Contacts of the helix formed by residues 997 - 1025 (chain B) in PDB entry 5MJ6
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 997 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B GLU* 3.8 26.7 - - + -
542B GLU* 3.3 17.0 - - - +
949B TRP* 6.0 0.7 - - + -
958B LEU* 3.9 34.8 - - + -
959B GLY* 4.7 3.6 - - - +
963B ILE* 6.2 0.9 - - + -
993B ALA 3.5 17.7 + - - +
994B THR* 3.0 25.2 + - + +
995B PHE 3.4 0.4 - - - -
996B ARG* 1.3 83.1 - - - +
998B ARG* 1.3 65.4 + - - +
999B CYS* 3.2 20.1 + - + +
1000B VAL* 3.4 8.9 + - + +
1001B GLN* 3.1 21.2 + - - +
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Residues in contact with ARG 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B SER* 3.8 21.7 + - - +
527B SER* 5.7 0.2 - - - +
528B HIS* 3.0 48.5 + - - +
532B SER* 4.0 13.7 + - - -
533B SER 4.3 11.9 + - - -
534B VAL* 4.8 3.0 - - - +
539B GLN* 4.3 17.1 + - - +
542B GLU* 2.9 50.2 + - + +
543B MET* 4.4 4.0 - - - -
996B ARG 3.8 0.4 + - - -
997B LEU* 1.3 73.2 - - - +
999B CYS* 1.3 55.6 + - - +
1001B GLN* 3.2 6.2 + - + +
1002B GLU* 2.7 44.7 + - + +
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Residues in contact with CYS 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B GLU* 4.5 13.5 - - - -
959B GLY* 4.3 24.2 - - - -
963B ILE* 5.3 4.0 - - + -
964B GLN* 3.9 45.1 - - - +
967B VAL* 4.4 13.9 - - + +
997B LEU* 3.2 13.2 - - + -
998B ARG* 1.3 76.9 - - - +
1000B VAL* 1.3 61.9 + - + +
1002B GLU* 3.8 5.0 - - - +
1003B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949B TRP* 5.9 1.1 - - + -
967B VAL* 5.1 3.6 - - + -
987B PHE* 3.8 56.3 - - + -
994B THR* 3.5 21.8 - - + +
995B PHE* 3.7 26.7 - - + +
997B LEU* 3.4 8.5 + - + +
998B ARG 3.3 0.2 - - - -
999B CYS* 1.3 77.6 - - + +
1001B GLN* 1.3 67.7 + - - +
1003B ALA* 3.1 6.8 + - - +
1004B LEU* 2.9 34.7 + - + +
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Residues in contact with GLN1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B SER* 4.0 16.7 - - - -
995B PHE* 2.7 50.7 + - - +
996B ARG* 4.1 22.9 + - - +
997B LEU 3.1 17.7 + - - +
998B ARG* 3.7 5.2 - - - +
1000B VAL* 1.3 77.8 - - - +
1002B GLU* 1.3 56.5 + - - +
1004B LEU* 3.3 14.7 + - - +
1005B GLU* 3.0 28.4 + - - +
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Residues in contact with GLU1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LYS* 3.4 48.8 + - - +
524B LEU* 3.8 18.7 - - + +
526B SER* 3.3 34.5 - - - +
527B SER* 4.3 6.9 - - - -
547B LEU* 5.9 0.7 - - - +
964B GLN* 3.8 5.6 - - - +
998B ARG* 2.7 28.0 + - - +
999B CYS* 3.8 5.2 - - - +
1001B GLN* 1.3 72.6 - - - +
1003B ALA* 1.3 57.7 + - - +
1005B GLU* 3.2 1.7 + - - +
1006B VAL* 2.9 36.0 + - + +
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Residues in contact with ALA1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967B VAL* 4.0 17.7 - - + -
968B ALA* 5.3 4.0 - - - +
971B THR* 3.7 24.7 + - + +
983B VAL* 5.3 7.2 - - + -
987B PHE* 5.8 0.2 - - + -
999B CYS 3.0 17.9 + - - +
1000B VAL* 3.1 5.4 + - - +
1002B GLU* 1.3 75.3 - - - +
1004B LEU* 1.3 62.9 + - - +
1006B VAL* 3.4 7.1 + - - +
1007B ILE* 3.2 29.6 + - - +
