Contacts of the helix formed by residues 977 - 998 (chain C) in PDB entry 5Y3R
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 977 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928C VAL* 4.4 16.3 - - - +
973C ALA 2.2 35.7 + - - +
976C VAL* 1.3 94.3 - - + +
978C GLN* 1.3 64.9 + - - +
979C VAL* 3.3 18.6 - - + +
980C THR* 2.9 38.9 + - - +
981C ARG* 3.4 5.9 + - - +
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Residues in contact with GLN 978 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973C ALA 3.6 0.8 + - - -
974C CYS* 4.3 9.7 + - - +
976C VAL 4.1 1.4 + - - -
977C ASP* 1.3 71.5 - - - +
979C VAL* 1.3 57.5 + - + +
981C ARG* 5.7 3.2 - - - +
982C GLN* 2.2 89.6 + - - +
985C GLU* 5.6 0.8 + - - -
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Residues in contact with VAL 979 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977C ASP* 2.9 27.9 - - + +
978C GLN* 1.3 81.0 - - + +
980C THR* 1.3 54.6 + - - +
982C GLN* 4.8 1.3 - - - -
983C LEU* 2.4 44.9 + - + +
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Residues in contact with THR 980 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927C LYS* 6.5 0.7 - - - -
928C VAL* 5.8 0.3 - - - -
931C CYS* 3.6 31.3 - - + -
969C LEU* 3.4 24.5 - - + +
973C ALA* 3.4 17.3 - - + -
976C VAL* 5.0 2.5 - - - +
977C ASP* 2.9 29.3 + - - +
979C VAL* 1.3 79.3 - - - +
981C ARG* 1.3 69.5 + - - +
983C LEU* 2.7 14.1 + - - -
984C TYR* 2.8 19.7 - - + -
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Residues in contact with ARG 981 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970C LEU* 3.0 63.2 + - + +
971C ARG 5.1 0.2 - - - -
973C ALA* 3.0 14.4 - - + +
974C CYS* 4.6 7.9 - - - +
977C ASP 3.4 3.9 + - - +
978C GLN* 4.7 3.1 - - - +
980C THR* 1.3 76.8 - - - +
982C GLN* 1.3 60.7 + - - +
984C TYR 2.9 2.6 + - - -
985C GLU* 2.2 59.2 + - - +
1026C ARG* 2.8 27.4 - - - +
1027C ASP* 2.8 37.8 + - - +
1031C ARG* 2.8 38.6 - - - +
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Residues in contact with GLN 982 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978C GLN* 2.2 68.1 + - - +
979C VAL* 4.8 1.6 - - - -
981C ARG* 1.3 79.5 - - - +
983C LEU* 1.3 56.8 + - - +
985C GLU* 3.4 17.0 - - - +
986C PRO* 3.0 24.8 - - + +
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Residues in contact with LEU 983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C CYS* 5.5 1.3 - - - -
935C HIS* 4.5 21.2 - - + +
979C VAL* 2.4 39.2 + - + +
980C THR* 2.7 14.7 + - - +
982C GLN* 1.3 72.6 - - - +
984C TYR* 1.3 86.8 + - + +
986C PRO* 3.4 14.4 - - - +
987C LEU* 4.3 5.7 + - - +
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Residues in contact with TYR 984 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931C CYS* 2.4 51.1 + - + +
932C GLU* 3.3 8.7 + - - -
934C LEU* 4.4 1.3 - - + -
935C HIS* 3.3 44.4 - - + +
966C PHE* 6.2 0.4 - + - -
969C LEU* 3.4 34.1 - - + -
970C LEU* 3.5 9.9 - - + -
980C THR* 2.8 27.9 + - + +
981C ARG 4.0 0.9 - - - +
983C LEU* 1.3 102.4 - - + +
985C GLU* 1.3 54.0 + - - +
986C PRO 3.4 0.4 - - - -
987C LEU* 3.0 14.7 + - + +
988C VAL* 2.6 38.4 + - + +
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Residues in contact with GLU 985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970C LEU* 3.4 4.0 - - + -
