Contacts of the helix formed by residues 921 - 938 (chain L) in PDB entry 1SOJ
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 ASN 921 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984G LEU* 5.0 0.2 - - - -
985G ALA* 3.4 12.0 - - - +
1071G ILE 2.9 28.3 + - - -
1072G TRP* 3.6 20.5 - - + -
918L GLU* 2.8 31.0 + - + +
920L SER* 1.3 79.3 + - - +
922L GLU* 1.3 66.0 + - - +
923L ASN* 2.8 24.9 + - - +
924L ASP* 3.1 20.1 + - + +
925L ARG* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 922 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982G PRO* 4.3 15.7 - - + +
983G GLN* 3.5 17.6 + - - +
984G LEU* 2.8 36.6 + - - +
985G ALA* 2.9 27.6 + - - +
986G LYS* 3.6 3.3 + - - +
810L GLU* 5.4 0.2 - - - +
881L ARG* 4.3 24.0 + - - +
920L SER 3.6 6.0 + - - +
921L ASN* 1.3 70.7 + - - +
923L ASN* 1.3 67.3 + - - +
925L ARG* 3.2 27.4 + - - +
926L LEU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 923 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985G ALA* 3.8 10.1 - - - +
986G LYS* 5.3 1.3 + - - +
1072G TRP 2.8 25.6 - - - +
1073G LYS* 3.0 26.5 - - - +
908L LYS* 5.4 0.2 - - - +
921L ASN* 2.8 13.8 + - - +
922L GLU* 1.3 82.7 + - - +
924L ASP* 1.3 64.2 + - - +
926L LEU* 3.1 11.6 + - - +
927L LEU* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 924 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071G ILE 5.0 0.2 - - - +
908L LYS* 3.2 44.0 + - - +
916L GLY 4.8 0.9 - - - +
917L ILE* 2.4 47.3 + - + +
918L GLU* 4.1 6.3 - - - +
921L ASN* 3.1 24.7 + - + +
923L ASN* 1.3 77.2 - - - +
925L ARG* 1.3 64.0 + - - +
927L LEU* 3.2 8.7 + - - +
928L VAL* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 925 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982G PRO* 5.7 5.9 - - - +
786L TYR* 5.9 0.2 - - - -
805L ASN 3.8 7.0 - - - -
806L ILE* 4.1 9.5 - - + +
807L PRO* 3.1 28.2 - - - +
810L GLU* 2.7 50.0 + - - +
881L ARG* 4.8 0.4 - - - +
918L GLU 5.3 0.2 + - - -
919L TRP* 2.8 48.6 + - + +
920L SER* 4.0 8.1 + - - +
921L ASN 3.0 8.2 + - - +
922L GLU* 3.4 39.7 + - - +
924L ASP* 1.3 77.1 - - - +
926L LEU* 1.3 62.5 + - - +
928L VAL* 3.2 9.3 + - - +
929L CYS* 3.0 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 926 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881L ARG* 6.3 0.4 - - - +
884L PHE* 4.4 13.7 - - + -
885L LEU* 4.5 22.4 - - + +
888L GLU* 4.0 43.7 - - + +
889L ALA* 5.2 1.6 - - + +
922L GLU 3.0 13.5 + - - +
923L ASN* 3.5 13.7 - - - +
925L ARG* 1.3 75.6 - - - +
927L LEU* 1.3 58.6 + - - +
929L CYS* 3.0 11.8 + - + +
930L GLN* 2.8 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 927 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901L PHE* 4.3 24.7 - - + +
904L GLU* 3.9 32.5 - - - +
905L PHE* 3.7 37.2 - - + +
908L LYS* 4.0 19.5 - - + -
917L ILE* 6.6 0.2 - - + -
923L ASN 2.9 13.4 + - - +
924L ASP* 3.5 10.3 - - - +
926L LEU* 1.3 76.9 - - - +
928L VAL* 1.3 62.3 + - + +
930L GLN* 3.2 15.3 + - - +
931L VAL* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 928 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802L LEU* 4.5 12.3 - - + -
806L ILE* 4.4 10.3 - - + -
905L PHE* 4.3 12.6 - - + -
917L ILE* 4.0 23.8 - - + -
919L TRP* 4.0 33.4 - - + -
924L ASP 3.0 17.4 + - - +
925L ARG 3.5 7.4 - - - +
927L LEU* 1.3 77.7 - - + +
929L CYS* 1.3 62.8 + - - +
931L VAL* 3.3 7.7 + - - +
932L CYS* 3.0 21.9 + - + +
1003L TYR* 4.8 4.9 - - + +
1008L LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 929 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753L THR* 6.2 0.2 - - - -
806L ILE* 4.0 33.7 - - - -
810L GLU* 4.7 12.3 - - - -
811L LEU* 4.7 3.1 - - - -
814L LEU* 3.3 33.1 - - + +
889L ALA* 6.0 1.1 - - + -
925L ARG 3.0 16.4 + - - +
926L LEU* 3.0 18.2 + - + +
928L VAL* 1.3 77.9 - - - +
930L GLN* 1.3 61.1 + - + +
932L CYS* 3.2 20.0 + - - +
933L ILE* 3.2 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 930 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888L GLU* 3.1 43.1 + - - +
889L ALA* 4.5 5.4 - - - -
892L ALA* 3.9 15.6 - - + +
901L PHE* 3.8 31.3 - - + -
