Contacts of the helix formed by residues 899 - 913 (chain A) in PDB entry 3N56
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 LYS 899 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 3.7 41.8 + - + +
427A LYS 4.2 8.3 - - - +
428A GLU* 6.1 1.8 - - - +
429A ARG* 5.0 21.7 - - - +
567A PHE* 3.4 18.1 - - - -
569A LEU* 6.5 0.4 - - - -
897A PRO* 4.1 0.9 - - - +
898A LYS* 1.3 78.3 - - + +
900A LEU* 1.3 68.3 + - - +
901A SER* 4.5 16.2 + - - +
902A ALA* 3.4 23.1 + - + +
903A GLU* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 4.9 6.6 + - - +
564A ASP* 3.9 28.0 - - + +
567A PHE* 3.6 18.5 - - + +
571A LYS* 4.2 18.2 - - + +
572A ALA* 4.0 11.2 - - - +
573A ASN* 3.7 32.5 - - - +
730A HIS* 3.7 38.4 - - + +
731A GLY* 4.0 4.3 - - - -
899A LYS* 1.3 73.5 - - - +
901A SER* 1.3 57.9 + - - +
903A GLU* 3.0 8.5 + - - +
904A SER* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 4.6 10.0 + - - -
573A ASN* 3.4 22.0 + - - +
632A LYS* 4.7 17.5 + - - +
899A LYS* 3.4 13.8 + - - +
900A LEU* 1.3 75.5 - - - +
902A ALA* 1.3 59.9 + - - +
904A SER* 3.7 1.9 - - - -
905A ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 4.5 18.6 - - - +
897A PRO* 4.0 20.1 - - + +
898A LYS 4.7 1.3 - - - +
899A LYS* 3.4 24.6 + - + +
900A LEU 3.3 0.6 - - - -
901A SER* 1.3 78.7 - - - +
903A GLU* 1.3 61.1 + - - +
905A ALA* 3.8 5.5 - - - +
906A LYS* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LYS* 3.0 17.5 + - - -
564A ASP* 4.9 1.4 - - - +
565A ASP* 5.3 0.5 + - - +
566A LYS* 3.7 22.9 + - - +
567A PHE* 3.2 23.4 - - - -
730A HIS* 3.5 14.6 + - + -
897A PRO* 3.9 25.5 - - + +
899A LYS 3.6 4.7 + - - +
900A LEU 3.0 10.0 + - - +
902A ALA* 1.3 77.6 - - - +
904A SER* 1.3 65.5 + - - +
906A LYS* 3.1 15.7 + - + +
907A TYR* 2.7 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ASN* 2.9 40.1 + - - +
575A ASN* 5.2 5.6 - - - -
632A LYS* 5.1 5.6 - - - -
728A LEU* 3.8 12.4 - - - +
730A HIS* 3.0 25.2 + - - +
900A LEU 2.9 6.7 + - - -
901A SER* 3.7 4.9 - - - -
903A GLU* 1.3 76.2 - - - +
905A ALA* 1.3 51.6 + - - -
907A TYR* 3.2 3.6 + - - +
908A TRP* 2.7 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A LYS* 6.0 2.0 - - - +
901A SER 2.9 19.6 + - - +
902A ALA* 3.8 7.0 - - - +
903A GLU 3.2 0.2 - - - -
904A SER* 1.3 76.2 - - - +
906A LYS* 1.3 57.2 + - - +
908A TRP* 3.8 7.4 - - - +
909A GLY* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A ARG* 4.5 10.7 + - - +
895A ASP 4.9 9.2 - - - -
897A PRO* 4.9 16.6 - - + -
902A ALA 3.3 11.3 + - - +
903A GLU* 3.1 13.5 + - + +
905A ALA* 1.3 79.9 - - - +
907A TYR* 1.3 69.2 + - + +
909A GLY* 3.7 1.6 + - - -
910A GLU* 3.5 23.7 + - - +
921A ASP* 3.1 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PRO 3.7 6.1 + - - -
547A TYR* 3.9 24.6 - + - -
548A PRO* 3.5 28.0 - - + -
562A LYS* 3.4 15.4 + - + -
566A LYS* 4.6 3.5 + - - -
728A LEU* 3.8 14.1 - - + -
730A HIS* 4.1 15.9 - + - -
903A GLU* 2.7 53.2 + - + +
904A SER 3.7 3.4 - - - +
906A LYS* 1.3 82.9 - - + +
908A TRP* 1.3 61.4 + - - +
910A GLU* 2.9 22.1 + - - +
911A ILE* 3.0 19.3 + - + +
918A PHE* 3.8 27.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ASN* 3.5 37.5 - - + +
576A PHE 3.9 0.7 - - - -
577A GLU* 3.7 29.6 - - + -
628A TYR* 3.5 42.0 - + - -
726A GLU 4.1 3.6 - - - -
727A ALA 4.3 2.7 - - - -
728A LEU* 3.8 30.7 - - + +
904A SER 2.7 21.7 + - - +
905A ALA* 3.8 9.2 - - - +
907A TYR* 1.3 69.5 - - - +
909A GLY* 1.3 61.5 + - - +
911A ILE* 4.3 17.0 - - + +
912A ILE* 2.9 66.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A ALA 2.9 16.9 + - - -
906A LYS 4.1 2.2 - - - -
908A TRP* 1.3 75.5 - - - +
910A GLU* 1.3 60.2 + - - +
912A ILE* 3.6 11.9 - - - +
913A SER* 3.0 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A LYS 3.5 15.5 + - - +
907A TYR 2.9 13.3 + - - +
909A GLY* 1.3 78.6 - - - +
911A ILE* 1.3 55.7 + - - +
913A SER* 4.0 2.9 + - - -
914A GLN* 3.9 0.2 - - - -
915A GLN* 3.1 18.2 + - - +
916A TYR* 2.9 27.4 + - - -
917A ASN 3.2 46.7 + - - +
918A PHE* 4.0 14.6 - - + +
920A ARG* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 911 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A TRP* 3.6 36.3 - - + +
577A GLU* 6.5 0.2 - - + -
726A GLU* 3.6 34.5 - - + +
728A LEU* 3.9 31.2 - - + -
907A TYR 3.0 17.8 + - - +
908A TRP* 3.8 20.2 - - + +
910A GLU* 1.3 76.3 - - - +
912A ILE* 1.3 68.2 + - + +
913A SER 3.2 1.3 - - - -
914A GLN* 3.0 20.1 + - - +
916A TYR* 3.9 12.8 + - + -
918A PHE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLU* 4.4 19.1 - - + +
765A ARG* 2.5 33.0 + - - +
908A TRP* 2.9 68.2 + - + +
909A GLY* 3.6 13.0 - - - +
911A ILE* 1.3 74.1 - - + +
913A SER* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 913 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLY 3.0 23.1 + - - -
910A GLU* 3.7 5.0 + - - -
912A ILE* 1.3 77.3 - - - +
914A GLN* 1.3 69.5 + - - +
915A GLN* 3.4 37.7 + - - +
1008A VAL* 5.5 1.6 - - - +
----------------------------------------------------------
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