Contacts of the helix formed by residues 458 - 468 (chain A) in PDB entry 4WTM
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 458 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASN* 2.8 31.3 + - - +
457A LEU* 1.3 76.7 - - - +
459A LEU* 1.3 63.2 + - - +
460A PRO* 3.3 4.3 - - - -
461A ALA* 3.0 19.7 + - + +
462A ILE* 3.1 27.1 + - + +
517A LYS* 2.9 33.8 + - - -
545A LEU* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 4.1 16.8 - - + -
412A ILE* 4.4 17.0 - - + -
413A ILE* 3.8 31.0 - - + -
429A PHE* 3.9 26.5 - - + -
430A PHE* 4.1 10.3 - - + -
454A VAL* 4.7 1.6 - - + -
455A ASN 3.9 1.5 + - - +
456A PRO* 3.2 24.8 + - + +
458A ASP* 1.3 76.1 - - - +
460A PRO* 1.3 71.2 - - + +
462A ILE* 3.3 11.5 + - + +
463A ILE* 2.8 39.2 + - + +
525A LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU 3.6 11.2 - - - +
458A ASP* 3.4 4.9 - - - -
459A LEU* 1.3 94.0 - - + +
461A ALA* 1.3 60.5 + - - +
464A GLU* 3.1 19.1 + - - +
472A PHE* 3.4 15.9 - - + -
520A VAL* 4.3 9.4 - - + +
521A CYS* 3.7 36.3 - - - +
524A TYR* 4.2 13.7 - - + -
525A LEU* 4.3 10.5 - - + -
539A LEU* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ASP* 3.0 15.2 + - + +
460A PRO* 1.3 76.4 - - - +
462A ILE* 1.3 67.2 + - - +
464A GLU 3.4 0.9 + - - -
465A ARG* 3.0 24.6 + - - +
539A LEU* 3.9 11.2 - - + +
541A GLU* 4.3 13.2 - - + -
542A ALA* 3.7 24.1 - - - +
545A LEU* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 4.6 12.6 - - + -
454A VAL* 3.6 31.6 - - + -
455A ASN 5.4 0.2 - - - +
458A ASP* 3.1 28.9 + - + +
459A LEU* 3.7 9.4 - - + +
461A ALA* 1.3 77.1 - - - +
463A ILE* 1.3 58.5 + - + +
465A ARG* 3.3 3.7 + - - +
466A LEU* 2.9 34.5 + - + +
545A LEU* 4.1 18.6 - - + -
547A LEU* 3.8 7.9 - - + +
550A TRP* 3.7 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 4.6 7.2 - - + +
413A ILE* 5.4 3.4 - - - -
416A ALA* 3.8 26.0 - - + -
426A MET* 3.7 29.8 - - + -
459A LEU* 2.8 33.3 + - + +
462A ILE* 1.3 78.3 - - + +
464A GLU* 1.3 60.7 + - - +
466A LEU* 4.6 0.4 - - - -
467A HIS* 2.8 36.8 + - + +
471A ALA* 3.9 15.7 - - + -
472A PHE* 3.6 22.7 - - + -
525A LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A PRO 3.1 15.4 + - - +
461A ALA 3.8 4.0 - - - +
463A ILE* 1.3 75.0 - - - +
465A ARG* 1.3 58.4 + - - +
468A GLY* 2.8 36.3 + - - -
469A LEU* 4.0 24.4 - - + +
472A PHE* 3.9 8.2 - - + -
538A PRO* 3.2 27.5 - - - +
539A LEU* 2.8 41.1 + - - +
542A ALA* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA 3.0 17.7 + - - +
462A ILE 3.5 4.9 - - - +
464A GLU* 1.3 81.9 - - - +
466A LEU* 1.3 60.5 + - - +
468A GLY 4.6 0.5 + - - -
542A ALA* 3.3 27.2 + - + +
543A ARG* 3.9 16.8 + - - +
545A LEU* 3.6 22.7 + - + +
546A ASP* 5.5 0.8 - - - +
547A LEU* 3.4 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 4.3 15.9 + - - +
197A PRO* 5.5 1.1 - - + -
198A ALA* 3.8 18.9 + - - +
413A ILE* 3.7 37.2 - - + +
462A ILE* 2.9 19.0 + - + +
463A ILE* 6.4 0.2 - - + -
465A ARG* 1.3 78.6 - - - +
467A HIS* 1.3 77.7 + - + +
547A LEU* 4.4 17.9 - - + +
550A TRP* 4.1 13.0 - - + -
551A PHE* 4.0 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 4.2 19.8 - - + +
198A ALA* 4.9 12.2 - - - +
413A ILE 2.8 26.3 + - - -
414A GLN 3.4 21.4 + - - -
416A ALA* 3.8 15.4 - - + +
417A PRO* 3.6 25.5 - - + +
463A ILE* 2.8 15.5 + - + +
466A LEU* 1.3 98.7 + - + +
468A GLY* 1.3 62.7 + - - +
470A ASP* 5.1 1.9 + - - +
471A ALA* 3.8 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ILE 3.4 0.4 + - - -
464A GLU* 2.8 29.1 + - - -
465A ARG 4.5 0.4 + - - -
466A LEU 3.8 0.2 - - - -
467A HIS* 1.3 77.5 - - - +
469A LEU* 1.3 65.2 + - - -
470A ASP* 3.1 3.4 - - - -
471A ALA* 3.0 22.5 + - - +
472A PHE* 4.6 0.9 - - - -
----------------------------------------------------------
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