926L LEU* 2.8 43.6 + - + +
927L LEU* 3.7 15.5 - - - +
929L CYS* 1.3 71.1 - - - +
931L VAL* 1.3 65.2 + - - +
932L CYS 3.0 1.8 - - - -
933L ILE* 3.1 10.7 - - - +
934L LYS* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 931 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901L PHE* 4.7 10.8 - - + +
902L LEU* 6.0 0.7 - - - -
905L PHE* 3.5 43.1 - - + -
927L LEU* 2.9 27.0 + - + +
928L VAL 3.7 4.3 - - - +
930L GLN* 1.3 76.7 - - + +
932L CYS* 1.3 57.5 + - - +
934L LYS* 3.3 9.3 - - - +
935L LEU* 3.1 26.4 + - + +
999L LEU* 4.2 21.1 - - + +
1002L SER* 6.5 0.2 - - - -
1003L TYR* 3.6 30.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 932 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749L VAL* 4.2 10.8 - - - -
752L LEU* 3.8 25.4 - - - +
753L THR* 3.6 30.1 - - - -
802L LEU* 5.1 0.7 - - - -
814L LEU* 4.3 4.5 - - + -
928L VAL* 3.0 11.9 + - + +
929L CYS* 3.2 15.0 - - - +
930L GLN 3.0 1.0 - - - -
931L VAL* 1.3 73.9 - - - +
933L ILE* 1.3 66.3 + - - +
934L LYS 3.0 1.1 - - - -
935L LEU* 2.9 7.6 + - - +
936L ALA* 2.8 21.8 + - - +
1003L TYR* 3.8 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 933 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745L VAL* 4.6 6.2 - - + +
749L VAL* 3.8 23.0 - - + +
814L LEU* 4.0 14.8 - - + +
817L ALA* 5.3 0.9 - - + -
818L ALA* 4.5 20.9 - - + +
821L HIS* 5.8 2.0 - - + -
889L ALA* 2.8 46.9 - - + +
890L ILE* 6.3 0.2 - - - -
892L ALA* 3.8 11.7 - - + -
893L THR* 4.0 15.0 - - + -
929L CYS 3.2 10.9 + - - +
930L GLN* 3.1 21.1 - - - +
932L CYS* 1.3 75.0 - - - +
934L LYS* 1.3 53.6 + - - +
936L ALA* 4.1 1.3 - - - -
937L ASP* 2.6 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 934 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892L ALA* 3.1 31.9 - - + +
893L THR* 4.4 8.5 - - - +
894L ASP 5.5 0.4 - - - +
895L LEU* 4.6 10.5 - - + +
898L HIS* 3.1 60.1 + - - +
901L PHE* 3.9 17.2 - - + +
902L LEU 5.1 0.2 - - - +
930L GLN 2.9 23.6 + - - +
931L VAL* 3.3 12.1 - - + +
933L ILE* 1.3 80.0 - - - +
935L LEU* 1.3 59.6 + - - +
937L ASP* 3.5 9.3 + - + +
938L ILE* 3.4 22.5 + - - +
999L LEU* 3.9 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677L TRP* 5.8 1.1 - - + -
752L LEU* 4.1 15.0 - - + -
931L VAL 3.1 12.5 + - - +
932L CYS* 2.9 9.2 + - - +
934L LYS* 1.3 71.0 - - - +
936L ALA* 1.3 67.4 + - - +
937L ASP 3.1 2.0 - - - -
938L ILE* 3.0 17.2 + - + +
939L ASN* 3.0 22.0 + - + +
942L ALA* 5.3 3.8 - - + -
996L VAL* 5.1 2.7 - - + -
999L LEU* 3.5 22.8 - - + +
1000L CYS* 3.6 31.9 - - - -
1003L TYR* 3.8 33.7 - - + -
1009L LEU* 4.5 8.3 - - + -
1061L LEU* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 936 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677L TRP* 5.9 0.4 - - - -
745L VAL* 3.5 20.8 - - + +
748L ALA* 3.3 31.2 - - + -
749L VAL* 3.5 29.8 - - + +
752L LEU* 4.6 4.6 - - + +
932L CYS 2.8 12.5 + - - +
933L ILE 3.8 0.9 - - - +
935L LEU* 1.3 74.1 - - - +
937L ASP* 1.3 57.8 + - - +
939L ASN* 2.7 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 937 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736L TYR* 4.1 2.1 + - - -
741L HIS* 2.9 20.3 + - - -
745L VAL* 3.9 7.6 - - + +
821L HIS* 2.7 14.4 + - - +
893L THR* 3.6 30.0 - - + +
895L LEU* 6.0 0.9 - - - +
933L ILE 2.6 21.6 + - - +
934L LYS* 3.7 7.9 - - + +
935L LEU 3.1 0.2 - - - -
936L ALA* 1.3 73.6 - - - +
938L ILE* 1.3 68.2 + - + +
939L ASN* 3.6 1.2 + - - +
2122L IBM 4.0 5.7 - - - +
2145L MG 2.0 32.7 - - - -
2146L MG 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 938 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895L LEU* 4.7 16.4 - - + -
898L HIS* 4.7 3.1 - - + +
934L LYS* 3.4 18.6 - - - +
935L LEU* 3.0 9.7 + - + +
937L ASP* 1.3 91.5 - - + +
939L ASN* 1.3 58.5 + - - +
940L GLY 3.1 7.3 + - - +
941L PRO* 3.8 3.3 - - - +
991L PHE* 4.0 11.2 - - + -
995L ILE* 3.7 21.1 - - + -
996L VAL* 3.4 42.4 - - + +
999L LEU* 3.9 17.5 - - + -
2122L IBM 3.7 23.3 - - + +
----------------------------------------------------------
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