Contacts of the helix formed by residues 921 - 938 (chain C) in PDB entry 1SO2
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908C LYS* 4.9 4.9 - - - +
918C GLU* 2.7 35.0 + - + +
920C SER* 1.3 79.6 + - - +
922C GLU* 1.3 63.4 + - - +
923C ASN* 2.8 39.1 + - - +
924C ASP* 3.4 20.8 + - - -
925C ARG* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C GLU* 5.7 0.2 - - - -
881C ARG* 3.5 45.2 + - - +
920C SER 3.6 3.9 + - - +
921C ASN* 1.3 74.1 + - - +
923C ASN* 1.3 69.3 + - - +
925C ARG* 3.5 24.7 + - - +
926C LEU* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 923 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921C ASN* 2.8 12.0 + - - +
922C GLU* 1.3 84.2 + - - +
924C ASP* 1.3 69.7 + - - +
926C LEU* 3.2 11.0 + - - +
927C LEU* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 924 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908C LYS* 3.3 44.4 + - - +
916C GLY 4.0 0.5 - - - +
917C ILE* 3.9 12.4 - - + +
918C GLU* 3.0 43.9 + - - +
921C ASN* 3.3 22.2 + - - +
923C ASN* 1.3 78.9 - - - +
925C ARG* 1.3 61.9 + - - +
927C LEU* 3.6 8.9 + - - +
928C VAL* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 925 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784C ILE* 5.5 6.6 - - - +
786C TYR* 6.0 0.2 - - - -
805C ASN 3.5 19.5 - - - -
806C ILE* 4.2 10.7 - - + +
807C PRO* 3.3 16.6 - - - +
810C GLU* 2.7 46.8 + - - +
919C TRP* 2.8 49.3 + - + +
920C SER* 3.3 21.0 + - - +
921C ASN 3.1 21.1 + - - +
922C GLU* 3.5 24.9 + - - +
923C ASN 3.1 0.2 - - - -
924C ASP* 1.3 75.3 - - - +
926C LEU* 1.3 65.4 + - - +
928C VAL* 3.3 8.5 + - - +
929C CYS* 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 926 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C GLU* 6.0 0.4 - - - -
884C PHE* 4.4 14.1 - - + -
885C LEU* 3.8 31.2 - - + +
888C GLU* 4.0 39.3 - - + +
889C ALA* 5.2 2.5 - - + +
922C GLU 3.2 14.4 + - - +
923C ASN* 3.2 13.7 + - - +
925C ARG* 1.3 75.4 - - - +
927C LEU* 1.3 63.6 + - - +
929C CYS* 3.0 14.1 + - + +
930C GLN* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 927 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C PHE* 4.1 27.6 - - + +
904C GLU* 4.0 32.1 - - + +
905C PHE* 3.8 32.1 - - + +
908C LYS* 4.4 16.2 - - + -
917C ILE* 5.8 2.9 - - + -
923C ASN 3.1 13.9 + - - +
924C ASP* 3.7 7.4 - - - +
926C LEU* 1.3 79.2 - - - +
928C VAL* 1.3 64.3 + - + +
930C GLN* 2.8 21.2 + - - +
931C VAL* 2.8 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 928 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C LEU* 4.5 11.4 - - + -
806C ILE* 4.1 20.6 - - + -
905C PHE* 4.5 6.1 - - + -
917C ILE* 4.3 19.5 - - + -
919C TRP* 4.1 27.6 - - + -
924C ASP 3.2 14.4 + - - +
925C ARG 3.5 8.1 - - - +
927C LEU* 1.3 78.9 - - + +
929C CYS* 1.3 58.3 + - - +
931C VAL* 3.4 7.5 + - - +
932C CYS* 2.8 29.5 + - + +
1003C TYR* 4.6 4.0 - - + +
1008C LEU* 4.4 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 929 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C ILE* 4.1 31.0 - - - -
810C GLU* 4.4 17.9 - - - -
811C LEU* 4.5 1.1 - - - -
814C LEU* 3.2 37.3 - - + +
889C ALA* 5.7 1.8 - - + -
925C ARG 3.0 18.0 + - - -
926C LEU* 3.0 17.3 + - + +
928C VAL* 1.3 76.2 - - - +
930C GLN* 1.3 58.6 + - - +
932C CYS* 3.4 5.1 - - - +
933C ILE* 2.8 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 930 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C GLU* 2.9 42.5 + - - +
889C ALA* 4.4 5.4 - - + +
892C ALA* 3.8 13.7 - - + -
901C PHE* 3.5 34.8 - - + -
926C LEU* 2.8 32.5 + - + +
927C LEU* 2.8 25.7 + - - +
929C CYS* 1.3 74.1 - - - +
931C VAL* 1.3 60.1 + - - +
933C ILE* 3.2 12.0 - - - +
