Contacts of the strand formed by residues 478 - 485 (chain D) in PDB entry 3KXX
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 LEU 478 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LEU* 4.8 5.8 - - + -
474D PRO 4.0 1.3 + - - +
475D ARG 3.6 17.1 + - - +
476D ASP 3.4 2.3 - - - -
477D ARG* 1.3 80.5 + - - +
479D VAL* 1.3 63.2 + - - +
480D LEU* 3.8 19.5 + - + +
495D ALA* 4.1 4.9 - - + -
496D GLU 3.5 15.0 - - - +
497D ALA* 4.1 14.1 - - + -
511D VAL* 4.2 2.9 - - + -
513D VAL* 3.7 37.7 - - + -
551D CYS* 4.3 14.1 - - - -
558D TYR* 4.4 7.6 - - + -
560D ILE* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D ARG 5.2 0.2 - - - -
478D LEU* 1.3 72.3 - - - +
480D LEU* 1.3 70.9 + - - +
481D GLY* 4.4 0.2 - - - -
495D ALA* 3.2 3.1 - - - -
496D GLU* 2.7 49.3 + - + +
498D ILE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D LEU* 3.8 28.4 + - + +
479D VAL* 1.3 81.8 - - - +
481D GLY* 1.3 63.6 + - - +
493D VAL* 4.4 6.5 - - + -
495D ALA* 3.7 3.1 - - - -
513D VAL* 4.2 10.8 - - + -
515D MET* 4.2 24.2 - - + -
558D TYR* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 481 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D VAL 3.5 1.9 + - - -
480D LEU* 1.3 78.4 - - - +
482D LYS* 1.3 66.4 + - - -
483D PRO* 4.5 1.0 - - - +
493D VAL* 4.5 6.4 - - - +
494D LEU* 2.6 22.5 + - - +
495D ALA* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 482 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D GLY* 1.3 72.8 - - - -
483D PRO* 1.3 78.3 - - + +
484D LEU* 5.4 7.4 - - + +
493D VAL* 3.7 1.3 - - - -
494D LEU* 3.0 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D GLY 4.0 1.3 - - - +
482D LYS* 1.3 96.0 - - + +
484D LEU* 1.3 62.5 + - - +
485D GLY* 3.3 6.3 - - - +
486D GLU* 5.5 5.2 - - + +
491D GLN* 4.0 19.1 - - - +
493D VAL* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D LYS* 4.6 8.1 - - - +
483D PRO* 1.3 75.1 - - - +
485D GLY* 1.3 57.2 + - - +
492D VAL* 2.8 30.6 + - + +
493D VAL 3.9 5.2 - - - -
494D LEU* 3.5 43.5 - - + +
512D ALA* 4.1 9.9 - - + -
563D TYR* 4.1 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D PRO* 3.3 5.7 - - - +
484D LEU* 1.3 81.2 - - - +
486D GLU* 1.3 64.2 + - - +
487D GLY 4.0 1.3 - - - -
491D GLN* 3.4 6.9 - - - +
492D VAL* 3.3 26.1 + - - +
----------------------------------------------------------
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