Contacts of the helix formed by residues 537 - 546 (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 ARG 537 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446M SER* 6.5 0.2 - - - -
534M ASN 3.9 6.1 + - - +
535M THR 3.9 0.4 - - - -
536M ARG* 1.3 80.3 - - - +
538M SER* 1.3 70.4 + - - +
539M GLN* 3.2 42.5 + - + +
540M LEU* 3.2 34.3 + - + +
541M LEU* 3.8 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 538 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537M ARG* 1.3 74.5 + - - +
539M GLN* 1.3 66.6 + - - +
540M LEU 3.3 0.2 - - - -
541M LEU* 3.3 21.3 - - - +
542M MET* 2.8 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 539 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537M ARG* 3.2 43.1 + - + +
538M SER* 1.3 84.1 - - - +
540M LEU* 1.3 59.4 + - + +
542M MET* 3.7 16.5 - - + +
543M LEU* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530M MET* 5.8 9.0 - - + -
533M GLU* 3.7 23.6 - - + +
534M ASN* 2.7 31.3 + - - +
536M ARG* 5.9 1.3 - - + -
537M ARG* 3.2 23.3 + - + +
539M GLN* 1.3 78.6 - - + +
541M LEU* 1.3 57.4 + - - +
543M LEU* 3.3 28.1 - - + +
544M PHE* 3.3 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444M ALA* 3.8 39.9 - - + +
445M LEU* 3.3 28.5 - - - +
446M SER* 3.7 14.6 - - - -
534M ASN* 3.9 14.3 + - + +
537M ARG 3.8 6.1 + - - +
538M SER* 3.3 29.8 - - - +
540M LEU* 1.3 77.2 - - - +
542M MET* 1.3 66.4 + - + +
543M LEU 3.2 1.0 + - - -
544M PHE* 3.4 20.5 + - + -
545M ASP* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 542 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444M ALA* 5.9 1.6 - - + -
538M SER* 2.8 52.5 + - - +
539M GLN* 3.2 16.1 + - + +
541M LEU* 1.3 83.8 - - + +
543M LEU* 1.3 59.6 + - - +
545M ASP* 4.3 2.7 - - - +
546M LYS* 2.9 47.8 + - + +
548M ARG* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530M MET* 5.1 11.0 - - + -
539M GLN 2.9 18.6 + - - +
540M LEU* 3.3 39.9 - - + +
542M MET* 1.3 77.8 - - - +
544M PHE* 1.3 81.3 + - + +
546M LYS* 4.2 19.1 - - - +
563M VAL* 4.9 4.9 - - - +
567M LEU* 3.3 55.0 - - + +
568M LEU* 5.8 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M THR* 4.0 14.4 - - - -
516M LEU* 4.9 8.1 - - + -
520M PHE* 4.8 30.6 - + + -
527M GLU* 5.3 8.1 - - - +
530M MET* 5.1 7.4 - - + -
531M TYR* 5.9 2.2 - - + -
534M ASN* 3.6 23.1 - - + -
540M LEU 3.3 24.5 - - - -
541M LEU* 3.6 12.3 - - + -
542M MET 3.2 0.2 - - - -
543M LEU* 1.3 89.0 - - + +
545M ASP* 1.3 99.8 + - - +
546M LYS 3.5 1.3 - - - -
547M PHE* 3.1 24.0 - - - -
563M VAL* 5.5 7.2 - - + -
567M LEU* 4.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 545 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M THR* 3.0 27.7 + - - +
442M PRO* 4.2 13.4 - - - +
444M ALA* 4.0 26.3 - - + +
445M LEU 5.5 0.7 - - - +
516M LEU* 5.2 4.3 - - - +
541M LEU* 3.0 18.5 + - - +
542M MET* 3.3 3.6 + - - -
544M PHE* 1.3 112.2 - - - +
546M LYS* 1.3 57.7 + - - +
547M PHE* 3.2 20.2 + - - -
548M ARG* 3.8 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 546 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542M MET* 2.9 26.7 + - + +
543M LEU* 4.2 15.9 - - - +
544M PHE 3.5 1.2 - - - -
545M ASP* 1.3 77.0 - - - +
547M PHE* 1.3 60.2 + - + +
548M ARG* 3.0 36.0 + - - +
549M SER* 4.0 14.0 + - - -
562M ALA 5.2 1.0 + - - -
563M VAL* 5.6 5.3 - - - +
566M ALA* 3.5 43.1 - - - +
----------------------------------------------------------
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