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Residues in contact with LEU1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980B LEU* 3.5 23.3 - - + +
983B VAL* 3.6 34.1 - - + +
984B GLN* 3.7 38.6 - - + +
995B PHE* 3.8 26.7 - - + -
1000B VAL* 2.9 27.4 + - + +
1001B GLN* 3.7 14.6 - - - +
1003B ALA* 1.3 73.8 - - - +
1005B GLU* 1.3 65.2 + - - +
1007B ILE* 3.3 3.4 + - + -
1008B GLN* 3.0 19.1 + - - +
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Residues in contact with GLU1005 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU* 3.6 19.5 - - + +
525B ASN* 2.9 37.0 + - - +
526B SER* 3.0 25.2 + - - +
1001B GLN 3.0 16.4 + - - +
1002B GLU 3.2 2.7 + - - +
1004B LEU* 1.3 77.3 - - - +
1006B VAL* 1.3 63.2 + - - +
1008B GLN* 3.1 10.8 + - + +
1009B LEU* 2.9 32.1 + - + +
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Residues in contact with VAL1006 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B LEU* 4.2 22.4 - - + -
972B TYR* 4.1 28.0 - - + +
1002B GLU* 2.9 23.2 + - + +
1003B ALA* 3.7 8.1 - - - +
1004B LEU 3.2 0.2 - - - -
1005B GLU* 1.3 76.5 - - - +
1007B ILE* 1.3 62.0 + - - +
1009B LEU* 3.1 11.7 + - + +
1010B ASN* 3.0 35.9 + - - +
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Residues in contact with ILE1007 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971B THR* 3.8 27.8 - - - +
974B PHE* 3.5 28.0 - - + +
976B THR 4.1 5.6 - - - +
980B LEU* 3.8 32.8 - - + +
983B VAL* 4.0 33.0 - - + -
1003B ALA 3.2 19.2 + - - +
1004B LEU* 3.7 7.6 - - - +
1005B GLU 3.3 0.2 - - - -
1006B VAL* 1.3 78.1 - - + +
1008B GLN* 1.3 63.7 + - - +
1010B ASN* 3.1 5.2 + - - +
1011B ILE* 2.9 28.8 + - + +
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Residues in contact with GLN1008 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B ASN* 6.0 0.7 - - - +
977B LYS* 6.0 1.2 - - - +
980B LEU* 3.5 27.6 - - + +
1004B LEU 3.0 13.7 + - - +
1005B GLU* 3.1 14.6 + - + +
1007B ILE* 1.3 75.5 - - - +
1009B LEU* 1.3 58.2 + - + +
1011B ILE* 3.4 21.9 + - - +
1012B GLN* 2.9 54.3 + - - +
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Residues in contact with LEU1009 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B LYS* 6.1 3.1 - - - +
523B SER* 5.8 1.3 - - - +
524B LEU* 3.4 33.2 - - + -
637B LEU* 3.8 36.9 - - + +
741B LEU* 4.5 9.6 - - + -
1005B GLU* 2.9 24.8 + - + +
1006B VAL* 3.5 10.8 - - + +
1007B ILE 3.1 0.2 - - - -
1008B GLN* 1.3 76.1 - - + +
1010B ASN* 1.3 61.2 + - - +
1012B GLN* 3.2 7.7 + - - +
1013B TRP* 2.9 30.9 + - - +
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Residues in contact with ASN1010 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 3.8 24.1 - - + +
972B TYR 2.8 30.4 + - - +
974B PHE 3.0 18.0 + - - +
975B SER* 3.1 21.5 - - - +
1006B VAL* 3.0 22.2 + - - +
1007B ILE* 3.1 9.3 + - - +
1009B LEU* 1.3 71.7 - - - +
1011B ILE* 1.3 66.4 + - - +
1013B TRP* 3.4 7.0 + - - +
1014B MET* 3.2 28.4 + - - +
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Residues in contact with ILE1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975B SER 3.5 26.9 - - - +
976B THR* 3.4 26.7 - - - +
977B LYS* 3.5 15.7 - - + +
