Contacts of the helix formed by residues 976 - 994 (chain A) in PDB entry 4AY6
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 ASP 976 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A LYS* 2.9 32.7 + - + +
973A LEU 4.3 2.2 - - - -
975A THR* 1.3 76.4 + - - +
977A LEU* 1.3 50.9 + - - +
978A GLU* 3.5 11.4 + - - +
979A TYR* 2.9 28.9 + - + +
980A LEU* 2.8 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TYR* 6.2 3.8 - - + -
832A ILE* 4.3 18.4 - - + -
974A GLY 4.2 11.4 - - - +
975A THR 3.0 24.7 + - - +
976A ASP* 1.3 71.8 + - - +
978A GLU* 1.3 65.3 + - - +
980A LEU* 3.6 14.2 - - + +
981A LYS* 3.1 23.0 + - - +
1019B ALA 5.5 7.2 - - - +
1021B ASN* 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A ASP* 3.1 9.3 + - - +
977A LEU* 1.3 79.2 - - - +
979A TYR* 1.3 65.0 + - - +
981A LYS* 3.4 29.6 + - - +
982A LYS* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A GLU* 3.5 33.5 + - + +
958A LEU* 6.5 0.2 - - + -
969A ILE* 5.3 5.0 - - + +
972A LYS* 3.6 51.2 + - + +
973A LEU* 3.8 27.6 - - + -
976A ASP* 2.9 25.5 + - - +
978A GLU* 1.3 76.3 - - - +
980A LEU* 1.3 68.9 + - - +
982A LYS* 2.9 32.2 + - + +
983A VAL* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ILE* 4.2 23.1 - - + -
909A ASP* 4.2 16.6 - - + +
910A VAL* 4.0 25.1 - - + -
932A PRO* 5.1 1.1 - - + -
973A LEU* 3.4 40.6 - - + +
974A GLY* 5.3 0.2 - - - -
976A ASP 2.8 14.7 + - - +
977A LEU* 3.6 14.8 - - + +
979A TYR* 1.3 75.3 - - - +
981A LYS* 1.3 63.4 + - - +
983A VAL* 3.2 1.4 + - - +
984A ARG* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 981 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A ILE* 5.0 10.1 + - - +
977A LEU 3.1 13.8 + - - +
978A GLU* 3.6 30.3 + - - +
979A TYR 3.2 0.2 - - - -
980A LEU* 1.3 79.3 - - - +
982A LYS* 1.3 62.7 + - - +
984A ARG* 4.0 8.1 - - - +
985A GLY* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 982 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A GLU 3.1 12.4 + - - +
979A TYR* 2.9 28.6 + - + +
981A LYS* 1.3 78.7 - - - +
983A VAL* 1.3 63.3 + - + +
985A GLY* 3.4 1.7 + - - -
986A LYS* 3.1 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 983 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A PRO* 4.0 12.8 - - + -
955A CYS* 5.5 0.7 - - - -
957A GLU* 4.9 13.5 - - + +
958A LEU* 3.9 34.5 - - + -
973A LEU* 4.0 9.6 - - + -
979A TYR* 3.0 47.5 + - + +
980A LEU 3.7 4.0 - - - +
982A LYS* 1.3 72.8 - - + +
984A ARG* 1.3 62.4 + - - +
986A LYS* 2.8 27.6 + - + +
987A VAL* 3.0 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A LYS* 4.7 8.9 - - - +
721A ASP* 2.9 35.7 + - - +
722A ASN* 4.2 3.8 - - - -
746A MET* 5.5 0.9 - - - -
906A GLN 3.7 14.8 + - - -
908A ALA 3.2 22.5 + - - -
909A ASP* 2.8 38.4 + - - +
929A ALA 4.8 2.2 + - - -
930A GLY 3.9 17.2 + - - +
931A THR* 3.8 11.1 + - - -
932A PRO* 3.6 27.8 - - + +
980A LEU* 2.9 37.8 + - + +
981A LYS* 4.0 7.0 - - - +
983A VAL* 1.3 72.1 - - - +
985A GLY* 1.3 63.3 + - - +
987A VAL* 3.6 2.5 + - - +
988A TRP* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A MET* 4.2 24.7 - - - +
981A LYS 3.0 15.8 + - - -
982A LYS 3.7 4.3 - - - -
984A ARG* 1.3 76.5 - - - +
986A LYS* 1.3 62.2 + - - +
988A TRP* 3.5 2.8 - - - +
