Contacts of the helix formed by residues 945 - 970 (chain A) in PDB entry 5IYB
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 945 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A ASP 5.6 0.7 - - - +
942A VAL* 3.6 11.3 + - + +
944A SER* 1.3 79.1 + - - +
946A ALA* 1.3 62.0 + - - +
947A HIS* 2.6 39.7 + - - +
948A ILE* 3.0 43.3 + - + +
949A GLN* 2.9 27.6 + - - +
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Residues in contact with ALA 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A SER 3.3 6.3 + - - +
945A ASN* 1.3 71.8 + - - +
947A HIS* 1.3 60.1 + - - +
949A GLN* 3.2 15.7 + - - +
950A ASN* 3.0 26.4 + - - +
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Residues in contact with HIS 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A ASN* 2.6 21.2 + - - +
946A ALA* 1.3 72.3 - - - +
948A ILE* 1.3 61.6 + - + -
950A ASN* 3.3 15.2 + - - +
951A GLU* 2.9 48.6 + - + +
1007A ILE* 6.3 0.7 - - + -
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Residues in contact with ILE 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A PHE* 6.3 0.7 - - + -
924A TYR* 3.2 8.0 + - + +
942A VAL* 3.7 36.1 - - + +
945A ASN* 3.0 44.8 + - + +
946A ALA 3.3 0.2 - - - -
947A HIS* 1.3 78.6 - - + +
949A GLN* 1.3 63.0 + - + +
951A GLU* 3.8 1.1 - - - +
952A LEU* 3.1 34.5 + - + +
1005A HIS* 4.1 13.5 - - + +
1006A PRO* 5.0 5.8 - - + -
1007A ILE* 3.6 32.1 - - + -
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Residues in contact with GLN 949 (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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924A TYR* 3.0 53.3 + - + +
942A VAL 5.8 1.3 - - - +
943A LEU 4.4 12.3 + - - -
944A SER 4.4 4.6 + - - -
945A ASN 2.9 25.3 + - - +
946A ALA* 3.2 13.6 + - - +
948A ILE* 1.3 78.4 - - + +
950A ASN* 1.3 60.7 + - - +
953A GLU* 3.2 30.3 + - + +
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Residues in contact with ASN 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A ALA 3.0 12.4 + - - +
947A HIS* 3.3 19.4 + - - +
949A GLN* 1.3 75.5 - - - +
951A GLU* 1.3 58.7 + - - +
953A GLU* 3.3 7.6 + - - +
954A ARG* 2.3 76.3 + - - +
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Residues in contact with GLU 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A HIS* 2.9 37.9 + - + +
948A ILE* 3.8 4.5 - - - +
950A ASN* 1.3 78.5 + - - +
952A LEU* 1.3 60.2 + - - +
954A ARG* 3.1 18.9 - - - +
955A GLU* 3.0 23.4 + - - +
1007A ILE* 4.3 21.5 - - + -
1010A VAL* 4.6 12.6 - - + +
1014A LYS* 2.6 32.2 + - - -
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Residues in contact with LEU 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A PHE* 3.9 33.4 - - + -
924A TYR* 3.1 28.7 - - + +
948A ILE* 3.1 27.3 + - + +
951A GLU* 1.3 72.6 - - - +
953A GLU* 1.3 59.7 + - - +
954A ARG 3.1 0.2 - - - -
955A GLU* 2.9 29.3 + - - +
956A PHE* 2.8 29.0 + - - +
1006A PRO* 4.6 11.2 - - + -
1007A ILE* 4.7 4.9 - - + -
1010A VAL* 3.7 18.2 - - + -
1051A SER* 3.7 13.5 - - - +
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Residues in contact with GLU 953 (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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921A ARG* 3.9 29.3 + - - +
922A PHE 5.5 0.7 - - - +
924A TYR* 4.4 17.4 - - + -
949A GLN* 3.2 20.8 + - + +
950A ASN* 3.5 7.9 - - - +
952A LEU* 1.3 76.4 - - - +
954A ARG* 1.3 65.4 + - - +
956A PHE* 4.5 14.4 - - - +
957A GLU* 3.2 29.3 + - - +
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Residues in contact with ARG 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A ASN* 2.3 61.0 + - - +
951A GLU* 3.1 28.7 - - - +
953A GLU* 1.3 78.3 - - - +
955A GLU* 1.3 59.0 + - - +
957A GLU* 3.1 26.9 + - - +
958A ARG* 3.4 24.8 + - - +
1014A LYS* 6.0 0.4 - - - +
