Contacts of the helix formed by residues 964 - 989 (chain A) in PDB entry 5XA0
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 964 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A PRO 4.2 6.1 - - - -
961A GLU 3.3 12.3 + - - +
962A LYS 3.1 1.4 + - - -
963A GLU* 1.3 74.3 - - - +
965A ILE* 1.3 60.3 + - - +
967A VAL* 2.4 27.0 + - - +
968A MET* 3.0 13.0 + - - +
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Residues in contact with ILE 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961A GLU 4.8 0.4 + - - -
962A LYS* 3.3 8.4 + - - +
964A ASP* 1.3 77.6 - - - +
966A MET* 1.3 61.3 + - - +
968A MET* 3.8 11.1 + - - +
969A ASP* 4.6 2.1 + - - +
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Residues in contact with MET 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A LYS* 3.0 17.7 + - + +
963A GLU* 3.8 11.2 - - + -
965A ILE* 1.3 76.3 - - - +
967A VAL* 1.3 58.7 + - - +
968A MET 3.3 0.2 - - - -
969A ASP* 3.1 12.2 + - - +
970A THR* 3.1 24.2 + - - -
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Residues in contact with VAL 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775A TYR* 6.5 1.3 - - - -
776A ASP* 6.1 6.1 - - + +
960A PRO 5.6 0.9 - - - -
963A GLU* 2.0 30.8 + - - +
964A ASP* 2.4 29.6 + - - +
966A MET* 1.3 67.4 - - - +
968A MET* 1.3 59.0 + - - -
970A THR* 3.7 10.5 - - - -
971A LYS* 2.9 29.8 + - - +
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Residues in contact with MET 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A ASP 3.0 8.2 + - - +
965A ILE* 4.3 8.5 - - - +
966A MET 3.3 0.6 - - - -
967A VAL* 1.3 76.4 - - - +
969A ASP* 1.3 62.0 + - - +
971A LYS* 3.2 7.3 + - - +
972A LEU* 3.0 21.9 + - - +
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Residues in contact with ASP 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856A ASP 5.8 0.4 - - - +
857A LYS* 5.8 7.2 - - + -
860A ASN* 5.4 16.8 - - + +
864A PHE* 5.6 0.2 - - - +
965A ILE 4.6 1.7 + - - +
966A MET* 3.1 12.7 + - - +
968A MET* 1.3 78.0 - - - +
970A THR* 1.3 62.6 + - - +
972A LEU* 3.1 17.7 + - - +
973A LYS* 3.1 14.0 + - - +
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Residues in contact with THR 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A ASP* 6.4 2.0 - - - -
963A GLU* 6.5 0.4 - - - -
966A MET* 3.1 15.7 + - - -
967A VAL* 3.8 11.2 - - - -
968A MET 3.3 0.2 - - - -
969A ASP* 1.3 76.8 - - - +
971A LYS* 1.3 56.3 + - - +
973A LYS* 3.3 7.0 + - - +
974A ILE* 3.0 28.3 + - - +
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Residues in contact with LYS 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A PRO 6.0 2.5 - - - +
967A VAL 2.9 18.7 + - - +
968A MET* 3.2 6.5 + - - +
970A THR* 1.3 76.4 - - - +
972A LEU* 1.3 55.9 + - - +
974A ILE* 4.2 5.5 - - - +
975A ILE* 2.9 32.1 + - - +
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Residues in contact with LEU 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864A PHE* 4.4 20.5 - - + +
968A MET 3.0 12.7 + - - +
969A ASP* 3.1 13.4 + - - +
971A LYS* 1.3 77.3 - - - +
973A LYS* 1.3 58.1 + - - +
975A ILE* 3.9 4.4 - - - +
976A GLU* 3.0 28.9 + - - +
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Residues in contact with LYS 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860A ASN* 5.6 12.8 - - + +
863A THR* 6.4 2.0 - - - -
864A PHE* 5.4 6.0 - - - +
867A VAL* 5.6 1.9 - - - +
899A HIS 4.4 20.3 - - - +
969A ASP 3.1 11.8 + - - +
970A THR* 3.3 8.7 + - - +
972A LEU* 1.3 76.0 - - - +
974A ILE* 1.3 61.2 + - - +
976A GLU* 4.2 4.2 - - - +
977A ILE* 3.0 27.4 + - - +
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Residues in contact with ILE 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ALA* 5.6 10.8 - - + -
899A HIS 5.5 0.4 + - - -
970A THR 3.0 16.1 + - - +
971A LYS* 4.2 6.1 - - - +
973A LYS* 1.3 75.1 - - - +
975A ILE* 1.3 57.4 + - - +
977A ILE* 3.4 7.4 + - - +
978A LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770A ASP* 6.2 2.0 - - - -
971A LYS 2.9 20.8 + - - +
972A LEU* 4.0 4.9 - - - +
974A ILE* 1.3 76.0 - - - +
976A GLU* 1.3 58.4 + - - +
978A LEU* 3.4 8.8 + - - +
979A GLN* 2.8 26.3 + - - +
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Residues in contact with GLU 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864A PHE* 4.6 2.5 - - - +
867A VAL* 3.1 36.1 - - + +
868A ASN* 3.3 16.8 - - + +
972A LEU 3.0 19.4 + - - +
973A LYS* 4.2 3.6 - - - +
975A ILE* 1.3 73.8 - - - +
977A ILE* 1.3 65.2 + - - +
978A LEU 3.1 1.1 - - - -
979A GLN* 3.6 8.0 - - - +
980A PHE* 2.9 26.0 + - - +
