Contacts of the helix formed by residues 870 - 884 (chain A) in PDB entry 4TWO
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 870 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ALA* 5.5 8.7 - - - +
807A VAL* 4.8 2.5 - - + -
865A ARG 5.8 1.2 + - - -
866A ASN* 5.9 4.7 + - - +
868A ARG 4.8 7.0 + - - +
869A PRO* 1.3 77.0 - - - +
871A PHE* 1.3 66.6 + - - +
872A GLU* 3.1 9.6 - - + +
873A GLN* 2.8 35.1 + - + +
874A ILE* 3.1 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ALA* 4.1 10.5 - - + +
734A MET* 3.5 42.0 - - + -
735A LYS* 3.6 23.1 - - + +
738A SER* 3.7 23.3 - - - +
803A SER* 3.9 5.8 - - - -
806A ASP* 3.8 23.3 - - + -
807A VAL* 3.7 33.2 - - + +
810A TYR* 3.8 26.0 - + + -
869A PRO 4.1 0.6 + - - -
870A LYS* 1.3 74.3 - - - +
872A GLU* 1.3 57.1 + - - +
874A ILE* 3.2 14.8 + - + +
875A VAL* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A LYS* 3.7 37.0 + - - +
870A LYS* 3.1 7.9 - - + +
871A PHE* 1.3 78.6 - - - +
873A GLN* 1.3 58.9 + - + +
875A VAL* 3.5 6.1 + - - +
876A SER* 2.8 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A ARG 4.7 0.5 - - - +
869A PRO* 3.3 16.7 - - + +
870A LYS* 2.8 43.9 + - + +
872A GLU* 1.3 76.5 - - + +
874A ILE* 1.3 60.4 + - - +
876A SER* 3.2 8.2 + - - -
877A ILE* 2.8 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A ALA* 3.8 14.1 - - + -
807A VAL* 4.0 13.7 - - + -
810A TYR* 3.7 31.6 - - + -
856A LEU* 4.4 11.4 - - + -
860A CYS* 3.9 25.1 - - - -
869A PRO* 3.9 15.5 - - + -
870A LYS 3.1 12.5 + - - +
871A PHE* 3.2 25.3 + - + +
873A GLN* 1.3 75.9 - - - +
875A VAL* 1.3 64.4 + - - +
877A ILE* 3.2 9.2 + - - +
878A LEU* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ARG* 3.7 26.4 - - - +
731A ALA* 3.7 13.0 - - + +
732A SER* 3.7 33.4 - - - +
735A LYS* 4.4 7.9 - - + -
871A PHE 2.9 19.6 + - - +
872A GLU* 3.7 8.7 - - - +
874A ILE* 1.3 73.9 - - - +
876A SER* 1.3 58.1 + - - +
878A LEU* 3.2 6.1 + - - +
879A ASP* 2.8 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A GLU* 2.8 25.0 + - - +
873A GLN* 3.2 12.5 + - - -
875A VAL* 1.3 74.4 - - - +
877A ILE* 1.3 65.8 + - - +
879A ASP* 3.3 8.9 + - - +
880A LYS* 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A ALA 5.8 1.3 - - - +
856A LEU* 4.0 39.9 - - + -
859A ASP* 5.6 3.1 - - - +
869A PRO* 5.0 7.2 - - + -
873A GLN* 2.8 34.4 + - + +
874A ILE* 3.5 6.1 - - - +
876A SER* 1.3 73.7 - - - +
878A LEU* 1.3 60.0 + - - +
880A LYS* 3.3 12.7 + - + +
881A LEU* 3.2 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A VAL* 3.9 14.3 - - + +
727A LEU* 3.5 21.3 - - + +
728A ARG* 3.6 22.0 - - + -
731A ALA* 4.2 3.1 - - + -
810A TYR* 3.2 26.7 - - + +
814A LEU* 5.7 0.4 - - + -
853A LEU* 4.0 20.4 - - + -
856A LEU* 4.0 20.0 - - + -
874A ILE* 2.9 29.5 + - + +
875A VAL* 3.8 2.9 - - - +
877A ILE* 1.3 74.6 - - - +
879A ASP* 1.3 62.7 + - - +
881A LEU* 3.3 8.5 + - + +
882A ILE* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ARG* 2.7 45.9 + - - +
875A VAL* 2.8 23.8 + - - +
876A SER* 3.7 8.9 - - - +
877A ILE 3.3 0.2 - - - -
878A LEU* 1.3 78.4 - - - +
880A LYS* 1.3 60.3 + - - +
882A ILE* 3.6 11.6 + - - +
883A ARG* 3.2 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A SER* 3.1 20.5 + - - +
877A ILE* 3.5 12.1 - - + +
878A LEU 3.2 0.2 - - - -
879A ASP* 1.3 75.9 - - - +
881A LEU* 1.3 66.6 + - + +
883A ARG* 3.1 27.9 + - - +
884A ASN* 3.2 14.9 + - - +
887A SER* 4.3 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ILE* 3.8 10.5 - - - +
724A VAL* 4.5 7.2 - - + -
852A ALA* 3.9 23.1 - - + +
853A LEU* 3.8 29.2 - - + -
856A LEU* 5.7 0.4 - - + -
877A ILE* 3.2 28.6 + - + +
878A LEU* 3.3 11.0 + - + +
880A LYS* 1.3 76.9 - - + +
882A ILE* 1.3 62.4 + - - +
884A ASN 3.6 17.2 - - - +
887A SER* 3.6 27.8 - - - +
888A LEU* 3.8 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A ILE* 3.9 23.3 - - + +
724A VAL* 3.5 22.0 - - + -
725A GLY* 4.1 23.3 - - - +
728A ARG* 4.3 18.4 - - + -
878A LEU 3.0 15.5 + - - +
879A ASP* 3.7 12.6 - - - +
880A LYS 3.2 0.2 - - - -
881A LEU* 1.3 77.3 - - - +
883A ARG* 1.3 67.0 + - + +
884A ASN 3.5 0.2 + - - -
885A PRO* 3.7 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ASP* 3.2 44.0 + - - +
880A LYS* 3.1 23.9 + - - +
882A ILE* 1.3 87.0 - - + +
884A ASN* 1.3 58.4 + - + +
885A PRO* 3.5 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A LYS 3.2 8.0 + - - +
881A LEU 3.6 4.6 - - - +
883A ARG* 1.3 80.9 - - + +
885A PRO* 1.3 54.8 - - - +
886A GLY* 2.9 7.0 - - - +
887A SER* 2.3 50.4 + - - +
----------------------------------------------------------
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