Contacts of the helix formed by residues 938 - 954 (chain A) in PDB entry 3NC0
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 GLY 938 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A ARG* 3.2 21.3 - - - +
891A ASP* 4.5 4.9 - - - -
894A LEU* 4.4 8.1 - - - -
935A HIS 3.5 2.2 + - - -
936A THR 3.4 0.6 - - - -
937A ALA* 1.3 76.5 - - - +
939A LEU* 1.3 54.7 + - - +
940A THR 3.0 3.6 + - - -
941A MET* 3.0 5.0 + - - +
942A HIS* 2.7 50.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 939 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930A VAL* 6.1 2.0 - - + -
935A HIS 5.0 0.2 - - - -
936A THR* 3.5 22.8 + - - +
937A ALA 3.2 2.9 - - - +
938A GLY* 1.3 75.7 - - - +
940A THR* 1.3 57.8 + - - +
942A HIS* 3.5 10.9 - - + +
943A ALA* 3.0 29.3 + - - +
1012A LYS* 4.0 22.9 - - + +
1015A LEU* 4.4 17.8 - - + +
1016A ARG* 3.5 51.8 - - + +
1019A LEU* 4.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 940 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A ALA 4.9 2.3 + - - -
938A GLY 3.2 0.6 - - - -
939A LEU* 1.3 75.8 - - - +
941A MET* 1.3 59.6 + - + +
943A ALA* 3.2 3.8 + - - +
944A SER* 2.7 43.7 + - - +
1008A ILE* 4.6 7.7 - - + +
1012A LYS* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A ASP* 4.3 12.1 - - - +
894A LEU* 3.6 30.3 - - + +
895A GLN* 3.6 46.4 - - + +
898A PHE* 4.3 20.9 - - + -
938A GLY* 3.0 5.3 + - - +
940A THR* 1.3 80.8 - - + +
942A HIS* 1.3 64.4 + - - +
944A SER* 3.3 13.7 + - - -
945A ILE* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A PHE* 5.0 4.7 - + - -
887A ARG* 5.5 2.0 + - - -
894A LEU* 3.7 31.6 - - + +
926A ILE* 4.6 7.5 - - - +
929A VAL* 3.5 30.1 + - + +
930A VAL* 4.1 32.2 - - + +
935A HIS* 3.6 27.6 + - + +
938A GLY* 2.7 31.1 + - - +
939A LEU* 3.5 9.0 - - + +
941A MET* 1.3 74.7 - - - +
943A ALA* 1.3 63.8 + - - +
945A ILE* 3.3 5.2 + - - +
946A LEU* 3.2 25.9 + - - +
1015A LEU* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 943 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A LEU 3.0 11.2 + - - +
940A THR 3.6 2.2 - - - +
942A HIS* 1.3 80.0 - - - +
944A SER* 1.3 63.3 + - - +
947A ALA* 3.0 24.5 + - - +
1008A ILE* 4.6 4.0 - - + +
1011A PHE* 3.3 32.4 - - + -
1012A LYS* 3.6 22.0 - - + +
1015A LEU* 3.4 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A PHE* 4.4 17.2 - - - -
940A THR* 2.7 30.5 + - - +
941A MET* 3.5 15.6 - - - -
942A HIS 3.2 0.2 - - - -
943A ALA* 1.3 77.4 - - - +
945A ILE* 1.3 64.7 + - - +
947A ALA* 3.6 2.3 - - - +
948A TYR* 3.0 23.6 + - - +
1008A ILE* 3.3 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 3.8 46.7 - - + +
897A LEU* 4.4 14.4 - - + -
898A PHE* 3.8 27.4 - - + +
901A LEU* 3.5 27.8 - - + -
926A ILE* 4.7 11.2 - - + -
941A MET* 3.1 18.7 + - - +
942A HIS* 3.8 3.8 - - - +
944A SER* 1.3 76.1 - - - +
946A LEU* 1.3 63.4 + - + +
948A TYR* 3.2 6.1 + - - +
949A MET* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A LEU* 3.6 30.3 - - + -
926A ILE* 3.7 31.9 - - + -
927A PHE* 3.5 36.1 - - + -
930A VAL* 4.9 4.9 - - + -
942A HIS 3.2 11.1 + - - +
