Contacts of the helix formed by residues 336 - 346 (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 LEU 336 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319M TRP* 4.8 4.7 - - - -
334M TYR* 3.3 16.8 + - - +
335M MET* 1.3 80.2 - - - +
337M SER* 1.3 62.7 + - - +
339M ASN* 3.1 13.5 - - - +
340M ALA* 3.5 12.0 - - - +
401M ARG 5.4 1.1 - - - +
402M LEU* 4.5 21.8 - - + -
403M LEU* 4.1 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334M TYR 5.1 0.2 + - - -
336M LEU* 1.3 79.6 - - - +
338M PRO* 1.4 69.5 - - - +
340M ALA* 3.2 6.5 + - - +
341M SER* 2.9 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 338 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334M TYR 4.9 4.0 - - - +
335M MET* 4.4 6.5 - - - -
336M LEU 4.0 7.0 - - - +
337M SER* 1.4 92.8 - - - +
339M ASN* 1.3 60.5 + - - +
341M SER* 3.1 8.6 + - - +
342M VAL* 3.0 33.3 + - + +
352M PHE* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 339 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319M TRP* 5.7 1.1 - - - -
335M MET* 3.0 33.0 + - - +
336M LEU 3.1 10.2 - - - +
338M PRO* 1.3 75.9 - - - +
340M ALA* 1.3 71.6 + - - +
342M VAL* 3.3 2.9 + - - +
343M CYS* 2.9 28.3 + - - +
348M LEU* 3.6 7.3 - - + +
352M PHE* 3.7 31.7 - - + -
368M PHE* 3.3 35.6 - - + -
402M LEU* 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319M TRP* 3.4 42.9 - - + +
336M LEU 3.5 15.0 - - - +
337M SER* 3.2 10.3 + - - +
339M ASN* 1.3 79.3 + - - +
341M SER* 1.3 61.1 + - - +
343M CYS* 3.3 9.6 + - - +
344M LEU* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337M SER* 2.9 16.2 + - - -
338M PRO* 3.1 12.1 + - - -
340M ALA* 1.3 74.1 - - - +
342M VAL* 1.3 64.8 + - - +
344M LEU* 3.1 12.4 + - - +
345M TYR* 3.0 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 342 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338M PRO 3.0 19.4 + - - +
339M ASN 3.3 7.4 + - - +
341M SER* 1.3 75.0 - - - +
343M CYS* 1.3 50.7 + - - +
345M TYR* 2.8 33.3 + - + +
346M SER* 2.3 45.5 + - - +
348M LEU* 4.3 3.6 - - + -
351M GLN* 3.3 30.1 - - + +
352M PHE* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 343 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317M VAL* 4.0 20.2 - - - -
318M TYR* 5.1 7.4 - - - -
319M TRP* 4.8 14.8 - - + -
339M ASN 2.9 13.9 + - - +
340M ALA* 3.4 13.7 - - - +
342M VAL* 1.3 75.7 - - - +
344M LEU* 1.3 61.9 + - - +
345M TYR 3.5 0.3 + - - -
346M SER 3.3 16.9 + - - +
347M PRO* 5.3 0.6 - - - +
348M LEU* 3.6 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319M TRP 5.2 3.1 - - - +
320M GLY* 3.7 24.2 - - - -
321M LYS 3.3 27.6 - - - +
322M ALA* 4.5 8.1 - - - +
340M ALA 2.9 13.3 + - - +
341M SER* 3.1 17.0 + - - +
343M CYS* 1.3 77.3 - - - +
345M TYR* 1.3 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 345 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341M SER* 3.0 38.1 + - - -
342M VAL* 2.8 33.5 + - + +
343M CYS 4.5 0.2 - - - -
344M LEU* 1.3 87.0 - - + +
346M SER* 1.3 67.7 + - - -
347M PRO* 4.7 0.5 - - - +
351M GLN* 4.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 346 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M VAL* 2.3 38.4 + - - +
343M CYS* 3.3 16.2 + - - -
344M LEU 3.7 1.0 - - - -
345M TYR* 1.3 83.8 - - - +
347M PRO* 1.3 84.1 + - - +
348M LEU 3.5 0.7 + - - -
350M GLU* 4.8 3.8 - - - +
351M GLN* 3.8 28.1 + - - +
----------------------------------------------------------
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