Contacts of the helix formed by residues 976 - 1001 (chain A) in PDB entry 6UHA
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 LEU 976 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974A LYS 4.0 2.9 + - - +
975A LEU* 1.3 78.5 - - - +
977A PRO* 1.3 82.0 - - + +
978A PRO* 3.7 15.5 - - + -
979A GLN* 3.0 37.2 + - + +
980A GLU* 3.0 12.2 + - - +
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Residues in contact with PRO 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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975A LEU 4.4 2.5 - - - +
976A LEU* 1.3 93.6 - - + +
978A PRO* 1.3 68.5 - - + +
980A GLU* 3.0 17.3 + - + +
981A ILE* 3.1 21.1 + - + +
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Residues in contact with PRO 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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976A LEU* 3.5 15.0 - - + -
977A PRO* 1.3 98.8 - - + +
979A GLN* 1.3 59.8 + - + +
981A ILE* 3.6 14.0 + - + +
982A LEU* 3.2 24.8 + - - +
1053A PRO* 4.2 23.2 - - + +
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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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974A LYS 5.0 0.7 - - - +
975A LEU* 3.8 21.9 - - + +
976A LEU* 3.0 45.0 + - + +
978A PRO* 1.3 79.8 - - + +
980A GLU* 1.3 57.4 + - - +
982A LEU* 3.5 13.2 - - + +
983A VAL* 3.2 27.5 + - - +
1041A VAL* 4.9 8.5 - - + +
1045A VAL* 4.3 16.4 - - - +
1050A ASN* 3.6 13.7 + - - +
1051A ILE* 3.3 32.9 + - + +
1052A GLU* 5.7 0.2 + - - -
1053A PRO* 5.4 4.3 - - + -
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Residues in contact with GLU 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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975A LEU* 4.3 12.6 - - + +
976A LEU 3.0 9.0 + - - +
977A PRO* 3.0 11.7 + - + +
979A GLN* 1.3 75.0 - - - +
981A ILE* 1.3 65.8 + - + +
982A LEU 3.0 1.6 - - - -
983A VAL* 3.0 23.4 + - - +
984A ASP* 3.3 22.2 + - - +
1038A ARG* 2.8 48.2 + - - +
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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 PRO* 3.1 17.3 + - + +
978A PRO* 3.8 14.8 - - + +
980A GLU* 1.3 76.6 - - + +
982A LEU* 1.3 60.2 + - - +
984A ASP* 3.6 13.3 + - - +
985A LYS* 3.2 39.6 + - - +
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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
----------------------------------------------------------
930A LEU* 3.6 16.4 - - + -
933A LEU* 5.1 7.6 - - + -
935A CYS* 3.5 22.7 - - - -
978A PRO 3.2 13.0 + - - +
979A GLN* 3.5 15.7 - - + +
980A GLU 3.0 0.8 - - - -
981A ILE* 1.3 76.1 - - - +
983A VAL* 1.3 65.7 + - - +
984A ASP 3.2 0.4 - - - -
985A LYS* 3.2 16.2 + - + +
986A LEU* 3.2 24.6 + - + +
1041A VAL* 5.8 4.7 - - + -
1051A ILE* 3.5 35.2 - - + +
1053A PRO* 4.7 18.6 - - + -
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Residues in contact with VAL 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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975A LEU* 3.7 22.2 - - + -
979A GLN 3.2 17.2 + - - +
980A GLU* 3.0 21.1 + - - +
982A LEU* 1.3 77.6 - - + +
984A ASP* 1.3 62.0 + - - +
986A LEU* 3.4 10.6 + - - +
987A ALA* 3.1 21.0 + - - +
1034A ARG* 3.8 29.2 - - + +
1037A LEU* 4.2 5.4 - - + +
1038A ARG* 3.9 20.2 - - + +
1041A VAL* 3.9 17.9 - - + -
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Residues in contact with ASP 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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980A GLU* 3.3 24.5 + - - +
981A ILE* 3.8 13.6 - - - +
982A LEU 3.2 0.4 - - - -
983A VAL* 1.3 75.5 - - - +
985A LYS* 1.3 61.6 + - + +
987A ALA* 3.2 7.3 + - - +
988A GLU* 2.8 32.9 + - - +
1022A TYR* 4.7 5.6 + - + +
