Contacts of the helix formed by residues 472 - 481 (chain A) in PDB entry 6ML4
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 ASP 472 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A THR* 3.7 16.9 - - + +
461A TYR* 3.9 2.0 - - - -
470A PHE* 3.3 10.3 - - - +
471A SER* 1.3 83.0 + - - +
473A SER* 1.3 66.6 + - - +
474A SER* 2.9 33.1 + - - -
475A ALA* 2.9 13.1 + - + -
476A LYS* 3.2 16.6 + - - +
7E G 6.0 0.4 - - - +
8E T 3.6 20.7 - - + +
9E C 2.9 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A THR* 5.5 1.0 + - - +
453A ARG* 4.7 2.9 + - - +
461A TYR* 3.5 45.3 + - - -
472A ASP* 1.3 75.1 + - - +
474A SER* 1.3 63.6 + - - +
476A LYS* 3.4 5.2 + - - +
477A ARG* 3.1 43.2 + - - +
10F C 5.5 7.0 - - - +
11F A 5.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ASP* 2.9 10.9 + - - -
473A SER* 1.3 79.2 + - - +
475A ALA* 1.3 59.8 + - - +
477A ARG* 3.4 15.1 + - - +
478A ARG* 2.8 33.0 + - - +
8E T 5.7 0.2 - - - -
9E C 4.4 0.2 - - - -
11F A 4.0 6.9 + - - -
12F G 2.8 34.4 + - - -
13F G 3.5 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A PHE* 3.8 22.0 - - + -
472A ASP* 2.9 18.4 + - + +
474A SER* 1.3 76.1 - - - +
476A LYS* 1.3 57.7 + - - +
478A ARG* 3.8 22.5 + - - +
479A HIS* 3.0 28.9 + - - +
6E G 5.0 0.7 + - - -
7E G 4.3 6.3 - - - +
8E T 3.7 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A TYR* 3.8 28.5 - - + -
462A SER 3.3 30.1 - - - +
463A CYS* 4.4 0.4 - - - +
464A SER 5.3 0.7 - - - +
470A PHE* 3.5 30.2 - - + -
472A ASP 3.2 7.1 + - - +
473A SER 3.6 8.3 - - - +
474A SER 3.2 0.2 - - - -
475A ALA* 1.3 75.5 - - - +
477A ARG* 1.3 68.5 + - + +
479A HIS* 3.1 3.1 + - - +
480A CYS* 3.0 47.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A SER* 3.1 28.2 + - - +
474A SER* 3.4 28.5 + - - +
476A LYS* 1.3 84.5 - - + +
478A ARG* 1.3 62.5 + - - +
480A CYS* 3.4 12.7 + - - +
481A ILE* 3.5 20.3 + - + +
10F C 4.1 2.0 - - - +
11F A 2.4 66.5 + - - +
12F G 3.2 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER 2.8 16.6 + - - +
475A ALA* 3.8 22.6 + - - +
477A ARG* 1.3 76.0 - - - +
479A HIS* 1.3 64.1 + - - +
481A ILE* 3.5 24.7 + - + +
482A LEU* 4.2 7.8 + - - +
500A ARG* 3.5 46.8 - - - +
502A ASP* 4.9 0.6 + - - -
6E G 3.5 26.8 + - - +
7E G 2.8 51.7 + - - -
8E T 3.7 5.1 + - - -
13F G 5.6 2.2 + - - -
14F A 3.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A CYS* 3.5 17.0 - - + +
466A CYS* 3.3 11.6 - - - -
468A LYS* 4.0 11.4 - - + +
470A PHE* 3.5 18.4 - + + -
475A ALA 3.0 18.5 + - - +
476A LYS 3.1 2.4 + - - +
478A ARG* 1.3 77.7 - - - +
480A CYS* 1.3 61.0 + - - +
482A LEU* 2.9 37.4 + - + +
483A HIS* 3.4 7.6 + + - -
604A ZN 2.0 36.3 - - - -
6E G 3.2 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A CYS* 3.9 27.6 - - - -
464A SER 5.2 0.9 - - - -
465A ILE* 5.1 4.4 - - + +
476A LYS* 3.0 52.0 + - - +
477A ARG* 3.9 7.0 - - - +
478A ARG 3.4 0.8 - - - -
479A HIS* 1.3 80.4 - - - +
481A ILE* 1.3 62.4 + - + +
482A LEU 3.3 0.3 + - - -
483A HIS* 3.3 22.5 + - + +
484A THR* 4.2 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ARG* 3.5 20.4 - - + +
478A ARG* 3.6 15.5 - - + +
479A HIS 3.1 1.0 + - - -
480A CYS* 1.3 77.1 - - + +
482A LEU* 1.3 65.7 + - + +
484A THR* 2.5 40.3 + - + +
485A GLY 3.8 1.0 + - - -
486A LYS* 4.7 14.6 + - + +
499A ALA* 5.5 8.7 - - + +
----------------------------------------------------------
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