Contacts of the helix formed by residues 560 - 574 (chain A) in PDB entry 4DK9
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 ASP 560 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A TYR* 3.5 39.3 + - + -
558A PRO* 3.7 2.2 - - - +
559A GLU* 1.3 78.9 - - - +
561A HIS* 1.3 65.1 + - - +
562A LYS* 3.6 11.4 + - - +
563A LEU* 3.2 28.2 + - + +
564A ASN* 2.8 32.4 + - - +
18C 3DR 3.4 32.9 + - - +
19C G 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLU 4.3 0.2 + - - -
560A ASP* 1.3 77.7 + - - +
562A LYS* 1.3 70.5 + - + +
564A ASN* 2.9 22.7 + - + +
565A LYS* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 5.8 1.6 - - + +
447A LEU* 3.6 35.1 - - + +
466A LEU* 4.9 10.4 - - - +
471A GLY* 5.4 5.1 - - - +
540A TYR* 5.3 2.5 - - - -
560A ASP* 3.6 10.5 + - - +
561A HIS* 1.3 82.4 - - + +
563A LEU* 1.3 57.7 + - - +
565A LYS* 3.0 19.9 + - + +
566A TYR 2.9 24.8 + - - -
18C 3DR 3.1 46.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 4.2 8.7 - - + +
449A GLN* 4.3 11.9 - - - +
540A TYR* 4.0 17.9 - - + -
543A ASP* 3.8 29.8 - - + +
544A SER* 3.8 17.7 - - - +
547A ILE* 4.1 14.8 - - + -
548A PHE* 3.9 28.0 - - + -
558A PRO* 4.0 15.9 - - + -
560A ASP* 3.2 21.7 + - + +
561A HIS 3.2 0.6 - - - -
562A LYS* 1.3 76.3 - - - +
564A ASN* 1.3 53.7 + - - +
566A TYR* 3.1 3.8 + - + +
567A HIS* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PRO* 3.2 36.3 + - - +
559A GLU* 3.9 7.1 - - - +
560A ASP 2.8 30.7 + - - +
561A HIS* 2.9 13.4 + - + +
563A LEU* 1.3 71.3 - - - +
565A LYS* 1.3 57.5 + - - +
567A HIS* 4.4 2.9 - - - +
568A ASP* 2.8 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PHE* 3.2 47.6 - - + -
561A HIS* 2.9 33.4 + - + +
562A LYS* 3.1 24.0 - - + +
564A ASN* 1.3 75.9 - - - +
566A TYR* 1.3 63.3 + - - +
568A ASP* 3.9 5.0 - - - +
569A TRP* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PRO* 3.6 8.4 - - + +
441A PRO* 2.6 49.4 + - + +
443A SER* 3.4 31.9 - - - -
445A PHE* 4.0 8.5 - - + -
447A LEU* 3.6 22.0 - - + -
450A GLU* 3.7 15.9 - - + -
547A ILE* 3.8 17.5 - - + -
548A PHE* 3.6 27.6 - + + -
562A LYS 2.9 5.3 + - - -
563A LEU* 3.6 6.1 - - + +
565A LYS* 1.3 73.6 - - - +
567A HIS* 1.3 56.2 + - - +
569A TRP* 3.0 11.4 + + - +
570A LEU* 2.8 50.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 4.1 14.3 - - + +
553A TRP* 2.9 43.4 - + - +
556A VAL* 3.2 17.7 + - + -
557A HIS* 5.5 0.2 + - - -
558A PRO* 3.7 27.4 - - + -
563A LEU 2.7 19.8 + - - +
564A ASN* 3.9 4.5 - - - +
566A TYR* 1.3 72.7 - - - +
568A ASP* 1.3 72.8 - - - +
569A TRP 2.9 1.3 - - - -
570A LEU* 2.8 16.7 + - - +
571A TRP* 2.9 47.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASN* 2.8 38.1 + - - +
565A LYS* 3.9 5.4 - - - +
567A HIS* 1.3 79.5 - - - +
569A TRP* 1.3 56.4 + - - +
571A TRP* 3.4 8.6 + - - +
572A GLU* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO* 4.1 21.1 - - + -
442A ARG 3.5 21.3 - - - -
443A SER* 3.8 17.9 - - - -
444A PRO* 3.8 30.9 - - + +
445A PHE* 3.4 19.3 - + + -
565A LYS 3.1 19.1 + - - +
566A TYR* 3.0 17.9 + + - +
567A HIS 2.9 0.6 - - - -
568A ASP* 1.3 75.4 - - - +
570A LEU* 1.3 77.5 + - + +
572A GLU* 3.6 6.0 + - + +
573A ASN* 3.1 55.1 + - + +
577A LEU 5.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TRP* 5.1 3.6 - - + -
441A PRO* 4.0 28.9 - - + -
547A ILE* 4.7 2.0 - - + -
553A TRP* 3.6 50.9 - - + +
566A TYR* 2.8 37.8 + - + +
567A HIS* 2.8 10.3 + - - +
569A TRP* 1.3 85.4 - - + +
571A TRP* 1.3 65.3 + - - +
573A ASN 2.9 13.6 + - - -
574A HIS* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A TRP* 3.5 14.6 - + - -
554A LYS* 3.6 46.5 + - + -
567A HIS* 2.9 56.4 + + - +
568A ASP* 3.6 11.0 - - - +
570A LEU* 1.3 73.2 - - - +
572A GLU* 1.3 63.5 + - + +
574A HIS* 3.2 35.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ASP* 3.1 31.9 + - - +
569A TRP* 3.7 9.1 - - + +
570A LEU 3.1 0.2 - - - -
571A TRP* 1.3 77.0 - - - +
573A ASN* 1.3 69.8 + - - +
574A HIS 4.0 0.2 - - - -
576A LYS* 5.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A TRP* 3.1 54.1 + - + +
570A LEU* 2.9 9.6 + - + -
572A GLU* 1.3 84.9 + - - +
574A HIS* 1.3 65.5 + - - +
575A GLU 3.3 3.4 - - - +
576A LYS* 3.2 24.2 + - + +
577A LEU 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A TRP* 3.5 37.7 - + + -
554A LYS* 4.1 20.8 + - - -
570A LEU* 2.9 20.0 + - + +
571A TRP* 3.2 34.3 + + - -
573A ASN* 1.3 75.6 - - - +
575A GLU* 1.3 84.7 + - + +
577A LEU* 3.0 32.4 + - - +
----------------------------------------------------------
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