1034A ARG* 3.3 31.5 + - - +
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Residues in contact with LYS 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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933A LEU* 4.7 17.6 - - + +
981A ILE* 3.2 33.2 - - - +
982A LEU* 3.2 17.9 + - + +
984A ASP* 1.3 78.8 - - + +
986A LEU* 1.3 57.4 + - - +
988A GLU* 3.4 15.6 + - - +
989A ASN* 2.9 32.2 + - - +
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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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926A THR* 4.5 17.5 - - + +
929A THR* 3.7 31.4 - - + +
930A LEU* 4.1 36.8 - - + -
933A LEU* 4.3 8.5 - - + -
982A LEU* 3.2 16.6 + - + +
983A VAL* 3.7 7.4 - - - +
985A LYS* 1.3 77.8 - - - +
987A ALA* 1.3 57.3 + - - +
989A ASN* 3.8 3.5 - - - +
990A ALA* 2.9 30.5 + - - +
1037A LEU* 3.5 20.4 - - + +
1041A VAL* 4.4 22.4 - - + -
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Residues in contact with ALA 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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983A VAL 3.1 13.8 + - - +
984A ASP* 3.2 6.7 + - - +
986A LEU* 1.3 76.8 - - - +
988A GLU* 1.3 62.1 + - - +
990A ALA* 3.3 4.6 + - - +
991A HIS* 3.1 22.7 + - - +
1022A TYR* 3.5 21.0 - - + +
1030A LYS 5.4 0.2 - - - +
1033A ASN* 4.6 7.0 + - + +
1034A ARG* 4.1 29.2 - - + +
1037A LEU* 3.4 12.2 - - + +
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Residues in contact with GLU 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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984A ASP 2.8 20.3 + - - +
985A LYS* 3.8 17.0 - - - +
987A ALA* 1.3 72.8 - - - +
989A ASN* 1.3 61.3 + - - +
991A HIS* 3.4 3.6 + - - +
992A ASN* 3.2 33.7 + - - +
1022A TYR* 3.6 44.9 - - + +
1023A ALA 5.5 0.7 + - - -
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Residues in contact with ASN 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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853A PRO* 3.4 7.1 - - - +
854A VAL* 2.9 55.7 + - + +
929A THR* 3.6 21.4 + - + +
933A LEU* 5.7 2.5 - - + -
985A LYS 2.9 17.7 + - - +
986A LEU* 4.0 5.6 - - - +
988A GLU* 1.3 75.4 - - - +
990A ALA* 1.3 60.2 + - - +
992A ASN* 3.2 7.1 + - - +
993A VAL* 2.8 39.7 + - - +
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Residues in contact with ALA 990 (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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922A MSE 5.3 13.2 - - + -
986A LEU 2.9 18.9 + - - +
987A ALA* 3.7 4.9 - - - +
989A ASN* 1.3 78.2 - - - +
991A HIS* 1.3 57.0 + - - +
993A VAL* 3.4 8.4 + - - +
994A TRP* 2.8 31.1 + - - +
1033A ASN* 4.0 19.5 - - - +
1037A LEU* 4.5 6.3 - - + -
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Residues in contact with HIS 991 (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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850A ILE* 5.0 1.3 - - + -
987A ALA 3.1 8.5 + - - +
988A GLU 3.5 9.0 - - - +
989A ASN 3.2 0.2 - - - -
990A ALA* 1.3 77.1 - - - +
992A ASN* 1.3 66.2 + - - +
994A TRP* 3.2 28.2 + + - -
995A ALA* 2.7 44.0 + - + +
1018A ARG* 3.5 18.8 - - + -
1020A VAL 2.8 25.8 + - - -
1022A TYR* 3.6 30.2 + + + -
1025A LEU* 3.5 27.6 - - + +
1033A ASN* 5.2 2.6 - - - +
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Residues in contact with ASN 992 (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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850A ILE* 4.2 7.9 - - - +
851A PRO* 3.5 44.3 + - - +
852A CYS 4.2 5.3 + - - -
853A PRO* 4.0 15.8 - - + +
988A GLU* 3.2 27.5 + - - +
989A ASN* 3.7 9.3 + - - +
991A HIS* 1.3 87.9 - - - +
993A VAL* 1.3 57.9 + - - +
995A ALA* 4.1 5.6 - - - +
996A LYS* 3.0 29.8 + - - +
