Contacts of the helix formed by residues 446 - 459 (chain A) in PDB entry 6DWZ
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 LYS 446 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 3.4 53.2 - - + -
442A MET* 3.3 28.0 - - + +
443A GLN 2.6 14.9 + - - +
444A GLN* 3.6 14.5 - - + +
445A GLU* 1.3 106.6 + - - +
447A VAL* 1.3 57.3 + - - +
449A GLN* 2.9 29.7 + - + +
450A ILE* 2.9 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A PHE* 4.2 13.0 - - + -
442A MET 5.4 0.4 - - - -
443A GLN* 3.2 48.0 - - - +
445A GLU 2.8 0.6 + - - -
446A LYS* 1.3 72.5 - - + +
448A ALA* 1.3 55.7 + - - +
450A ILE* 3.5 14.1 - - + +
451A LYS* 2.6 42.4 + - + +
524A PHE* 3.6 23.3 - - + -
528A ARG* 4.2 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU* 2.6 28.6 + - + +
447A VAL* 1.3 76.8 - - - +
449A GLN* 1.3 68.0 + - - +
451A LYS* 3.7 4.1 - - - +
452A GLU* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.9 17.3 - - + +
445A GLU* 3.2 32.7 - - - +
446A LYS* 2.9 13.4 + - + +
448A ALA* 1.3 79.7 - - - +
450A ILE* 1.3 57.3 + - + +
452A GLU* 3.7 15.4 + - - +
453A PHE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 5.5 1.8 - - + -
430A TYR* 3.8 22.9 - - + +
431A THR* 3.9 19.3 - - + +
434A PHE* 3.4 38.8 - - + -
442A MET* 4.5 5.4 - - + -
446A LYS* 2.9 27.6 + - + +
447A VAL* 3.5 21.8 - - + +
448A ALA 3.1 0.2 - - - -
449A GLN* 1.3 75.0 - - + +
451A LYS* 1.3 56.3 + - - +
453A PHE* 3.0 6.5 + - - +
454A CYS* 2.4 59.0 + - - -
524A PHE* 3.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 2.6 27.5 + - + +
448A ALA* 3.7 4.7 - - - +
450A ILE* 1.3 71.5 - - - +
452A GLU* 1.3 56.8 + - - +
454A CYS 3.0 0.2 + - - -
455A LEU* 2.7 53.0 + - + +
521A SER 5.9 1.8 - - - -
524A PHE* 3.3 51.1 - - + -
525A GLU* 2.7 23.0 + - - +
528A ARG* 5.4 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ALA 3.1 14.6 + - - +
449A GLN* 3.7 14.8 - - - +
451A LYS* 1.3 77.2 - - - +
453A PHE* 1.3 66.3 + - - +
455A LEU* 4.2 4.6 - - - +
456A SER* 3.0 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.6 28.9 - - + -
428A TRP* 3.6 48.5 - + - -
431A THR* 3.7 26.5 - - + -
449A GLN 2.9 16.9 + - - +
450A ILE* 3.2 8.1 - - - +
452A GLU* 1.3 79.8 + - - +
454A CYS* 1.3 76.1 + - - +
456A SER* 2.9 17.4 + - - -
457A LYS* 3.2 37.1 + - + +
557A LEU* 4.9 6.7 - - + -
561A LEU* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A THR* 4.1 13.5 - - - -
435A PHE* 4.3 8.5 - - - -
450A ILE* 2.4 42.2 + - - +
453A PHE* 1.3 79.1 - - - +
455A LEU* 1.3 65.2 + - - +
457A LYS* 3.3 3.3 + - - +
458A MET* 3.1 32.5 + - - +
524A PHE* 3.6 24.5 - - + -
554A LEU* 5.4 1.8 - - + -
557A LEU* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LYS* 2.7 42.3 + - + +
452A GLU* 4.2 3.8 - - - +
454A CYS* 1.3 73.1 - - + +
456A SER* 1.3 65.2 + - - +
457A LYS 3.2 0.5 - - - -
458A MET* 2.8 23.3 + - + -
459A GLU* 3.5 20.6 - - + +
520A PRO* 3.9 17.0 - - + +
521A SER* 3.8 39.3 - - - +
524A PHE* 5.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A GLU* 3.0 25.4 + - - -
453A PHE* 2.9 8.6 + - - -
455A LEU* 1.3 75.6 - - - +
457A LYS* 1.3 63.4 + - - +
459A GLU* 3.8 11.7 - - - +
460A ASP* 4.2 5.9 - - - +
461A LEU* 5.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 3.5 27.5 + - - -
244A LYS* 5.2 0.2 - - - +
261A ILE* 5.7 3.2 - - - +
428A TRP* 3.3 31.3 - - + -
453A PHE* 3.2 32.4 + - + +
454A CYS 3.7 6.7 - - - +
455A LEU 2.8 1.6 + - - -
456A SER* 1.3 82.8 - - - +
458A MET* 1.3 69.1 + - - +
459A GLU 3.3 1.6 + - - -
460A ASP* 3.3 3.6 - - - +
461A LEU* 3.3 37.4 - - + +
557A LEU* 4.0 24.5 - - + -
561A LEU* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A CYS* 3.1 28.9 - - - +
455A LEU* 2.8 17.1 + - + +
457A LYS* 1.3 76.9 - - - +
459A GLU* 1.3 67.0 + - + +
461A LEU 3.6 1.2 + - - -
462A GLU* 2.6 36.6 - - - +
520A PRO* 3.2 36.6 - - + +
523A GLU* 4.5 1.6 - - + -
524A PHE* 5.6 2.0 - - - -
553A LYS* 3.8 36.3 - - + +
554A LEU* 3.8 26.7 - - + -
557A LEU* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU* 3.5 23.9 - - + +
456A SER* 3.8 10.4 - - - +
457A LYS 3.3 0.6 + - - -
458A MET* 1.3 77.8 - - + +
460A ASP* 1.3 98.8 + - - +
461A LEU 3.1 0.2 + - - -
462A GLU* 3.9 11.3 + - - +
520A PRO* 4.4 24.9 - - + -
553A LYS* 5.6 5.4 - - - +
----------------------------------------------------------
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