Contacts of the strand formed by residues 451 - 458 (chain A) in PDB entry 3KN5
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 451 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS* 3.3 33.7 - - - +
443A CYS 3.5 4.0 - - - -
444A VAL* 4.4 2.2 - - + +
449A ASN 3.8 1.9 + - - +
450A GLN* 1.3 84.2 + - - +
452A PHE* 1.3 69.5 + - - +
500A LEU* 3.8 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 3.9 19.1 - + - -
442A LYS* 3.5 10.4 - - - +
443A CYS* 2.9 35.3 + - - -
445A HIS* 3.9 13.5 - + + -
448A SER* 5.8 0.2 - - - -
450A GLN* 3.4 50.7 - - + -
451A ALA* 1.3 78.0 - - - +
453A ALA* 1.3 62.0 + - - +
485A HIS* 3.7 35.2 - + + -
497A VAL* 3.7 20.4 - - + -
498A MET 3.4 16.6 - - - +
499A GLU* 4.3 4.3 - - - -
500A LEU* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ANP 3.8 35.2 - - + +
432A LEU* 3.9 18.4 - - + -
440A CYS* 4.2 6.3 - - - -
441A ARG 3.4 5.2 - - - -
443A CYS* 4.5 0.4 - - - -
452A PHE* 1.3 78.0 - - - +
454A VAL* 1.3 60.9 + - - +
497A VAL* 3.4 4.7 - - - +
498A MET* 2.8 36.1 + - + +
499A GLU 4.3 0.7 - - - +
500A LEU* 4.1 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PHE* 3.7 23.6 - - + -
425A LEU* 3.9 26.9 - - + -
439A ILE 3.7 0.5 - - - +
440A CYS* 3.1 7.3 - - - -
441A ARG* 2.7 50.2 + - + +
443A CYS* 4.1 14.1 - - - -
453A ALA* 1.3 76.6 - - - +
455A LYS* 1.3 66.0 + - - +
456A ILE* 3.9 23.4 + - + +
495A PHE* 4.2 2.9 - - + -
496A LEU 3.3 14.8 - - - +
497A VAL* 3.9 6.5 - - + -
498A MET* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A SER* 4.0 23.6 - - - -
439A ILE 3.4 11.4 - - - +
440A CYS* 4.3 9.6 - - + +
454A VAL* 1.3 72.1 - - - +
456A ILE* 1.3 61.1 + - - +
457A ILE* 3.9 19.9 - - + +
468A GLU* 2.8 36.5 + - - +
494A THR 3.5 4.3 - - - +
495A PHE* 3.6 0.2 - - - -
496A LEU* 2.9 44.1 + - + +
498A MET* 5.2 7.5 - - + +
565A ASP* 3.4 21.4 + - - +
567A GLY* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PHE* 5.6 0.2 - - + -
420A TYR* 5.1 1.3 - - - +
425A LEU* 4.1 26.0 - - + -
437A PHE 4.0 0.3 - - - +
438A SER* 3.2 4.5 - - - -
439A ILE* 2.9 42.2 + - + +
441A ARG* 4.6 11.7 - - + +
454A VAL* 4.0 23.8 - - + +
455A LYS* 1.3 75.2 - - - +
457A ILE* 1.3 62.7 + - - +
493A HIS* 3.7 35.2 - - + +
494A THR 3.5 2.9 - - - -
495A PHE* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER 4.9 0.4 - - - +
437A PHE 3.4 10.1 - - - +
438A SER* 4.1 9.4 - - - -
455A LYS* 3.9 28.0 - - + +
456A ILE* 1.3 81.3 - - - +
458A SER* 1.3 73.3 - - - +
461A MET* 3.9 19.5 - - + -
465A THR* 3.7 31.4 - - + +
468A GLU* 4.1 13.7 - - - +
493A HIS* 3.1 8.2 - - - -
494A THR* 2.8 35.7 + - - +
496A LEU* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.0 30.1 + - - -
457A ILE* 1.3 76.3 - - - +
459A LYS* 1.3 59.9 + - - +
460A ARG* 2.9 28.0 + - - +
461A MET* 2.8 26.9 + - - +
462A GLU* 3.9 1.7 + - - +
465A THR* 4.9 0.7 - - - +
492A LEU 3.6 1.6 + - - -
493A HIS* 3.5 20.0 + - - -
494A THR* 5.6 0.4 - - - -
----------------------------------------------------------
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