Contacts of the helix formed by residues 474 - 485 (chain A) in PDB entry 4EGC
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 GLY 474 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 4.6 4.2 - - - +
472A PRO 3.5 4.8 + - - -
473A LEU* 1.3 75.9 - - - +
475A ALA* 1.3 66.8 + - - -
476A VAL* 3.4 3.8 - - - -
477A GLY* 3.2 5.0 + - - +
478A LYS* 3.0 25.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
474A GLY* 1.3 70.8 - - - -
476A VAL* 1.3 59.5 + - - +
478A LYS* 3.3 8.7 + - - +
479A TYR* 3.0 27.6 + - - +
482A ARG* 4.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 6.2 2.0 - - - +
474A GLY* 5.3 1.6 - - - -
475A ALA* 1.3 79.3 - - - +
477A GLY* 1.3 61.9 + - - +
479A TYR* 3.3 17.6 + - + +
480A ARG* 2.9 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 5.9 4.9 - - - -
473A LEU* 4.0 20.4 - - - -
474A GLY 3.2 9.5 + - - +
476A VAL* 1.3 84.9 - - - +
478A LYS* 1.3 62.6 + - - +
480A ARG* 3.2 12.4 + - - +
481A VAL* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A TYR* 3.8 38.4 - - + +
466A GLU* 5.7 0.7 - - - -
473A LEU* 4.0 34.6 + - + +
474A GLY 3.0 20.3 + - - +
475A ALA* 3.7 6.3 - - - +
477A GLY* 1.3 72.5 - - - +
479A TYR* 1.3 66.8 + - - +
481A VAL* 3.2 3.7 + - - +
482A ARG* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ALA 3.0 14.2 + - - +
476A VAL* 3.3 24.0 + - + +
478A LYS* 1.3 76.5 - - - +
480A ARG* 1.3 82.0 + - + +
482A ARG* 3.4 25.7 + - - +
483A ARG* 3.2 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 2.9 50.9 + - - +
477A GLY* 3.2 11.2 + - - +
479A TYR* 1.3 93.7 - - + +
481A VAL* 1.3 64.7 + - + +
483A ARG* 3.1 8.1 + - - +
484A LYS* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 6.3 1.1 - - + -
461A HIS* 3.8 31.6 - - + +
462A TYR* 3.8 17.3 - - + -
465A ALA* 3.6 27.8 - - + -
473A LEU* 4.1 11.9 - - + -
477A GLY 3.0 18.6 + - - +
478A LYS 3.2 6.3 + - - +
480A ARG* 1.3 76.2 - - + +
482A ARG* 1.3 59.5 + - + +
484A LYS* 3.1 6.1 + - - -
485A PHE* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 4.1 25.4 - - + -
462A TYR* 2.8 38.9 + - + +
475A ALA 4.9 1.8 + - - -
478A LYS* 3.0 26.6 + - - +
479A TYR* 3.6 35.8 - - - +
480A ARG 3.3 0.2 - - - -
481A VAL* 1.3 78.8 - - - +
483A ARG* 1.3 60.0 + - + +
485A PHE 3.4 20.3 - - - +
486A PRO* 3.5 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A TYR* 3.2 50.4 + - + +
480A ARG* 3.1 11.2 + - - +
482A ARG* 1.3 78.9 - - - +
484A LYS* 1.3 62.6 + - - +
486A PRO* 4.1 11.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
468A LEU* 6.1 2.8 - - - +
480A ARG 3.0 15.4 + - - +
481A VAL* 3.1 5.6 + - - +
483A ARG* 1.3 78.6 - - - +
485A PHE* 1.3 94.0 + - + +
486A PRO* 3.6 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TRP* 3.1 18.6 + + + +
458A LEU* 5.3 2.4 - - - +
461A HIS* 3.4 45.1 - + + +
465A ALA* 6.2 1.8 - - + -
481A VAL* 2.9 29.6 + - + +
482A ARG* 3.4 9.1 - - - +
484A LYS* 1.3 122.9 - - + +
486A PRO* 1.3 68.9 - - - +
487A LEU 3.7 0.3 + - - -
----------------------------------------------------------
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