989A LYS* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A GLY 3.4 21.5 + - - -
955A CYS* 4.0 10.1 - - - -
957A GLU* 2.6 35.2 + - - +
982A LYS* 3.1 19.2 + - + +
983A VAL* 2.8 17.6 + - + +
985A GLY* 1.3 75.4 - - - +
987A VAL* 1.3 51.1 + - - +
989A LYS* 3.0 6.5 + - - +
990A GLN* 2.7 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A LEU* 3.9 13.7 - - + +
930A GLY* 3.5 29.4 - - - +
931A THR 3.9 6.5 - - - +
932A PRO* 3.8 26.9 - - + -
950A LEU* 6.2 0.2 - - + -
953A LEU* 4.6 17.3 - - + +
955A CYS* 4.6 12.7 - - - -
958A LEU* 4.7 3.1 - - + -
983A VAL* 3.5 15.0 - - + +
984A ARG 3.7 6.5 - - - +
986A LYS* 1.3 74.6 - - - +
988A TRP* 1.3 63.7 + - - +
990A GLN* 4.3 5.4 - - - +
991A ARG* 2.9 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 988 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU 3.7 12.8 - - - -
706A LYS 3.3 11.7 + - - -
707A LYS* 4.0 1.6 - - + -
708A LYS* 3.3 60.3 - - + -
746A MET* 3.7 33.3 - - + -
762A LEU* 4.5 18.1 - - - +
763A ASN 5.5 0.8 + - - +
906A GLN* 4.3 5.2 - - - -
929A ALA* 3.7 21.3 - - - -
930A GLY* 3.9 6.7 - - - +
984A ARG 3.0 15.0 + - - +
985A GLY* 3.5 8.3 - - - +
987A VAL* 1.3 79.7 - - - +
989A LYS* 1.3 66.0 + - + +
991A ARG* 3.0 61.9 + - - +
992A ILE* 4.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU 5.2 11.4 - - - +
985A GLY 3.0 15.9 + - - +
986A LYS* 3.0 5.4 + - - +
988A TRP* 1.3 81.8 - - + +
990A GLN* 1.3 76.7 + - - +
992A ILE* 3.1 17.2 + - - +
993A SER* 3.3 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A LEU* 3.3 40.0 + - + +
954A GLY* 5.1 2.9 - - - +
955A CYS* 4.8 4.3 - - - -
986A LYS* 2.7 42.5 + - + +
987A VAL* 3.8 2.2 - - - +
989A LYS* 1.3 93.7 + - - +
991A ARG* 1.3 58.3 + - - +
993A SER* 3.6 11.0 + - - -
994A SER* 2.7 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A LEU 3.2 18.2 + - - -
706A LYS* 2.8 30.4 + - - +
927A LEU* 3.8 12.8 - - + +
928A TRP* 2.7 53.3 + - + +
930A GLY 4.5 1.8 - - - +
953A LEU* 3.7 13.0 - - + +
987A VAL* 2.9 13.2 + - + +
988A TRP* 3.0 56.3 + - - +
989A LYS 3.1 0.4 + - - -
990A GLN* 1.3 76.4 - - - +
992A ILE* 1.3 77.5 + - + +
994A SER* 4.4 2.5 + - - +
997A PHE* 3.4 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 992 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A ALA* 6.2 0.7 - - + -
706A LYS* 4.1 22.0 - - + +
928A TRP* 3.9 32.1 - - + -
988A TRP 4.5 4.0 - - - +
989A LYS* 3.1 9.3 + - - +
990A GLN 3.0 0.6 - - - -
991A ARG* 1.3 94.2 - - + +
993A SER* 1.3 66.9 + - - +
994A SER 3.2 9.0 - - - +
997A PHE* 6.1 0.2 - - + -
998A ASN* 5.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 993 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LYS* 3.3 41.1 + - - +
990A GLN* 3.6 11.9 + - - -
992A ILE* 1.3 79.6 - - - +
994A SER* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 994 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A CYS 3.7 11.0 - - - -
953A LEU* 3.4 19.3 - - - +
990A GLN* 2.7 40.9 + - - +
991A ARG* 4.4 2.9 + - - +
992A ILE 3.2 11.3 - - - +
993A SER* 1.3 77.8 + - - +
995A PRO* 1.4 74.2 - - - +
996A LEU* 3.2 14.8 + - - +
997A PHE 4.6 1.0 + - - -
998A ASN* 4.6 4.7 + - - +
----------------------------------------------------------
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