1022A TYR* 4.5 6.4 - - - +
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Residues in contact with VAL 993 (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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853A PRO* 3.3 29.4 - - + -
854A VAL 5.3 2.2 - - - +
929A THR* 5.8 0.9 - - - +
989A ASN* 2.8 27.9 + - - +
990A ALA* 3.6 8.5 - - - +
992A ASN* 1.3 74.0 - - - +
994A TRP* 1.3 69.0 + - + +
996A LYS* 3.3 4.1 + - - +
997A ASP* 3.0 22.9 + - + +
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Residues in contact with TRP 994 (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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990A ALA 2.8 20.9 + - - +
991A HIS* 3.6 38.1 - + - +
993A VAL* 1.3 75.5 - - - +
995A ALA* 1.3 74.0 + - + +
997A ASP* 3.2 10.3 + - - +
998A ARG* 3.0 58.1 + - + +
1016A ASN* 3.2 31.6 - - - -
1018A ARG* 3.4 17.5 - - + -
1019A LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 995 (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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850A ILE* 4.2 20.6 - - + -
991A HIS* 2.7 27.3 + - + +
992A ASN* 4.1 5.2 - - - +
994A TRP* 1.3 81.6 - - + +
996A LYS* 1.3 61.5 - - - +
998A ARG* 4.4 0.4 - - - +
999A ILE* 2.9 39.2 + - + +
1019A LEU* 3.7 22.4 - - + -
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Residues in contact with LYS 996 (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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852A CYS* 5.4 6.7 - - + +
853A PRO* 3.5 32.0 + - + +
992A ASN 3.0 19.8 + - - +
993A VAL* 3.6 4.9 - - - +
995A ALA* 1.3 75.7 - - - +
997A ASP* 1.3 61.4 + - - +
999A ILE* 4.1 6.5 - - - +
1000A LYS* 3.2 36.3 + - - +
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Residues in contact with ASP 997 (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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993A VAL* 3.0 14.3 + - + +
994A TRP* 3.4 12.8 - - - +
996A LYS* 1.3 74.5 - - - +
998A ARG* 1.3 100.1 + - - +
1000A LYS* 3.1 18.0 + - - +
1001A GLN* 3.1 31.4 + - - +
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Residues in contact with ARG 998 (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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994A TRP* 3.0 51.0 + - + +
995A ALA 4.0 2.7 - - - +
997A ASP* 1.3 100.6 + - - +
999A ILE* 1.3 63.0 + - - +
1001A GLN* 3.1 35.2 + - - +
1003A TRP* 2.9 72.9 + - + +
1016A ASN* 5.8 0.4 - - - +
1019A LEU* 4.5 10.8 - - + -
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Residues in contact with ILE 999 (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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850A ILE* 4.5 28.7 - - + +
995A ALA* 2.9 25.3 + - + +
996A LYS* 4.1 6.3 - - - +
998A ARG* 1.3 75.6 - - - +
1000A LYS* 1.3 64.5 + - - +
1002A GLY* 3.0 14.7 + - - -
1003A TRP 3.6 19.3 + - - +
1004A THR* 5.7 0.4 - - - -
1019A LEU* 4.1 13.7 - - + -
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Residues in contact with LYS1000 (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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996A LYS* 3.2 28.8 + - - +
997A ASP* 3.1 12.6 + - - +
999A ILE* 1.3 78.1 - - - +
1001A GLN* 1.3 64.3 + - + +
1002A GLY* 3.2 1.4 + - - -
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Residues in contact with GLN1001 (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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997A ASP* 3.2 28.7 + - - +
998A ARG* 3.1 27.6 + - - +
1000A LYS* 1.3 78.3 - - + +
1002A GLY* 1.3 57.3 + - - +
1003A TRP* 3.7 13.5 - - + +
1014A LYS* 3.1 24.8 + - - +
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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