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Residues in contact with GLU 955 (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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951A GLU 3.0 11.5 + - - +
952A LEU* 2.9 34.1 + - + +
954A ARG* 1.3 75.5 - - - +
956A PHE* 1.3 59.9 + - - +
958A ARG* 3.3 9.9 + - - +
959A MET* 2.9 41.5 + - + +
1010A VAL* 3.3 23.1 - - + +
1046A ARG* 4.5 2.0 - - - +
1049A LEU 4.7 1.6 - - - +
1050A CYS* 3.7 33.1 - - - +
1051A SER* 3.8 6.5 + - - -
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Residues in contact with PHE 956 (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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916A PHE* 3.7 32.3 - + - -
917A GLU* 4.1 20.4 - - + -
920A PHE* 4.1 19.1 - - + -
921A ARG* 3.5 51.6 - - + -
952A LEU 2.8 16.0 + - - +
953A GLU* 4.3 15.3 - - - +
954A ARG 3.6 0.2 - - - -
955A GLU* 1.3 71.5 - - - +
957A GLU* 1.3 63.8 + - - +
959A MET* 3.2 8.6 + - + +
960A ARG* 2.8 38.9 + - + +
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Residues in contact with GLU 957 (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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953A GLU* 3.2 20.3 + - - +
954A ARG* 3.1 37.9 + - - +
956A PHE* 1.3 80.4 - - + +
958A ARG* 1.3 62.2 + - + +
960A ARG* 3.4 14.9 + - - +
961A GLU* 2.8 36.8 + - + +
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Residues in contact with ARG 958 (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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954A ARG 3.4 11.8 + - - +
955A GLU* 3.3 12.9 + - - +
956A PHE 3.2 0.2 - - - -
957A GLU* 1.3 84.7 - - + +
959A MET* 1.3 53.8 + - - +
961A GLU* 3.2 8.7 + - + +
962A ASP* 2.7 49.9 + - - +
1014A LYS* 6.3 1.0 - - - +
1046A ARG* 4.3 19.5 - - - +
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Residues in contact with MET 959 (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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908A THR* 4.6 9.2 - - + +
916A PHE* 4.2 19.3 - - + -
920A PHE* 5.0 7.2 - - + -
955A GLU* 2.9 35.8 + - + +
956A PHE* 3.2 14.6 + - + +
958A ARG* 1.3 75.3 - - - +
960A ARG* 1.3 56.6 + - - +
962A ASP* 3.4 7.6 + - - +
963A ARG* 2.8 30.5 + - - +
1043A ILE* 4.6 2.2 - - - +
1046A ARG* 3.5 45.8 - - + +
1047A SER* 3.7 28.7 - - - -
1050A CYS* 5.1 4.3 - - + -
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Residues in contact with ARG 960 (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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916A PHE* 4.4 17.9 - - + -
956A PHE* 2.8 27.7 + - + +
957A GLU* 3.8 13.4 + - - +
959A MET* 1.3 74.9 - - - +
961A GLU* 1.3 101.7 + - - +
963A ARG* 3.4 15.8 - - - +
964A GLU* 3.2 63.4 + - - +
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Residues in contact with GLU 961 (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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957A GLU* 2.8 25.5 + - + +
958A ARG* 3.5 8.1 - - + +
960A ARG* 1.3 110.8 + - - +
962A ASP* 1.3 60.7 + - - +
964A GLU* 3.1 10.4 + - - +
965A VAL* 3.0 28.8 + - - +
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Residues in contact with ASP 962 (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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908A THR* 5.9 1.8 - - + -
958A ARG* 2.7 35.1 + - - +
959A MET* 3.4 9.0 + - - +
961A GLU* 1.3 69.9 - - - +
963A ARG* 1.3 55.9 + - - +
965A VAL* 3.1 11.4 + - - +
966A LEU* 2.7 37.7 + - - +
1039A LEU* 5.0 5.5 - - - +
1043A ILE* 3.8 25.2 - - + +
1046A ARG* 3.0 40.0 + - - -
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Residues in contact with ARG 963 (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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908A THR* 3.1 39.2 + - + +
