Contacts of the strand formed by residues 474 - 480 (chain D) in PDB entry 1YKN
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 474 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 4.0 17.9 - - - +
8C THR* 3.7 45.8 - - + +
10C SER* 4.1 20.0 - - - +
137C ILE* 6.1 0.4 - - + -
138C HIS* 4.5 7.4 - - + -
311D ARG* 4.2 6.3 - - - +
316D HIS* 4.2 5.2 - - + -
464D GLY* 3.4 1.7 - - - -
465D ILE* 2.8 44.0 + - + +
472D THR 4.0 5.4 - - - +
473D LYS* 1.4 79.6 - - - +
475D ILE* 1.3 69.8 + - - +
476D THR* 4.2 8.3 - - + -
525D ILE* 4.8 0.4 - - + -
526D VAL 4.7 1.1 - - - +
527D LEU* 4.3 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 3.4 12.2 + - - +
11C GLN 3.2 25.2 + - - +
12C THR 4.5 0.7 - - - +
13C ALA* 3.8 32.3 - - + +
21C LEU* 3.9 28.0 - - + -
67C PHE* 4.7 1.3 - - + -
131C PHE* 3.6 40.0 - - + -
138C HIS* 5.2 1.2 + - - -
400D TRP* 4.3 9.9 - - + -
462D HIS* 5.6 0.4 - - - +
463D PHE 3.3 11.9 - - - +
464D GLY* 4.1 4.9 - - - -
473D LYS* 4.0 11.0 - - - +
474D LEU* 1.3 74.5 - - - +
476D THR* 1.3 70.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 4.2 17.0 - - + -
9C PRO 3.0 22.5 + - - -
10C SER* 4.5 0.2 - - - -
11C GLN* 3.8 10.8 - - - +
462D HIS* 3.3 7.1 - - - +
463D PHE* 2.6 49.5 + - + +
465D ILE* 4.2 14.8 - - + -
474D LEU* 4.6 4.7 - - + -
475D ILE* 1.3 80.0 - - - +
477D GLN* 1.3 71.1 + - - +
504D LEU* 3.6 12.3 - - - +
523D PHE* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 3.9 16.3 - - + +
12C THR* 3.4 22.5 + - - +
457D ARG* 2.8 35.2 + - - +
460D HIS* 3.0 18.8 - - + -
461D ILE 3.3 4.9 - - - +
462D HIS* 3.6 17.6 - - + +
476D THR* 1.3 92.9 + - - +
478D LEU* 1.3 61.2 + - - +
479D TYR* 3.1 17.9 + - + +
491D ILE* 4.3 1.8 - - - +
504D LEU* 3.5 27.0 - - - +
523D PHE* 4.3 4.0 - - - -
1550D DHB 3.2 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D VAL* 3.6 21.5 - - + -
460D HIS* 3.0 29.5 - - - +
461D ILE* 2.7 25.8 + - + +
463D PHE* 3.6 28.1 - - + -
477D GLN* 1.3 74.8 - - - +
479D TYR* 1.4 69.7 + - - +
480D PHE* 3.4 36.3 - - + -
504D LEU 3.8 3.8 - - - -
506D ALA* 3.8 14.4 - - + -
523D PHE* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLN* 2.7 26.6 + - - -
457D ARG* 3.0 30.2 + - - -
458D PRO* 4.0 15.9 - - + -
459D ALA 3.8 9.0 - - - +
460D HIS* 3.7 22.9 - - + -
477D GLN* 3.1 17.0 + - + -
478D LEU* 1.4 73.1 - - - +
480D PHE* 1.4 62.8 + - - +
486D ILE* 3.8 21.8 - - + -
492D VAL* 3.3 26.5 - - + +
501D VAL* 5.5 2.0 - - + -
504D LEU* 2.9 40.2 + - + +
505D ILE* 3.4 7.3 - - + -
506D ALA* 2.6 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D ILE* 3.9 21.3 - - + -
380D VAL* 5.0 2.0 - - + -
443D LYS* 3.7 25.6 - - + +
444D PRO* 3.9 35.0 - - + -
459D ALA* 3.7 28.9 + - + -
460D HIS* 4.4 1.6 - - - -
461D ILE* 4.0 10.8 - - + -
478D LEU* 3.4 27.4 - - + -
479D TYR* 1.4 75.1 - - - +
481D GLU* 1.3 69.4 + - - +
482D GLY 3.2 0.5 + - - -
483D ASP* 3.1 25.5 + - + +
486D ILE* 3.5 5.2 - - - +
505D ILE* 4.0 2.7 - - - -
506D ALA* 4.2 1.1 - - + -
521D TYR* 3.8 37.7 - + + -
----------------------------------------------------------
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