
296M GLN* 1.3 72.0 + - + +
298M LEU* 3.9 3.5 - - - +
299M ALA* 3.0 29.3 + - - +
488M ALA* 3.4 39.9 - - + +
494M GLU* 4.0 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 296 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292M VAL* 3.0 27.3 + - + +
293M LYS* 3.1 30.5 + - - +
295M LEU* 1.3 83.5 - - + +
297M GLN* 1.3 60.3 + - - +
299M ALA* 3.7 6.6 - - - +
300M GLN* 2.9 65.0 + - - +
470M LEU* 4.9 17.2 - - + +
472M PRO* 6.0 5.5 - - - +
478M LEU* 5.8 0.9 - - - +
479M ASN* 6.2 0.2 - - - +
488M ALA* 5.6 4.9 - - + -
494M GLU* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 297 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293M LYS* 2.9 28.3 + - - +
294M ASN* 3.4 24.4 - - - +
295M LEU 3.2 0.2 - - - -
296M GLN* 1.3 77.2 - - - +
298M LEU* 1.3 64.3 + - + +
300M GLN* 3.2 20.1 - - - +
301M ASP* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294M ASN* 2.9 21.1 + - + +
295M LEU* 4.3 3.1 - - - +
297M GLN* 1.3 78.1 - - + +
299M ALA* 1.3 57.4 + - - +
301M ASP* 3.8 12.1 - - + +
302M ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295M LEU 3.0 20.9 + - - +
296M GLN* 3.7 6.5 - - - +
298M LEU* 1.3 77.0 - - - +
300M GLN* 1.3 56.4 + - - +
302M ALA* 3.3 5.5 + - - +
303M ASP* 2.9 26.8 + - - +
482M MET* 4.9 13.6 - - + +
494M GLU* 3.4 21.5 - - + +
498M ILE* 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 300 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M GLN* 2.9 44.4 + - - +
297M GLN* 3.2 26.6 + - - +
299M ALA* 1.3 76.7 - - - +
301M ASP* 1.3 64.8 + - - +
303M ASP* 3.4 9.8 - - - +
304M LEU* 2.8 28.1 + - - +
308M GLN* 5.4 0.7 - - - +
478M LEU* 4.2 22.9 - - + +
482M MET* 5.9 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 301 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M ILE* 5.4 7.4 - - - +
256M ARG* 5.3 4.2 + - - +
297M GLN* 2.9 38.5 + - - +
298M LEU* 3.9 14.4 + - + +
299M ALA 3.2 0.2 - - - -
300M GLN* 1.3 85.1 + - - +
302M ALA* 1.3 59.5 + - - +
304M LEU* 3.5 9.7 + - + +
305M ALA* 2.8 26.5 + - - +
424M ARG* 4.5 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 302 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298M LEU 2.9 17.9 + - - +
299M ALA* 3.3 5.6 + - - +
301M ASP* 1.3 77.0 - - - +
303M ASP* 1.3 57.1 + - - +
305M ALA* 3.2 10.2 + - - +
306M LEU* 3.0 31.6 + - + +
495M ARG* 6.3 2.0 - - + -
498M ILE* 4.0 22.2 - - + -
499M LEU* 5.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 303 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299M ALA 2.9 14.7 + - - +
300M GLN* 3.4 14.8 - - + +
301M ASP 3.2 0.2 - - - -
302M ALA* 1.3 76.7 - - - +
304M LEU* 1.3 53.9 + - - +
306M LEU* 2.9 4.3 + - - +
307M LEU* 2.4 46.3 + - - +
308M GLN* 3.3 29.9 + - - +
478M LEU* 5.5 5.8 - - - +
481M ARG* 6.1 2.9 - - - +
482M MET* 5.0 17.7 - - + +
485M ASN* 5.3 4.3 - - - +
498M ILE* 4.6 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300M GLN 2.8 16.7 + - - +
301M ASP* 3.9 9.6 - - - +
303M ASP* 1.3 72.1 + - - +
305M ALA* 1.3 64.5 + - - +
306M LEU* 3.1 3.3 + - - -
308M GLN* 3.3 48.6 - - - +
309M VAL* 4.7 3.6 - - - +
310M PHE* 5.8 1.3 - - + -
420M GLU* 4.1 29.1 - - + +
424M ARG* 3.8 39.7 - - - +
430M PHE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M MET 5.8 2.9 - - - +
182M ASP* 5.5 3.1 - - - +
256M ARG* 4.7 15.3 - - - +
301M ASP 2.8 15.8 + - - +
302M ALA* 3.2 15.9 + - - +
304M LEU* 1.3 79.3 - - - +
306M LEU* 1.3 66.9 + - + +
420M GLU* 4.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M ALA* 3.0 11.0 + - + +
303M ASP* 2.9 6.5 + - - +
304M LEU 4.4 2.0 - - - -
305M ALA* 1.3 87.8 - - + +
307M LEU* 1.3 82.5 + - + +
308M GLN 3.9 1.7 + - - -
498M ILE* 3.4 40.4 - - + +
499M LEU* 3.8 25.4 - - + -
501M VAL* 5.7 0.4 - - + -
502M PRO* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303M ASP* 2.4 32.3 + - - +
306M LEU* 1.3 99.6 - - + +
308M GLN* 1.3 61.0 + - - +
309M VAL* 5.7 0.7 - - - -
432M ALA* 3.8 15.1 - - - +
434M VAL* 6.1 0.4 - - + -
435M GLY* 3.7 31.4 - - - +
436M GLY 5.9 1.1 - - - +
501M VAL* 5.6 10.3 - - + -
502M PRO* 6.5 0.7 - - + -
----------------------------------------------------------
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