Contacts of the helix formed by residues 461 - 470 (chain A) in PDB entry 4COO
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 461 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE* 3.9 33.4 - - + +
438A LEU* 3.7 17.8 - - + +
439A ARG* 4.2 27.4 - - + +
443A PHE 4.4 7.6 - - - +
444A ASP* 2.9 38.5 + - + +
460A THR* 1.3 71.8 - - - +
462A GLY* 1.3 57.8 + - - +
464A MET* 3.8 2.5 - - - +
465A LEU* 3.0 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP 4.7 0.4 + - - -
460A THR* 3.3 3.6 + - - -
461A LEU* 1.3 80.6 - - - +
463A ASN* 1.3 56.2 + - - +
465A LEU* 3.4 7.1 + - - +
466A SER* 2.9 30.3 + - - -
199B SER* 4.1 7.4 - - - -
200B PRO* 3.8 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 3.1 22.0 + - - +
462A GLY* 1.3 73.2 - - - +
464A MET* 1.3 63.9 + - - +
466A SER* 4.5 0.9 - - - +
467A SER* 2.7 34.5 + - - -
482A VAL* 3.4 31.1 + - + +
484A TYR* 3.1 26.8 + - + +
194B ASN* 4.1 6.3 + - - +
196B ARG* 2.9 38.1 + - - +
199B SER* 3.9 6.0 - - - -
201B GLU* 3.1 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A CYS* 3.5 38.8 - - - +
434A THR* 4.1 17.7 - - + -
435A ILE* 3.4 25.8 - - + -
459A VAL* 4.3 8.1 - - + -
460A THR 3.0 18.8 + - - +
461A LEU* 3.8 0.9 - - - +
463A ASN* 1.3 77.1 - - - +
465A LEU* 1.3 58.2 + - - +
467A SER* 3.4 2.7 + - - -
468A LEU* 3.0 30.4 + - + +
473A VAL* 4.5 2.5 - - - -
479A VAL* 3.7 29.8 - - + -
482A VAL* 3.9 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ILE* 3.6 26.7 - - + -
439A ARG* 5.7 4.5 - - - -
461A LEU* 3.0 39.4 + - + +
462A GLY* 3.8 5.8 - - - +
464A MET* 1.3 74.7 - - - +
466A SER* 1.3 60.6 + - - +
468A LEU* 3.6 8.0 - - + +
469A LEU* 2.8 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A GLY 2.9 18.5 + - - -
463A ASN* 4.0 4.9 - - - -
465A LEU* 1.3 76.3 - - - +
467A SER* 1.3 58.7 + - - +
469A LEU* 3.8 7.1 - - - +
470A ALA* 2.9 32.1 + - - +
196B ARG* 2.8 27.6 + - - -
198B ASP* 2.5 39.6 + - - -
199B SER* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASN* 2.7 26.6 + - - -
464A MET 3.6 4.7 - - - -
466A SER* 1.3 78.3 - - - +
468A LEU* 1.3 59.6 - - - +
470A ALA 3.5 0.5 + - - -
471A GLY 3.2 2.9 + - - -
472A LYS* 2.8 42.1 + - - +
473A VAL* 3.6 8.0 + - - -
482A VAL* 3.8 29.1 - - - +
196B ARG* 3.6 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A CYS* 4.4 8.5 - - + +
432A GLY* 5.0 2.2 - - - +
435A ILE* 3.7 30.1 - - + -
464A MET* 3.0 26.8 + - + +
465A LEU* 3.6 10.3 - - + +
467A SER* 1.3 72.9 - - - +
469A LEU* 1.3 71.6 + - + +
471A GLY* 3.0 14.9 + - - -
473A VAL* 3.6 25.0 - - + +
474A GLN 3.8 2.5 - - - -
475A PRO* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 2.8 37.7 + - + +
466A SER* 3.9 5.4 - - - +
468A LEU* 1.3 81.7 - - + +
470A ALA* 1.3 59.8 + - - +
471A GLY 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A SER 2.9 18.0 + - - +
467A SER 4.0 3.1 - - - +
468A LEU 3.2 0.2 - - - -
469A LEU* 1.3 76.4 - - - +
471A GLY* 1.3 60.0 + - - +
472A LYS* 3.3 20.3 + - + +
196B ARG* 3.7 26.9 - - - +
----------------------------------------------------------
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