Contacts of the strand formed by residues 464 - 470 (chain A) in PDB entry 3D8F
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 464 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 3.4 22.0 - - + +
402A SER* 2.7 34.7 + - - +
455A VAL* 3.3 8.3 - - - -
456A GLY 3.2 20.1 + - - +
460A GLY 4.3 1.2 - - - +
461A ARG* 3.3 38.0 + - - +
462A GLU 3.4 3.0 - - - -
463A ARG* 1.3 81.0 + - - +
465A PHE* 1.3 59.6 + - - +
481A VAL* 5.0 2.2 - - + -
482A PHE 3.4 6.5 - - - +
483A ARG* 3.4 16.8 + - - +
488A ALA* 3.5 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 4.7 0.9 - - - -
424A LEU* 3.8 32.1 - - + -
431A LEU* 4.2 4.3 - - + -
453A TRP* 3.7 15.7 - + + -
454A GLY 3.1 22.0 - - - -
463A ARG 3.6 1.8 + - - -
464A ASP* 1.3 73.0 - - - +
466A ALA* 1.3 75.1 + - - +
467A TYR* 4.0 22.0 - + + -
480A HIS 3.6 1.0 - - - +
481A VAL* 3.3 3.1 - - - +
482A PHE* 2.5 50.5 + + + +
484A CYS* 3.7 20.9 - - - -
488A ALA* 4.0 13.5 - - + -
491A ILE* 3.9 18.2 - - + -
492A ALA 4.5 3.4 - - - -
495A LEU* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 3.8 18.8 - - + -
398A ILE* 3.6 27.6 - - + +
453A TRP* 3.2 6.7 - - - +
454A GLY 3.1 28.6 + - - +
464A ASP 4.1 0.6 + - - -
465A PHE* 1.3 85.0 - - - +
467A TYR* 1.3 61.3 + - - +
479A CYS* 4.0 11.0 - - - -
480A HIS 3.3 8.3 - - - +
481A VAL* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.9 33.5 - - + +
433A LEU* 5.2 1.7 - - - +
443A HIS* 4.0 25.5 + - - -
445A GLN* 4.0 19.9 - - + +
450A ILE* 3.9 21.1 - - + -
452A VAL 3.4 10.3 - - - +
453A TRP* 4.2 1.6 - - + +
465A PHE* 4.0 14.8 - + + -
466A ALA* 1.3 74.6 - - - +
468A VAL* 1.3 72.4 + - - +
469A ALA* 4.1 7.4 - - + -
478A LYS 3.6 0.3 - - - +
479A CYS* 3.2 2.6 - - - -
480A HIS* 2.8 61.7 + + + -
482A PHE* 3.4 34.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A MET* 4.2 8.5 - - - -
385A LEU* 4.3 19.3 - - + -
394A VAL* 4.1 16.8 - - + -
450A ILE* 3.3 3.8 - - - -
451A ARG* 2.5 45.3 + - + -
452A VAL* 3.0 26.5 + - + +
467A TYR* 1.3 82.8 - - - +
469A ALA* 1.3 59.4 + - - +
477A LEU* 4.8 3.6 - - + -
478A LYS 3.1 21.5 - - - +
479A CYS* 3.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.0 38.8 - - + +
449A SER 3.8 11.9 - - - +
450A ILE* 4.5 0.9 - - - -
451A ARG* 4.6 2.7 - - - +
467A TYR* 4.1 12.0 - - + -
468A VAL* 1.3 76.3 - - - +
470A ARG* 1.3 66.9 + - - +
471A ASP* 3.6 1.2 + - - -
477A LEU* 4.3 3.6 - - - -
478A LYS* 3.0 31.5 + - - +
480A HIS* 5.0 3.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PO4 2.6 52.4 + - - +
382A GLU* 3.6 21.6 + - - +
445A GLN* 4.6 2.1 - - - +
449A SER 4.7 3.2 + - - -
469A ALA* 1.3 80.4 - - - +
471A ASP* 1.3 64.5 + - - +
472A LYS* 3.6 19.1 + - + +
475A GLN* 2.6 74.4 + - - +
476A MET 3.2 5.2 - - - +
477A LEU* 3.9 30.0 - - + +
----------------------------------------------------------
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