Contacts of the strand formed by residues 474 - 479 (chain D) in PDB entry 3DLX
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 ALA 474 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D HIS* 4.9 0.2 - - + -
469D ILE 4.5 0.2 - - - -
471D THR* 3.1 33.0 + - - +
472D GLU 3.7 1.0 - - - -
473D LYS* 1.3 80.6 - - + +
475D VAL* 1.3 69.6 + - - +
476D PHE* 3.7 16.8 - - + -
486D LEU* 3.2 27.8 - - + -
488D GLU 3.5 6.3 - - - +
489D LEU* 4.1 3.8 - - - +
490D TRP 4.5 0.7 - - - +
498D VAL* 3.9 11.4 - - + -
515D MET* 4.5 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ARG* 4.0 39.0 - - + +
468D ARG* 3.7 30.1 - - + +
469D ILE 3.3 12.6 - - - +
470D ILE* 4.5 7.4 - - + -
474D ALA* 1.3 82.2 - - - +
476D PHE* 1.3 65.4 + - - +
486D LEU* 3.4 8.5 - - - +
487D ILE* 3.1 34.8 + - + -
488D GLU* 3.1 23.5 + - + +
515D MET* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D HIS* 4.1 14.1 - + - -
452D ILE* 5.7 2.7 - - + -
468D ARG* 3.1 10.1 - - - -
469D ILE* 3.0 52.0 + - + +
471D THR* 4.9 3.4 - - + -
474D ALA* 3.7 16.8 - - + -
475D VAL* 1.3 78.4 - - - +
477D ASP* 1.3 67.7 + - - +
478D VAL* 3.7 0.7 - - - +
484D LEU* 3.7 37.9 - - + -
485D THR 3.9 2.0 - - - -
486D LEU* 3.9 33.4 - - + -
498D VAL* 3.4 31.0 - - + -
502D THR* 4.4 10.8 - - + -
506D PHE* 4.4 9.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D LYS* 6.0 0.5 - - - -
467D ASN 3.8 6.7 - - - +
468D ARG* 3.0 31.2 + - - +
476D PHE* 1.3 74.6 - - - +
478D VAL* 1.3 63.1 + - - +
483D GLY 4.5 0.2 - - - -
484D LEU* 3.4 3.5 - - - +
485D THR* 2.9 44.9 + - - +
487D ILE* 3.4 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D SER 4.3 1.3 - - - +
406D LYS 3.5 12.6 - - - +
407D TYR 3.7 2.0 - - - +
408D GLY* 3.4 38.4 - - - +
466D VAL* 3.3 21.0 - - + +
467D ASN* 3.2 21.8 + - - +
468D ARG 4.4 0.2 - - - +
469D ILE* 4.1 19.3 - - + -
476D PHE 3.7 9.9 - - - +
477D ASP* 1.3 80.5 - - - +
479D ASP* 1.3 63.5 + - - +
483D GLY 3.4 3.1 - - - -
484D LEU* 3.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D TYR* 3.5 17.7 - - - -
478D VAL* 1.3 75.3 - - - +
480D LYS* 1.3 63.6 + - - +
481D LYS* 3.2 10.4 + - - +
482D LYS* 2.7 41.2 + - + +
483D GLY* 2.5 32.1 + - - +
----------------------------------------------------------
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