Contacts of the helix formed by residues 468 - 479 (chain T) in PDB entry 6FF7
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 468 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A LYS 4.4 12.8 - - - +
1211A ASP* 5.1 6.1 - - + -
1279A VAL* 5.1 15.3 - - + +
466T SER 3.5 6.6 - - - +
467T LEU* 1.3 82.3 - - + +
469T PHE* 1.3 62.7 + - - +
470T GLU* 3.6 7.9 - - + +
471T GLU* 5.3 0.4 - - + +
472T CYS* 4.1 9.5 + - - +
506T PHE* 5.7 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A LYS* 4.4 12.8 + - + +
468T ASP* 1.3 74.5 - - - +
470T GLU* 1.3 64.5 + - - +
471T GLU 3.2 2.2 - - - -
472T CYS* 4.0 7.1 - - - +
473T ALA* 3.4 23.6 + - - +
506T PHE* 4.1 10.1 - - + +
509T LEU* 4.2 9.6 - - + +
510T LEU* 3.5 36.3 - - + +
513T ARG* 5.4 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 470 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350A ILE* 4.6 21.5 - - + -
24S SER* 4.5 10.8 - - - -
468T ASP* 3.6 4.7 - - + +
469T PHE* 1.3 80.1 - - - +
471T GLU* 1.3 58.2 + - - +
473T ALA* 4.2 3.9 - - - +
474T HIS* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 471 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333A VAL 4.2 11.4 - - - +
1334A LEU* 4.6 15.3 - - + +
466T SER* 4.2 13.6 - - - -
467T LEU 3.7 19.2 + - - +
468T ASP* 5.3 1.0 - - + +
469T PHE* 3.2 0.8 - - - +
470T GLU* 1.3 81.0 - - - +
472T CYS* 1.3 60.9 + - - +
474T HIS* 3.2 7.2 + - - +
475T LYS* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 472 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462T ALA* 4.7 6.6 - - - +
463T ILE* 4.3 27.6 - - + -
466T SER* 4.3 11.0 - - - +
468T ASP 4.1 14.5 + - - +
469T PHE* 3.9 6.8 + - - +
471T GLU* 1.3 78.4 - - - +
473T ALA* 1.3 63.4 + - - +
475T LYS* 3.3 3.3 + - - +
476T LEU* 2.9 25.4 + - - +
510T LEU* 5.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 473 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S SER* 3.9 23.3 - - - -
469T PHE 3.4 17.5 + - - +
470T GLU 4.2 0.4 - - - +
471T GLU 3.3 0.4 - - - -
472T CYS* 1.3 74.7 - - - +
474T HIS* 1.3 66.9 + - - +
476T LEU* 3.2 5.8 + - - +
477T LEU* 2.9 26.3 + - - +
510T LEU* 5.5 6.1 - - + +
513T ARG* 4.8 13.5 - - + -
514T PHE 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 474 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353A PHE* 5.4 12.1 - - + -
21S ARG 5.5 3.1 - - - +
22S ASN* 5.6 2.0 - - - -
23S LEU* 4.7 20.7 - - + +
24S SER* 4.6 3.0 - - - +
470T GLU 3.2 14.8 + - - +
471T GLU* 3.2 12.9 + - - +
473T ALA* 1.3 79.1 - - - +
475T LYS* 1.3 65.6 + - - +
477T LEU* 3.1 5.8 + - - +
478T LYS* 2.8 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462T ALA* 4.5 20.2 - - + +
466T SER* 5.8 4.0 - - - -
471T GLU 2.8 17.9 + - - +
472T CYS* 3.8 4.7 - - - +
474T HIS* 1.3 72.8 - - - +
476T LEU* 1.3 63.5 + - - +
478T LYS* 3.3 16.1 + - - +
479T MET* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 476 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459T ILE* 6.3 3.6 - - + -
462T ALA* 5.3 7.1 - - + +
472T CYS 2.9 19.2 + - - +
473T ALA* 3.6 6.5 - - - +
475T LYS* 1.3 74.0 - - - +
477T LEU* 1.3 68.9 + - - +
479T MET* 3.2 17.0 + - - +
480T GLU 4.1 1.4 + - - -
481T PHE* 4.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 3.8 25.8 - - + +
473T ALA 2.9 12.1 + - - +
474T HIS 3.4 7.9 - - - +
476T LEU* 1.3 76.3 - - - +
478T LYS* 1.3 52.6 + - - +
479T MET 2.7 12.6 + - - -
480T GLU* 2.7 19.9 + - - -
481T PHE 4.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 478 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU* 5.8 3.4 - - + -
474T HIS 2.8 20.4 + - - +
475T LYS* 3.7 9.6 - - - +
476T LEU 3.2 0.4 - - - -
477T LEU* 1.3 71.3 - - - +
479T MET* 1.3 55.7 + - - +
480T GLU* 3.3 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 479 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475T LYS 3.3 8.8 + - - +
476T LEU* 3.2 12.5 + - - +
477T LEU 2.7 6.2 + - - -
478T LYS* 1.3 72.9 - - - +
480T GLU* 1.3 67.3 + - - +
481T PHE* 3.1 7.6 + - + +
----------------------------------------------------------
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