Contacts of the helix formed by residues 924 - 937 (chain A) in PDB entry 2R2P
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 924 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A SER* 6.5 0.9 - - - -
858A ALA* 5.0 10.5 - - + +
861A VAL* 5.1 1.3 - - + -
919A ARG 4.9 6.5 + - - -
920A ASN* 4.9 15.6 + - - +
922A ARG 4.6 7.2 + - - +
923A PRO* 1.3 80.7 - - - +
925A PHE* 1.3 64.8 + - - +
926A ASP* 3.2 22.0 - - - +
927A GLU* 2.7 29.3 + - - +
928A ILE* 3.1 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A SER* 4.0 11.2 - - - +
788A MET* 3.5 47.8 - - + -
789A LYS* 3.6 22.0 - - + -
792A SER* 4.3 14.8 - - - -
857A SER* 3.8 14.1 - - - -
860A ASP* 3.7 25.6 - - + -
861A VAL* 3.5 26.0 - - + +
864A TYR* 3.7 27.1 - + + -
923A PRO 3.9 0.6 + - - -
924A LYS* 1.3 72.5 - - - +
926A ASP* 1.3 57.4 + - - +
928A ILE* 3.1 17.2 + - + +
929A VAL* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A LYS* 3.8 36.7 - - + +
924A LYS* 3.2 21.3 - - - +
925A PHE* 1.3 77.8 - - - +
927A GLU* 1.3 75.2 + - - +
929A VAL* 3.4 5.1 + - - +
930A ASN* 3.1 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A ARG 4.5 0.5 - - - +
923A PRO* 3.2 17.6 - - + +
924A LYS* 2.7 40.0 + - + +
926A ASP* 1.3 85.8 + - - +
928A ILE* 1.3 64.8 + - - +
930A ASN* 3.4 7.4 + - - +
931A MET* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A SER* 3.6 23.1 - - - +
861A VAL* 3.9 25.8 - - + -
864A TYR* 3.6 28.7 - - + +
910A LEU* 4.1 13.0 - - + -
914A CYS* 4.3 2.2 - - - -
923A PRO* 3.8 17.9 - - + +
924A LYS 3.1 14.3 + - - +
925A PHE* 3.4 28.3 - - + +
927A GLU* 1.3 76.6 - - - +
929A VAL* 1.3 62.2 + - - +
931A MET* 3.2 9.8 + - - +
932A LEU* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A ARG* 3.6 38.3 - - - +
785A SER* 3.2 39.3 - - - +
786A ALA* 3.8 8.5 - - + +
789A LYS* 4.6 8.5 - - + -
925A PHE 3.0 19.5 + - - +
926A ASP* 3.7 9.6 - - - +
927A GLU 3.3 0.2 - - - -
928A ILE* 1.3 74.6 - - - +
930A ASN* 1.3 62.6 + - - +
932A LEU* 3.4 4.1 + - - +
933A ASP* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ASP* 3.1 25.4 + - - +
927A GLU* 3.7 7.3 - - - +
929A VAL* 1.3 84.0 - - - +
931A MET* 1.3 55.6 + - - +
933A ASP* 3.5 13.5 + - - +
934A LYS* 3.1 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A LEU* 3.4 41.1 - - + -
913A ASP* 5.3 5.8 - - - +
923A PRO* 4.1 14.1 - - + -
927A GLU* 3.0 38.5 + - + +
928A ILE* 3.2 5.6 + - - +
930A ASN* 1.3 72.3 - - + +
932A LEU* 1.3 65.3 + - - +
934A LYS* 3.3 14.7 + - + +
935A LEU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 932 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A VAL* 3.9 17.6 - - + +
781A LEU* 3.5 20.2 - - + +
782A ARG* 3.6 22.4 - - + +
785A SER* 4.0 6.7 - - - +
864A TYR* 3.3 26.0 - - - +
868A MET* 4.9 1.6 - - + -
907A LEU* 3.8 28.9 - - + -
910A LEU* 3.8 13.7 - - + -
928A ILE* 3.0 21.4 + - + +
929A VAL 3.8 3.6 - - - +
931A MET* 1.3 74.7 - - - +
933A ASP* 1.3 65.1 + - - +
935A LEU* 3.0 19.4 + - + +
936A ILE* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 933 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A ARG* 2.7 45.4 + - - +
929A VAL* 2.9 24.1 + - - +
930A ASN* 3.6 13.4 + - - +
931A MET 3.4 0.2 - - - -
932A LEU* 1.3 76.4 - - - +
934A LYS* 1.3 59.2 + - + +
936A ILE* 3.4 9.3 + - - +
937A ARG* 3.0 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 934 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A ASN* 3.1 29.8 + - - +
931A MET* 3.4 16.8 - - + +
932A LEU 3.1 0.2 - - - -
933A ASP* 1.3 78.3 - - + +
935A LEU* 1.3 58.9 + - + +
937A ARG* 3.4 8.2 + - - +
938A ASN* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A VAL* 6.0 0.7 - - + -
775A ILE* 3.9 7.6 - - + +
778A VAL* 4.3 14.4 - - + -
904A PRO* 5.7 2.7 - - + -
906A ALA* 4.4 17.9 - - + -
907A LEU* 3.9 39.5 - - + +
910A LEU* 6.0 0.7 - - + -
931A MET 3.2 15.3 + - - +
932A LEU* 3.0 19.8 + - + +
934A LYS* 1.3 71.7 - - + +
936A ILE* 1.3 66.9 + - - +
937A ARG 3.1 1.8 - - - -
938A ASN* 3.1 23.5 + - - +
941A HIS* 3.3 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 936 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A ILE* 3.9 26.9 - - + +
778A VAL* 3.8 23.1 - - + -
779A GLY* 4.2 18.2 - - - -
782A ARG* 4.3 19.5 - - + -
932A LEU 3.1 14.2 + - - +
933A ASP* 3.8 11.4 - - - +
935A LEU* 1.3 76.3 - - - +
937A ARG* 1.3 61.0 + - + +
942A HIS* 2.7 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 937 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A ARG* 5.2 1.8 - - - +
933A ASP* 3.0 48.5 + - - +
934A LYS* 3.6 7.6 - - - +
935A LEU 3.1 0.8 - - - -
936A ILE* 1.3 82.7 - - + +
938A ASN* 1.3 58.0 + - - +
939A PRO* 3.4 11.3 - - - +
942A HIS* 5.0 0.7 - - - -
----------------------------------------------------------
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