Contacts of the helix formed by residues 936 - 949 (chain A) in PDB entry 3LZB
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 936 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ASN* 6.0 0.7 - - - +
805A GLU* 3.0 38.0 + - - -
870A GLN* 4.4 16.3 + - - +
873A VAL* 4.7 1.3 - - - -
934A ARG 4.7 3.6 - - - +
935A PRO* 1.3 76.2 - - - +
937A PHE* 1.3 60.6 + - - +
938A ARG* 3.2 43.4 - - + +
939A GLU* 3.0 31.2 + - + +
940A LEU* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 937 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ALA* 4.0 11.1 - - + +
801A MET* 3.5 53.4 - - + -
802A ASN* 3.8 23.1 - - + +
805A GLU* 3.8 15.9 - - + +
869A HIS* 3.8 15.0 - - + -
872A ASP* 3.7 19.1 - - + -
873A VAL* 3.7 24.9 - - + +
876A TYR* 3.7 26.0 - + + -
935A PRO 4.2 0.4 + - - -
936A LYS* 1.3 74.9 - - - +
938A ARG* 1.3 58.2 + - - +
940A LEU* 2.9 16.6 + - + +
941A ILE* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 938 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ASN* 3.9 20.3 - - - +
936A LYS* 3.3 45.9 - - + +
937A PHE* 1.3 73.5 - - - +
939A GLU* 1.3 76.3 + - + +
941A ILE* 3.3 14.0 + - + +
942A ILE* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 939 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A LYS* 3.7 22.1 + - - -
934A ARG 4.8 0.7 - - - +
935A PRO* 3.7 7.9 - - + +
936A LYS* 3.0 41.6 + - + +
938A ARG* 1.3 86.6 + - + +
940A LEU* 1.3 54.4 + - - +
942A ILE* 3.2 10.0 + - - +
943A GLU* 2.8 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 940 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ALA* 4.2 11.2 - - + +
873A VAL* 4.3 8.7 - - + -
876A TYR* 3.7 28.9 - - + -
922A ILE* 3.7 30.5 - - + -
926A CYS* 4.3 11.4 - - - -
935A PRO* 3.9 19.7 - - + -
936A LYS 2.9 19.7 + - - +
937A PHE* 2.9 25.1 + - + +
939A GLU* 1.3 76.4 - - - +
941A ILE* 1.3 65.3 + - - +
943A GLU* 4.5 6.1 - - - +
944A PHE* 3.1 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 4.4 6.0 - - + +
798A ALA* 3.8 21.8 - - + -
799A LYS* 3.8 36.1 - - + +
802A ASN* 3.4 38.1 - - + +
937A PHE 2.8 18.4 + - - +
938A ARG* 3.5 10.1 - - + +
940A LEU* 1.3 74.1 - - - +
942A ILE* 1.3 60.0 + - + +
944A PHE* 4.2 0.7 - - - +
945A SER* 2.5 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A ARG* 3.1 21.4 + - + +
939A GLU* 3.2 10.1 + - - +
941A ILE* 1.3 85.8 - - + +
943A GLU* 1.3 67.3 + - + +
945A SER* 3.3 7.3 + - - -
946A LYS* 3.1 23.5 + - + +
949A ARG* 4.5 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A ILE* 3.5 33.4 - - + +
925A LYS* 5.6 0.9 + - - -
935A PRO* 4.6 7.6 - - - +
939A GLU* 2.8 48.9 + - + +
940A LEU* 4.1 9.2 - - - +
941A ILE 3.4 0.2 - - - -
942A ILE* 1.3 76.6 - - + +
944A PHE* 1.3 59.2 + - - +
946A LYS* 3.4 12.8 + - - +
947A MET* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LEU* 3.7 26.6 - - + +
794A CYS* 3.5 32.3 - - + -
795A VAL* 3.5 22.1 - - + +
876A TYR* 3.6 28.5 - + - -
880A VAL* 4.4 12.6 - - + -
884A MET* 4.6 4.7 - - + -
919A VAL* 4.9 8.3 - - + -
922A ILE* 3.9 33.9 - - + -
923A MET* 5.8 1.6 - - + -
940A LEU* 3.1 29.6 + - + +
943A GLU* 1.3 75.4 - - - +
945A SER* 1.3 59.9 + - - +
947A MET* 3.3 12.7 + - - +
948A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 3.7 21.0 - - - +
799A LYS* 5.1 1.4 - - - -
941A ILE* 2.5 30.5 + - - +
942A ILE* 3.3 8.9 - - - -
944A PHE* 1.3 77.3 - - - +
946A LYS* 1.3 61.7 + - - +
948A ALA* 3.4 5.4 + - - +
949A ARG* 3.3 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942A ILE* 3.1 10.8 + - + +
943A GLU* 3.5 14.8 - - - +
944A PHE 3.2 0.2 - - - -
945A SER* 1.3 81.2 - - - +
947A MET* 1.3 66.3 + - - +
949A ARG* 3.1 44.2 + - - +
950A ASP* 3.9 2.6 + - - +
953A ARG* 6.1 0.2 - - - +
954A TYR* 3.7 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LEU* 4.2 10.5 - - + -
918A ASP* 3.8 11.2 - - + +
919A VAL* 3.3 46.9 - - + +
922A ILE* 3.9 18.2 - - + -
943A GLU* 3.2 18.4 + - - +
944A PHE* 3.3 19.7 + - - +
946A LYS* 1.3 85.0 - - + +
948A ALA* 1.3 58.2 + - - +
949A ARG 3.0 0.4 - - - -
950A ASP 3.1 27.4 - - - +
951A PRO* 3.1 6.4 - - - +
954A TYR* 3.3 43.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A GLN* 3.0 23.2 + - - +
791A LEU* 3.9 20.6 - - + +
792A ASN* 3.7 23.8 - - - +
795A VAL* 4.7 1.8 - - + -
944A PHE 2.9 17.1 + - - +
945A SER* 3.8 7.6 - - - +
946A LYS 3.2 0.2 - - - -
947A MET* 1.3 75.0 - - - +
949A ARG* 1.3 56.4 + - - +
950A ASP 3.1 3.4 - - - -
951A PRO* 2.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942A ILE* 4.5 3.0 + - - +
945A SER* 3.3 20.5 + - - +
946A LYS* 3.1 58.9 + - - +
947A MET 3.0 0.4 - - - -
948A ALA* 1.3 78.8 - - - +
950A ASP* 1.3 59.4 + - + +
951A PRO* 3.6 1.8 - - - +
----------------------------------------------------------
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