978C GLN* 5.6 0.4 + - - -
981C ARG* 2.2 55.8 + - - +
982C GLN* 3.4 21.6 - - - +
984C TYR* 1.3 72.8 - - - +
986C PRO* 1.3 68.0 - - + +
987C LEU 2.9 4.3 - - - -
988C VAL* 2.9 27.0 - - - +
989C MET* 2.9 16.0 + - - +
1026C ARG* 3.9 6.1 + - - -
1031C ARG* 3.2 26.2 - - - +
2776C ARG* 4.5 0.2 - - - -
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Residues in contact with PRO 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982C GLN 3.0 28.9 - - - +
983C LEU 3.4 10.8 - - - +
985C GLU* 1.3 85.8 - - + +
987C LEU* 1.3 55.5 + - - +
989C MET* 5.3 0.2 - - - -
990C GLN* 2.8 12.0 + - - +
2775C TYR* 6.4 1.3 - - + -
2776C ARG* 2.0 49.8 + - - +
2779C ASP* 5.5 0.7 - - - +
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Residues in contact with LEU 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935C HIS* 3.4 50.9 - - + +
938C VAL* 4.5 26.7 - - + -
939C MET* 4.6 9.0 - - + -
983C LEU 4.3 2.2 + - - +
984C TYR* 3.0 22.5 + - + +
985C GLU 2.9 0.8 - - - -
986C PRO* 1.3 78.2 - - - +
988C VAL* 1.3 67.8 + - + +
989C MET 3.1 1.6 - - - -
990C GLN* 2.9 34.0 - - + +
991C LEU* 2.9 23.3 + - + +
2783C ILE* 5.8 1.1 - - + -
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Residues in contact with VAL 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966C PHE* 4.9 13.2 - - + -
970C LEU* 3.7 24.9 - - + -
984C TYR* 2.6 21.9 + - + +
985C GLU* 2.9 25.1 - - - +
987C LEU* 1.3 74.1 - - + +
989C MET* 1.3 58.5 + - + +
991C LEU* 2.9 29.0 - - + +
992C ILE* 3.0 15.1 + - + +
1009C LEU* 6.0 6.1 - - + -
1031C ARG* 3.0 40.8 - - - +
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Residues in contact with MET 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985C GLU* 2.9 18.9 + - + +
988C VAL* 1.3 79.6 - - + +
990C GLN* 1.3 59.1 + - - +
991C LEU 3.1 1.6 - - - -
992C ILE* 3.1 13.7 - - + +
993C HIS* 2.9 30.7 + - - +
1030C GLY 3.8 10.5 - - - +
1031C ARG* 3.3 36.8 - - - +
1034C ARG* 3.4 43.1 + - + -
2776C ARG* 3.1 29.7 + - - +
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Residues in contact with GLN 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939C MET* 4.4 8.3 - - - +
986C PRO* 2.8 19.1 + - - +
987C LEU* 2.9 50.2 + - + +
989C MET* 1.3 73.1 - - - +
991C LEU* 1.3 65.9 + - - +
993C HIS* 4.2 1.7 - - - +
994C TRP* 3.2 19.8 + - - +
2776C ARG* 3.1 17.2 - - - +
2779C ASP* 2.9 39.5 - - + +
2782C ASP* 5.2 2.6 - - - +
2783C ILE* 3.3 34.0 - - + +
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Residues in contact with LEU 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C VAL* 6.5 0.7 - - + -
942C LEU* 6.2 1.3 - - + -
959C TYR* 3.8 18.4 - - - +
963C LYS* 3.5 17.9 - - + +
987C LEU* 2.9 13.9 + - + +
988C VAL* 2.9 17.9 - - + +
990C GLN* 1.3 76.4 - - - +
992C ILE* 1.3 59.1 + - + +
994C TRP* 2.7 36.0 + - + +
995C PHE* 3.3 29.0 - - + -
1002C GLU* 3.5 14.6 - - - +
1006C THR* 3.2 31.4 - - + +
1009C LEU* 4.5 7.0 - - + -
2783C ILE* 4.9 2.2 - - - -
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Residues in contact with ILE 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988C VAL* 3.0 15.7 + - + +
989C MET* 3.0 26.0 + - + +
991C LEU* 1.3 76.0 - - + +
993C HIS* 1.3 50.8 + - - +
995C PHE* 3.4 13.9 - - + -
996C THR* 2.6 37.6 + - - +