909A LEU* 5.7 0.3 - - - +
910A LYS* 2.7 28.3 + - - +
911A PRO 3.7 2.8 + - - -
912A SER 3.7 8.7 + - - -
913A ASN* 3.9 12.3 + - - +
916A PHE* 3.0 65.3 - - - +
959A MET 2.8 16.7 + - - +
960A ARG* 3.4 13.6 - - - +
962A ASP* 1.3 76.1 - - - +
964A GLU* 1.3 64.9 + - + +
966A LEU* 3.5 7.1 + - - +
967A ARG* 2.9 54.4 + - + +
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Residues in contact with GLU 964 (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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960A ARG* 3.2 42.5 + - - +
961A GLU* 3.1 12.5 + - - +
962A ASP 3.1 0.6 - - - -
963A ARG* 1.3 83.2 - - + +
965A VAL* 1.3 62.2 + - + +
967A ARG* 3.4 19.9 + - - +
968A VAL* 3.5 15.7 + - - +
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Residues in contact with VAL 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A GLU 3.0 17.6 + - - +
962A ASP* 3.1 13.2 + - - +
964A GLU* 1.3 77.0 - - + +
966A LEU* 1.3 62.2 + - - +
968A VAL* 3.1 12.6 + - + +
969A ILE* 3.1 37.4 + - + +
1039A LEU* 4.6 17.5 - - + -
1043A ILE* 6.3 2.5 - - + -
202E ARG* 4.9 14.6 - - - +
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Residues in contact with LEU 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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906A LEU* 4.1 12.1 - - + -
908A THR* 4.2 22.4 - - + +
909A LEU* 3.8 30.3 - - + +
962A ASP 2.7 18.4 + - - +
963A ARG* 3.8 6.5 - - - +
964A GLU 3.4 0.2 - - - -
965A VAL* 1.3 73.6 - - - +
967A ARG* 1.3 61.5 + - - +
969A ILE* 3.3 13.3 + - + -
970A PHE* 3.1 50.8 + - + +
1040A LEU* 4.2 7.6 - - + -
1043A ILE* 3.8 29.6 - - + -
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Residues in contact with ARG 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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908A THR 5.1 0.9 - - - -
909A LEU* 4.1 26.1 + - + +
910A LYS 3.2 7.5 + - - -
911A PRO* 4.7 0.6 + - - +
913A ASN* 4.5 2.8 + - - -
963A ARG* 2.9 65.1 + - - +
964A GLU* 3.8 15.9 + - - +
965A VAL 3.3 0.8 - - - -
966A LEU* 1.3 73.1 - - - +
968A VAL* 1.3 66.0 + - + +
970A PHE 3.7 16.0 - - - +
971A PRO* 3.7 6.9 - - - +
1322A ILE* 3.9 15.1 - - - +
1326A GLY* 3.2 25.6 + - - -
1327A GLU* 5.1 0.8 - - - +
1328A PHE* 3.7 41.7 - - + +
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Residues in contact with VAL 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A GLU 3.5 15.7 - - - +
965A VAL* 3.1 11.1 + - + +
967A ARG* 1.3 77.1 - - + +
969A ILE* 1.3 65.3 + - + +
970A PHE 3.5 0.2 + - - -
971A PRO* 3.6 14.5 - - - +
196E PRO* 5.6 1.9 - - - +
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Residues in contact with ILE 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A VAL* 3.1 33.3 + - + +
966A LEU* 3.3 21.0 + - + +
968A VAL* 1.3 76.8 - - + +
970A PHE* 1.3 90.2 + - + +
971A PRO* 3.1 9.2 - - - +
1039A LEU* 4.5 12.3 - - + -
1040A LEU* 5.3 5.2 - - + -
1043A ILE* 5.5 2.9 - - + -
196E PRO* 4.8 15.1 - - + +
197E SER 3.9 16.4 - - - +
201E GLY* 4.3 25.1 - - - +
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Residues in contact with PHE 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A LEU* 3.9 7.2 - - + -
909A LEU* 4.3 9.0 - - + +
966A LEU* 3.1 40.5 + - + +
967A ARG* 3.7 7.2 - - - +
969A ILE* 1.3 98.7 - - + +
971A PRO* 1.3 56.8 - - - +
972A THR* 3.0 13.2 - - - +
973A GLY* 2.8 20.6 + - - +
974A ASP* 3.8 24.2 - - + +
977A VAL* 3.5 32.8 - - + -
1040A LEU* 4.1 13.9 - - + -
1328A PHE* 4.4 4.5 - - - -
197E SER 4.2 9.0 - - - -
198E GLU* 4.5 16.2 - - + -
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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
------------------------------------------------------------
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