Contacts of the strand formed by residues 469 - 475 (chain D) in PDB entry 2QY0
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 ARG 469 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D PHE* 3.5 34.0 - - + -
464D THR 3.5 5.6 - - - +
465D ASN* 4.0 4.0 + - - +
468D GLY* 1.3 75.3 - - - +
470D GLY* 1.3 61.2 + - - +
509D VAL* 3.7 29.9 - - - +
513D MET* 5.4 1.4 - - - +
579D PHE* 3.0 30.9 + - + +
580D GLY* 5.0 0.4 - - - -
586D ILE* 4.6 13.3 - - - +
587D ALA 2.9 27.5 + - - -
588D HIS* 5.1 3.8 + - - -
634D GLN* 3.9 12.0 + - + +
635D GLY* 3.4 26.8 - - - +
637D SER* 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D PHE* 3.8 4.7 - - - -
464D THR* 2.9 40.3 + - - +
468D GLY 3.6 0.2 + - - -
469D ARG* 1.3 79.8 - - - +
471D GLY* 1.3 58.1 + - - -
486D THR* 4.9 7.6 - - - -
579D PHE* 5.0 3.2 - - - -
635D GLY 3.3 15.0 - - - +
637D SER* 3.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 471 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D GLN* 3.9 7.0 - - - -
462D VAL* 3.3 12.3 - - - -
464D THR* 4.3 8.6 + - - +
470D GLY* 1.3 74.8 - - - -
472D GLY* 1.3 52.9 + - - -
482D THR* 2.7 29.1 + - - -
486D THR* 5.1 0.7 + - - +
579D PHE* 5.6 1.3 - - - -
635D GLY 3.9 3.1 + - - -
636D ASP* 4.7 2.2 - - - -
637D SER 2.7 14.7 + - - -
638D GLY* 3.1 9.3 - - - -
639D GLY* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 472 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D TRP* 5.1 0.7 - - - -
461D GLN* 3.5 10.6 + - - +
462D VAL* 2.9 38.5 + - - +
464D THR* 5.7 0.2 - - - -
471D GLY* 1.3 73.7 - - - -
473D ALA* 1.3 60.1 + - - +
480D ILE* 4.4 2.7 - - - -
481D LEU 3.2 14.6 - - - -
482D THR* 4.2 2.2 - - - -
638D GLY 3.2 9.3 + - - -
639D GLY* 3.9 4.5 - - - +
640D VAL* 5.1 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 473 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D TRP* 3.3 16.6 - - + -
462D VAL* 3.9 4.4 - - - +
472D GLY* 1.3 73.5 - - - +
474D LEU* 1.3 62.8 + - - +
475D LEU* 3.4 1.3 + - + +
480D ILE* 3.5 1.4 - - - +
481D LEU* 2.9 43.9 + - + +
559D ILE* 4.0 19.7 - - + -
638D GLY 4.4 0.2 + - - -
640D VAL* 3.4 30.1 - - + -
653D ALA* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D TRP* 2.9 19.9 + - - +
462D VAL* 3.8 7.4 - - + +
473D ALA* 1.3 71.0 - - - +
475D LEU* 1.4 64.6 + - - +
476D GLY 3.6 21.5 - - - +
478D ARG* 4.3 7.2 - - - +
479D TRP 3.4 24.0 - - - +
480D ILE* 4.6 3.8 - - + -
504D LEU* 4.3 15.7 - - + -
546D LEU* 4.9 1.8 - - + -
550D VAL* 4.0 13.5 - - + -
552D LEU* 4.2 3.8 - - + -
556D LEU* 3.7 34.1 - - + -
557D LEU 4.1 2.0 - - - -
558D PRO* 3.1 17.2 - - + +
559D ILE* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ALA 4.1 7.4 - - - +
474D LEU* 1.4 77.6 - - - +
476D GLY* 1.3 66.6 + - - +
478D ARG 3.7 0.2 + - - -
479D TRP* 2.7 43.8 + - + +
481D LEU* 4.0 24.9 - - + +
543D LEU* 4.4 6.1 - - + -
558D PRO* 3.8 2.0 - - - -
559D ILE* 3.2 35.7 - - + +
561D LEU* 4.1 26.7 - - + -
680D ILE* 4.0 27.4 - - + -
684D MET* 4.2 15.0 - - - -
800D GOL 4.3 4.7 - - - +
----------------------------------------------------------
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