945A ILE* 1.3 77.4 - - - +
947A ALA* 1.3 65.1 + - - +
949A MET* 2.7 18.6 + - - +
950A PHE* 2.8 28.7 + - + -
1001A LEU* 5.3 0.4 - - + -
1011A PHE* 3.6 20.4 - - + -
1015A LEU* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A ALA 3.0 16.9 + - - +
944A SER* 3.6 5.2 - - - +
946A LEU* 1.3 77.7 - - - +
948A TYR* 1.3 57.9 + - - +
950A PHE* 3.9 2.7 - - - +
951A ASN* 2.8 32.5 + - - +
1004A LEU 5.0 0.2 - - - +
1005A ASN* 3.9 21.5 - - - +
1008A ILE* 4.8 10.8 - - + -
1011A PHE* 3.6 28.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A PHE* 4.7 17.5 - + + -
901A LEU* 4.1 31.2 + - + -
902A GLN* 4.1 20.0 - - + +
905A ALA* 3.7 24.8 - - - +
944A SER 3.0 13.4 + - - +
945A ILE* 3.4 11.9 - - - +
946A LEU 3.1 0.2 - - - -
947A ALA* 1.3 76.0 - - - +
949A MET* 1.3 68.5 + - + +
951A ASN* 3.5 7.0 + - + +
952A LEU* 2.9 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 4.1 30.7 - - + -
919A PHE* 3.3 52.6 - - + +
922A ILE* 4.4 17.7 - - + -
923A LEU* 4.2 21.8 - - + -
926A ILE* 5.6 0.7 - - - -
945A ILE* 2.9 34.5 + - - +
946A LEU* 2.7 16.9 + - - +
948A TYR* 1.3 73.9 - - + +
950A PHE* 1.3 58.9 + - - +
952A LEU* 3.2 10.3 - - + +
953A VAL* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A PHE* 6.2 0.4 - + - -
923A LEU* 4.2 14.6 - - + -
927A PHE* 3.9 17.5 - + - -
946A LEU* 2.8 57.5 + - + +
947A ALA 3.9 4.3 - - - +
949A MET* 1.3 69.7 - - - +
951A ASN* 1.3 60.6 + - - +
952A LEU 3.0 1.6 - - - -
953A VAL* 2.8 32.8 + - + +
954A GLU* 3.4 10.7 + - - +
974A ILE* 5.0 2.7 - - + -
978A VAL* 4.5 13.9 - - + -
1001A LEU* 3.4 48.9 - - + +
1002A PHE* 3.7 37.2 - + + -
1005A ASN* 4.5 3.1 - - + -
1011A PHE* 3.9 10.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A ALA 2.8 19.3 + - - +
948A TYR* 3.7 7.9 - - + +
950A PHE* 1.3 76.5 - - - +
952A LEU* 1.3 58.0 + - - +
954A GLU* 3.6 2.8 + - - +
955A GLU* 2.8 30.9 - - - +
1005A ASN* 3.0 35.2 + - - +
1006A GLN* 3.5 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 5.8 4.0 - - + +
905A ALA* 6.2 0.2 - - + -
915A TYR* 3.5 35.9 - - + +
919A PHE* 4.8 10.3 - - + -
948A TYR* 2.9 46.7 + - + +
949A MET* 3.2 12.1 - - + +
951A ASN* 1.3 78.4 - - - +
953A VAL* 1.3 62.8 + - - +
954A GLU 3.2 0.5 + - - -
955A GLU* 3.2 1.0 + - - -
956A GLY* 3.0 34.0 + - - +
957A LYS* 3.5 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A PHE* 3.5 28.0 - - + -
949A MET 2.9 25.2 + - - +
950A PHE* 2.8 20.7 + - + +
952A LEU* 1.3 80.5 - - + +
954A GLU* 1.3 55.8 + - - +
955A GLU* 3.1 7.6 + - - +
957A LYS* 4.8 11.1 - - + +
970A ASN* 4.2 14.8 - - + +
971A GLN* 3.8 21.6 + - + +
974A ILE* 3.7 32.8 - - + -
1002A PHE* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A PHE 3.8 11.6 - - - +
951A ASN 4.0 1.8 - - - +
952A LEU 3.2 1.6 - - - -
953A VAL* 1.3 76.8 - - - +
955A GLU* 1.3 79.1 + - - +
971A GLN* 4.5 21.5 + - - +
1002A PHE* 3.2 41.7 - - + +
1005A ASN* 3.4 16.5 + - - -
1046A GLN* 4.9 2.7 - - - +
1049A LYS* 3.8 12.1 + - - -
----------------------------------------------------------
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