Contacts of the helix formed by residues 470 - 485 (chain A) in PDB entry 4E9F
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 SER 470 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 1.3 77.9 - - - +
471A GLY* 1.3 58.7 + - - +
472A LYS* 4.0 7.9 + - - +
473A MET* 3.3 25.5 + - - +
474A ALA* 3.0 23.4 + - - +
6C G 3.5 26.8 + - - +
7C 3DR 3.4 13.2 - - - -
8D G 6.3 0.2 - - - -
9D C 5.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 3.6 23.7 - - - +
469A THR 3.6 1.8 + - - -
470A SER* 1.3 66.7 - - - +
472A LYS* 1.3 65.7 + - - +
473A MET 3.1 2.2 - - - -
474A ALA 4.3 0.2 - - - -
475A ILE* 3.0 35.4 + - - +
476A PRO* 3.9 0.2 - - - +
562A LYS* 4.7 4.7 - - - -
7C 3DR 3.0 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER* 3.3 8.7 - - - +
471A GLY* 1.3 75.1 - - - +
473A MET* 1.3 73.8 + - - +
476A PRO* 3.2 22.5 - - - +
9D C 4.4 5.6 - - - +
10D T 3.3 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A THR* 5.0 3.4 - - + -
470A SER* 3.3 19.3 + - - +
471A GLY 3.1 0.2 - - - -
472A LYS* 1.3 97.9 - - + +
474A ALA* 1.4 63.8 + - - +
475A ILE 3.5 0.2 - - - -
476A PRO* 3.3 10.8 - - - +
477A VAL* 3.6 10.9 - - - +
505A PRO* 5.9 2.7 - - + +
506A LEU* 3.5 20.6 - - + +
6C G 6.2 1.6 - - - +
8D G 3.6 18.2 - - - +
9D C 3.4 47.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 3.4 39.0 - - + +
466A LEU* 4.0 12.8 - - + -
469A THR* 3.9 6.1 - - + -
470A SER 3.0 16.6 + - - +
471A GLY* 4.3 0.2 - - - -
473A MET* 1.4 77.3 - - - +
475A ILE* 1.3 59.7 + - + +
477A VAL* 3.2 4.9 + - - +
478A LEU* 2.8 26.7 + - - +
506A LEU* 3.8 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 3.7 40.2 - - + -
462A ALA* 5.1 2.2 - - + +
465A PHE* 5.6 1.1 - - + -
466A LEU* 4.2 18.2 - - + -
471A GLY* 3.0 28.3 + - - +
474A ALA* 1.3 72.1 - - + +
476A PRO* 1.4 68.2 - - + +
478A LEU* 3.0 25.8 + - + +
479A TRP* 3.1 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 3.9 0.4 - - - +
472A LYS 3.2 25.8 - - - +
473A MET* 3.3 9.4 - - - +
475A ILE* 1.4 93.1 - - + +
477A VAL* 1.4 60.6 + - + +
479A TRP* 3.3 20.6 + - + +
480A LYS* 3.4 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A PHE* 3.9 4.0 - - + -
473A MET 3.6 14.6 - - - +
474A ALA 3.2 7.5 + - - +
475A ILE 3.2 0.6 - - - -
476A PRO* 1.4 75.1 - - + +
478A LEU* 1.4 65.2 + - - +
480A LYS* 3.0 10.5 + - + +
481A PHE* 2.9 20.4 + - - +
502A LEU* 3.6 39.5 - - + +
503A LEU* 4.7 0.4 - - + -
505A PRO* 5.4 9.2 - - + -
506A LEU* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 4.2 13.9 - - + -
458A LYS 4.9 0.9 - - - +
461A ILE* 3.8 29.2 - - + -
462A ALA* 3.8 29.2 - - + +
465A PHE* 3.7 25.0 - - + -
474A ALA 2.8 16.4 + - - +
475A ILE* 3.2 26.2 - - + +
477A VAL* 1.4 72.5 - - - +
479A TRP* 1.4 74.4 + - + +
481A PHE* 3.2 3.6 + - + +
482A LEU* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 4.2 10.8 - - + -
451A THR* 4.4 7.4 - - - -
452A LEU* 4.0 23.6 - - + -
475A ILE* 3.1 45.0 + - + +
476A PRO* 3.8 13.7 - - + +
477A VAL 3.3 0.4 - - - -
478A LEU* 1.4 83.6 - - + +
480A LYS* 1.4 61.9 + - - +
482A LEU* 3.3 29.4 + - + +
483A GLU* 3.1 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO 3.4 8.8 + - - +
477A VAL* 3.0 14.8 + - + +
479A TRP* 1.4 77.6 - - - +
481A PHE* 1.3 61.4 + - - +
483A GLU* 3.4 17.4 + - - +
484A LYS* 3.4 33.8 + - - +
502A LEU* 3.9 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TRP* 4.0 21.5 - + - -
461A ILE* 3.8 25.4 - - + -
465A PHE* 3.5 25.4 - + + -
477A VAL 2.9 7.4 + - - +
478A LEU* 3.4 7.9 - - + +
480A LYS* 1.3 78.2 - - - +
482A LEU* 1.3 64.3 + - + +
484A LYS 3.3 1.4 + - - -
485A TYR* 2.8 70.9 + + + -
491A ALA* 4.7 1.6 - - + -
499A VAL* 4.0 23.6 - - + -
502A LEU* 3.7 20.8 - - + +
516A ILE* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 4.8 1.6 - - + -
457A TRP* 3.7 29.6 - - + -
458A LYS* 4.0 39.0 - - + +
461A ILE* 4.7 4.0 - - + -
478A LEU* 2.9 47.0 + - + +
479A TRP* 3.3 26.9 + - + +
481A PHE* 1.3 81.2 - - + +
483A GLU* 1.3 63.6 + - - +
485A TYR 3.7 4.9 - - - +
486A PRO* 3.2 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A TRP* 3.1 27.5 + - - +
480A LYS* 3.5 17.5 + - - +
482A LEU* 1.3 77.7 - - - +
484A LYS* 1.4 61.2 + - - +
486A PRO* 3.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS* 3.4 20.3 + - - +
481A PHE 3.3 3.4 + - - +
483A GLU* 1.4 80.6 - - - +
485A TYR* 1.4 98.7 + - + +
486A PRO* 3.5 7.7 - - - +
490A VAL* 4.3 5.2 - - - +
498A ASP* 5.5 6.8 + - - +
502A LEU* 4.4 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TRP* 3.4 12.5 - - - -
481A PHE* 2.8 61.7 + + + +
482A LEU* 3.4 10.8 - - - +
484A LYS* 1.4 109.8 - - + +
486A PRO* 1.4 64.1 - - - +
487A SER 3.3 4.6 + - - -
490A VAL* 4.2 17.3 - - + -
491A ALA* 4.5 13.5 - - + -
494A ALA* 3.7 26.9 - - + +
498A ASP* 4.0 13.7 + - - +
499A VAL* 3.9 28.8 + - + +
502A LEU* 4.5 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