934C LYS* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 931 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C PHE* 4.8 9.9 - - + +
902C LEU* 6.0 0.4 - - - -
905C PHE* 3.4 46.0 - - + -
927C LEU* 2.8 30.0 + - + +
928C VAL 3.8 4.0 - - - +
930C GLN* 1.3 72.5 - - + +
932C CYS* 1.3 58.3 + - - +
934C LYS* 3.3 10.0 + - + +
935C LEU* 3.0 27.8 + - + +
999C LEU* 4.0 22.6 - - + +
1002C SER* 6.6 0.2 - - - -
1003C TYR* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 932 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C VAL* 4.1 10.8 - - - -
752C LEU* 3.8 30.2 - - - +
753C THR* 4.1 19.5 - - + -
802C LEU* 5.7 0.2 - - + -
814C LEU* 4.1 6.5 - - + -
928C VAL* 2.8 21.5 + - + +
929C CYS* 3.4 9.4 - - - +
931C VAL* 1.3 75.2 - - - +
933C ILE* 1.3 64.9 + - - +
935C LEU* 3.5 4.7 + - - +
936C ALA* 3.0 24.4 + - - +
1003C TYR* 3.7 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 933 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C VAL* 4.3 9.9 - - + -
749C VAL* 3.9 18.1 - - + +
814C LEU* 3.9 10.3 - - + +
817C ALA* 4.2 13.5 - - + -
818C ALA* 4.2 25.4 - - - +
821C HIS* 4.8 4.7 - - + -
889C ALA* 3.8 27.8 - - + +
890C ILE 4.7 0.2 - - - +
892C ALA* 4.6 2.5 - - + -
893C THR* 4.0 21.6 - - + +
929C CYS 2.8 18.6 + - - +
930C GLN* 3.2 18.8 - - - +
932C CYS* 1.3 75.5 - - - +
934C LYS* 1.3 61.6 + - - +
936C ALA* 3.8 0.4 - - - +
937C ASP* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 934 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C ALA* 3.3 30.8 + - + +
893C THR* 4.8 4.4 - - - +
895C LEU* 4.0 16.6 - - - +
898C HIS* 3.0 56.7 + - - +
901C PHE* 4.1 23.6 - - + -
902C LEU 5.6 0.4 - - - +
930C GLN 2.9 22.1 + - - +
931C VAL* 3.5 11.0 - - + +
932C CYS 3.1 0.2 - - - -
933C ILE* 1.3 75.5 - - + +
935C LEU* 1.3 67.8 + - - +
937C ASP* 2.9 17.7 + - - +
938C ILE* 3.3 16.4 + - - +
999C LEU* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C TRP* 4.9 3.1 - - + -
752C LEU* 3.6 23.6 - - + -
931C VAL 3.0 13.6 + - - +
932C CYS* 3.9 3.8 - - - +
934C LYS* 1.3 77.9 - - - +
936C ALA* 1.3 68.3 + - - +
938C ILE* 3.3 5.1 + - - +
939C ASN* 3.2 27.9 + - + -
942C ALA* 6.2 2.0 - - + -
999C LEU* 3.6 19.4 - - + +
1000C CYS* 4.3 26.0 - - - -
1003C TYR* 4.0 39.7 - - + -
1009C LEU* 4.4 10.1 - - + -
1061C LEU* 4.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 936 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C VAL* 3.6 17.1 - - + +
748C ALA* 3.5 28.3 - - + -
749C VAL* 3.5 22.2 - - + +
752C LEU* 4.8 1.8 - - + -
932C CYS 3.0 18.6 + - - +
933C ILE 3.8 2.9 - - - +
935C LEU* 1.3 80.4 - - - +
937C ASP* 1.3 59.7 + - - +
939C ASN* 2.9 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 937 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C MG 2.1 30.5 - - - -
736C TYR* 3.8 5.5 + - - -
741C HIS* 2.8 29.7 + - - -
745C VAL* 3.7 6.1 - - + -
821C HIS* 3.0 13.8 + - - +
893C THR* 3.7 26.9 - - + +
895C LEU* 6.1 1.4 - - - +
933C ILE 3.0 13.0 + - - +
934C LYS* 2.9 14.3 + - - +
936C ALA* 1.3 78.5 - - - +
938C ILE* 1.3 65.0 + - + +
939C ASN* 3.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 938 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C 666 3.5 28.8 - - + +
736C TYR* 4.9 0.2 - - - -
895C LEU* 4.7 19.5 - - + -
898C HIS* 5.0 2.2 - - + +
934C LYS* 3.6 13.2 - - - +
935C LEU* 3.5 7.0 - - - +
936C ALA 3.3 0.4 - - - -
937C ASP* 1.3 86.2 - - + +
939C ASN* 1.3 62.0 + - - +
940C GLY 3.4 3.8 + - - -
941C PRO* 3.6 5.5 - - - +
991C PHE* 4.0 18.8 - - + -
995C ILE* 3.9 26.7 - - + -
996C VAL* 3.8 25.4 - - + +
999C LEU* 3.9 21.3 - - + -
----------------------------------------------------------
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