1006C THR* 4.2 21.5 - - + -
1009C LEU* 5.6 1.8 - - + -
1031C ARG* 3.8 17.3 - - + +
1034C ARG* 3.4 33.7 - - + +
1035C GLU* 3.5 25.8 - - + +
1038C LYS* 3.9 3.2 - - + +
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Residues in contact with HIS 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989C MET 2.9 15.3 + - - +
990C GLN 4.2 2.9 - - - +
991C LEU 2.8 0.6 + - - -
992C ILE* 1.3 75.1 - - - +
994C TRP* 1.3 64.1 + - - +
996C THR* 2.3 25.7 + - - -
997C ASN* 3.0 12.0 + - + +
1034C ARG* 3.1 26.9 - - - +
1038C LYS* 3.1 34.1 - - + +
1041C ILE* 3.3 7.8 - - + +
2774C SER* 3.7 0.2 - - - -
2776C ARG* 3.1 26.8 + - + +
2777C HIS* 2.9 61.9 + + - -
2780C LEU* 5.8 2.5 - - + +
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Residues in contact with TRP 994 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C LEU* 3.3 27.8 - - + +
946C THR* 4.5 14.4 - - + -
990C GLN 3.2 14.0 + - - +
991C LEU* 2.7 18.0 + - + +
993C HIS* 1.3 78.7 - - - +
995C PHE* 1.3 60.8 + - - +
997C ASN* 3.2 2.5 + - - +
998C ASN* 2.3 59.5 + - - +
1001C PHE* 5.0 3.8 - - - -
1002C GLU* 2.9 32.0 + - - -
2776C ARG 5.7 0.6 + - - -
2780C LEU* 2.9 54.3 - - + +
2783C ILE* 3.2 40.2 - - + -
2784C GLN* 3.7 16.2 - - + -
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Residues in contact with PHE 995 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991C LEU* 3.3 12.8 - - + -
992C ILE* 3.4 31.0 - - + -
994C TRP* 1.3 81.0 - - - +
996C THR* 1.3 66.4 + - + +
998C ASN* 2.7 26.8 - - - +
999C LYS 2.6 29.1 - - - +
1000C LYS* 4.4 0.3 - - - -
1001C PHE* 4.5 2.5 - - + -
1002C GLU* 3.1 46.2 - - + +
1003C SER* 3.1 37.5 - - - -
1006C THR* 3.1 36.3 - - + -
1054C VAL* 5.2 5.6 - - + -
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Residues in contact with THR 996 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992C ILE 2.6 21.4 + - - +
993C HIS 2.3 29.1 + - - -
995C PHE* 1.3 92.7 - - + +
997C ASN* 1.3 59.6 + - - +
998C ASN 2.8 13.2 - - - +
1000C LYS* 3.9 26.7 + - - +
1035C GLU* 5.8 5.8 - - + +
1038C LYS* 2.9 25.5 + - + +
1039C TRP* 6.3 2.7 - - - -
1042C LYS* 3.9 8.0 + - - +
1054C VAL* 5.6 4.0 - - + -
1055C ASN* 5.2 6.5 - - - +
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Residues in contact with ASN 997 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993C HIS* 3.0 11.8 + - + +
994C TRP 3.9 2.7 - - - +
996C THR* 1.3 75.2 - - - +
998C ASN* 1.3 59.7 + - - +
1038C LYS* 2.9 23.1 - - - +
1041C ILE* 5.1 0.4 - - - +
1042C LYS* 2.2 51.8 + - - +
2777C HIS* 2.9 38.5 + - + -
2780C LEU* 5.4 7.8 - - + +
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Residues in contact with ASN 998 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994C TRP* 2.3 73.7 + - + +
995C PHE* 2.7 23.2 - - - +
996C THR 2.8 12.7 - - - +
997C ASN* 1.3 81.3 - - - +
999C LYS* 1.3 61.6 + - - +
1000C LYS* 4.8 1.6 - - - +
1001C PHE* 4.8 7.4 - - + -
1042C LYS* 4.3 1.6 + - - -
2780C LEU* 4.3 11.5 - - - +
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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
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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) + - + + + + + -
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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