Contacts of the helix formed by residues 346 - 353 (chain M) in PDB entry 5M64
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 346 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345M GLU* 1.3 80.8 + - - +
347M THR* 1.3 72.7 + - + +
349M LEU* 3.4 5.6 + - - +
350M ALA* 3.2 19.9 + - - +
357M PRO* 4.5 16.6 - - + +
360M VAL* 4.8 5.5 - - + +
361M VAL* 3.7 31.6 - - + -
364M PHE* 3.6 33.4 - - + -
371M VAL* 4.6 2.9 - - + -
392M TYR* 6.3 0.4 - - + -
393M LYS* 3.3 33.9 - - + +
394M ILE* 3.9 17.5 - - - +
395M ALA* 4.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B PRO* 6.0 6.3 - - + -
345M GLU* 4.4 0.2 - - - +
346M ILE* 1.3 83.8 - - + +
348M PRO* 1.3 68.1 - - - +
350M ALA* 3.3 7.6 + - - +
351M HIS* 3.0 38.9 + - + +
357M PRO* 5.6 9.2 - - + -
392M TYR* 2.6 47.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345M GLU* 3.5 29.2 - - + -
347M THR* 1.3 98.6 - - - +
349M LEU* 1.3 67.4 + - + +
351M HIS* 3.3 11.3 + - + +
352M GLU* 3.1 29.8 + - - +
382M PHE* 4.9 15.0 - - + -
392M TYR* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246M LYS* 6.2 1.1 - - - +
332M ILE* 5.1 0.4 - - + -
333M LEU* 4.1 17.3 - - + -
336M ILE* 3.7 28.0 - - + -
340M ASP* 5.6 0.9 - - - +
344M VAL* 3.7 21.3 - - + -
345M GLU* 3.4 25.1 - - + +
346M ILE 3.4 4.6 + - - +
347M THR 3.3 0.6 - - - -
348M PRO* 1.3 84.1 - - + +
350M ALA* 1.3 61.8 + - - +
352M GLU* 3.3 23.3 - - - +
353M LEU* 3.1 45.2 + - + +
360M VAL* 4.4 15.6 - - + +
364M PHE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ASP* 5.4 0.9 - - - +
865B THR 4.0 3.1 - - - +
346M ILE 3.2 11.2 + - - +
347M THR* 3.3 8.0 + - - +
349M LEU* 1.3 79.0 - - - +
351M HIS* 1.3 64.8 + - + +
353M LEU* 4.9 0.2 - - - -
354M ASN* 3.3 2.4 + - - -
355M LEU 3.1 43.3 + - - +
357M PRO* 3.8 32.5 - - + -
360M VAL* 4.1 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 351 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ASP* 3.1 46.8 + - - -
867B ASN* 3.5 23.0 + - - +
242M TYR* 4.4 6.5 + - - +
347M THR* 3.0 34.7 + - + +
348M PRO* 3.8 9.2 - - + +
349M LEU 3.3 0.2 - - - -
350M ALA* 1.3 80.1 - - + +
352M GLU* 1.3 61.2 + - - +
354M ASN* 3.4 18.0 + - - +
357M PRO* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M TYR* 3.5 62.7 + - + +
246M LYS* 5.4 9.9 + - - -
273M GLU* 5.0 6.9 - - - +
336M ILE* 4.2 8.3 - - - +
348M PRO* 3.1 19.0 + - - +
349M LEU* 3.3 37.1 - - - +
351M HIS* 1.3 77.4 - - - +
353M LEU* 1.3 72.9 + - + +
354M ASN* 3.4 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269M LEU* 6.6 0.2 - - + -
272M TYR* 3.1 42.7 + - + -
329M LEU* 4.6 7.6 - - + -
332M ILE* 3.6 45.3 - - + -
333M LEU* 6.4 0.2 - - + -
336M ILE* 5.2 2.0 - - + -
349M LEU* 3.1 35.1 + - + +
350M ALA* 4.9 0.4 - - - -
352M GLU* 1.3 92.7 - - + +
354M ASN* 1.3 69.4 + - - +
355M LEU* 3.4 18.8 + - + +
360M VAL* 5.5 1.8 - - + -
----------------------------------------------------------
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