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Residues in contact with ILE 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A VAL* 5.0 1.4 - - - +
895A LEU* 6.3 3.6 - - + -
973A LYS 3.0 19.8 + - - +
974A ILE* 3.5 8.1 - - - +
976A GLU* 1.3 73.8 - - - +
978A LEU* 1.3 56.9 + - - +
980A PHE* 3.8 4.8 - - - +
981A ILE* 3.0 31.2 + - - +
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Residues in contact with LEU 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A ARG* 6.3 3.1 - - + -
770A ASP* 4.9 17.0 - - + -
974A ILE 2.9 19.0 + - - +
975A ILE* 3.5 10.1 - - - +
977A ILE* 1.3 77.5 - - - +
979A GLN* 1.3 49.2 + - - +
981A ILE* 3.7 6.0 - - - -
982A LEU* 2.6 39.5 + - - +
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Residues in contact with GLN 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A ASN* 4.8 7.0 - - + -
871A ARG* 2.9 25.0 - - + +
975A ILE 2.8 17.2 + - - +
976A GLU* 3.0 10.0 + - - +
978A LEU* 1.3 75.9 - - - +
980A PHE* 1.3 62.3 + - - +
982A LEU* 4.0 4.2 - - - +
983A ASN* 2.9 24.6 + - - +
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Residues in contact with PHE 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A VAL 4.8 1.6 - - - +
870A ALA* 4.7 6.5 - - + -
871A ARG* 3.1 26.8 - - - +
874A ILE* 5.6 2.4 - - + +
976A GLU 2.9 15.2 + - - +
977A ILE* 3.8 4.9 - - - +
979A GLN* 1.3 74.8 - - - +
981A ILE* 1.3 62.5 + - - +
982A LEU 3.1 0.2 + - - -
983A ASN* 4.1 0.2 - - - +
984A VAL* 3.0 30.1 + - - +
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Residues in contact with ILE 981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977A ILE 3.0 19.9 + - - +
978A LEU* 4.1 6.1 - - - +
980A PHE* 1.3 76.2 - - - +
982A LEU* 1.3 53.1 + - - +
984A VAL* 5.2 1.1 - - - -
985A ARG* 2.3 44.7 + - + +
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Residues in contact with LEU 982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978A LEU 2.6 22.0 + - - +
979A GLN* 4.0 5.2 - - - +
980A PHE 3.1 0.2 - - - -
981A ILE* 1.3 79.1 - - - +
983A ASN* 1.3 59.4 + - - +
985A ARG* 4.5 0.2 - - - -
986A LEU* 2.8 38.3 + - + +
987A ASP* 3.0 2.6 + - - +
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Residues in contact with ASN 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871A ARG* 3.8 24.0 - - + +
872A ASN* 5.5 0.4 - - - -
875A TYR* 3.8 18.6 - - + +
979A GLN 2.9 19.4 + - - +
980A PHE 4.1 0.7 - - - +
982A LEU* 1.3 74.2 - - - +
984A VAL* 1.3 62.5 + - - +
987A ASP* 2.5 37.4 + - + +
988A TYR 3.4 1.2 + - - -
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Residues in contact with VAL 984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A ILE* 4.6 19.2 - - + +
875A TYR* 5.2 2.0 - - - +
888A THR* 5.9 7.2 - - - -
980A PHE 3.0 16.5 + - - +
981A ILE* 5.1 1.3 - - - -
983A ASN* 1.3 75.4 - - - +
985A ARG* 1.3 63.8 + - - +
988A TYR* 3.1 9.7 + - - +
989A ARG* 2.8 26.6 + - + +
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Residues in contact with ARG 985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A ILE* 2.3 35.2 + - + +
982A LEU* 4.5 0.4 - - - -
984A VAL* 1.3 78.1 - - - +
986A LEU* 1.3 56.8 + - + +
989A ARG* 2.8 39.7 + - - +
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Residues in contact with LEU 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 3.2 27.6 + - - +
982A LEU* 2.8 29.7 + - + +
985A ARG* 1.3 75.1 - - + +
987A ASP* 1.3 63.4 + - - +
988A TYR 3.3 0.4 + - - -
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Residues in contact with ASP 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743A MET* 5.1 13.0 - - + -
745A LEU* 5.4 1.8 - - - +
746A ASP* 4.6 9.3 + - - +
875A TYR* 4.9 8.3 - - + -
982A LEU 3.0 4.2 + - - -
983A ASN* 2.5 42.3 + - + +
986A LEU* 1.3 74.2 - - - +
988A TYR* 1.3 63.4 + - + +
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Residues in contact with TYR 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 5.6 2.2 - - - -
983A ASN 3.4 0.6 + - - -
984A VAL* 3.1 11.5 + - - +
986A LEU 4.3 0.7 - - - -
987A ASP* 1.3 84.3 - - + +
989A ARG* 1.3 57.7 + - - +
991A SER* 5.7 4.3 - - - -
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Residues in contact with ARG 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 5.9 3.8 - - - +
984A VAL* 2.8 16.0 + - + +
985A ARG* 2.8 38.5 + - + +
986A LEU 4.6 0.6 + - - -
988A TYR* 1.3 72.6 - - - +
990A ILE* 1.3 72.4 + - + +
991A SER* 3.4 8.3 + - - -
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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
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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