980B LEU* 4.1 10.3 - - + -
1007B ILE* 2.9 28.6 + - + +
1008B GLN* 3.5 24.5 - - - +
1009B LEU 3.2 0.2 - - - -
1010B ASN* 1.3 77.5 - - - +
1012B GLN* 1.3 62.5 + - - +
1014B MET* 3.4 3.6 + - - +
1015B GLU* 3.2 38.7 + - + +
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Residues in contact with GLN1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.0 36.4 - - + +
638B ASN* 4.0 24.7 - - - +
1008B GLN* 2.9 44.9 + - - +
1009B LEU* 3.2 13.2 + - - +
1011B ILE* 1.3 75.9 - - - +
1013B TRP* 1.3 63.5 + - - +
1015B GLU* 3.0 22.1 + - - +
1016B LYS* 3.0 25.3 + - - +
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Residues in contact with TRP1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 5.9 0.2 - - - +
736B PHE 5.3 0.8 + - - -
739B ALA 4.9 0.2 - - - -
740B GLY* 3.3 44.0 - - - +
746B LEU* 4.2 14.2 - - + +
775B ILE* 3.9 46.4 - - + -
778B LEU* 5.5 13.0 - - + -
779B LEU* 5.1 1.8 - - + -
1009B LEU 2.9 16.6 + - - +
1010B ASN* 3.7 9.0 - - - +
1011B ILE 3.3 0.2 - - - -
1012B GLN* 1.3 75.3 - - - +
1014B MET* 1.3 84.2 + - + +
1016B LYS* 4.6 1.6 - - - -
1017B ASN* 2.8 56.0 + - + +
1018B LEU* 5.1 0.7 - - - -
1021B LEU* 4.0 19.5 - - + -
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Residues in contact with MET1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LEU* 5.2 10.5 - - + -
779B LEU* 3.9 15.7 - - + -
782B LEU* 3.5 34.5 - - + -
784B TYR* 4.2 3.4 - - + -
975B SER* 4.4 9.2 - - - +
1010B ASN 3.2 16.9 + - - +
1011B ILE* 3.8 4.7 - - - +
1012B GLN 3.2 0.6 - - - -
1013B TRP* 1.3 101.4 - - + +
1015B GLU* 1.3 64.7 + - - +
1018B LEU* 3.0 69.3 + - + +
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Residues in contact with GLU1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B ILE* 3.2 30.1 + - + +
1012B GLN* 3.0 25.5 + - - +
1014B MET* 1.3 77.5 - - + +
1016B LYS* 1.3 61.0 + - + +
1018B LEU 4.7 1.0 + - - -
1019B LYS* 5.6 2.1 + - - +
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Residues in contact with LYS1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B GLY 6.3 0.7 - - - -
741B LEU 5.3 0.2 - - - -
742B GLY* 4.1 36.7 + - - +
744B VAL 5.6 2.2 + - - -
745B PRO* 5.8 4.4 - - - +
1012B GLN* 3.0 16.0 + - + +
1013B TRP* 3.8 3.4 - - - +
1015B GLU* 1.3 80.8 - - + +
1017B ASN* 1.3 75.6 + - - +
1018B LEU 3.8 0.4 - - - -
1019B LYS 5.3 0.5 + - - -
1020B SER* 4.8 4.9 + - - -
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Residues in contact with ASN1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B ALA 3.4 23.6 + - - +
740B GLY* 3.9 1.4 - - - -
744B VAL 5.3 0.3 - - - +
745B PRO* 5.5 0.2 - - - +
746B LEU* 3.3 36.1 + - + +
1013B TRP* 2.8 58.5 + - + +
1016B LYS* 1.3 93.5 + - - +
1018B LEU* 1.3 63.2 + - - +
1019B LYS 3.3 2.5 - - - -
1020B SER* 3.4 7.5 + - - -
1021B LEU* 3.0 25.4 + - - +
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Residues in contact with LEU1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779B LEU* 4.0 9.0 - - + -
784B TYR* 3.5 31.4 - - + +
787B LEU* 3.7 25.6 - - + -
1013B TRP* 4.1 2.6 + - - -
1014B MET* 3.0 55.2 + - + +
1015B GLU 4.7 0.4 + - - -
1016B LYS 3.8 1.0 - - - -
1017B ASN* 1.3 78.3 - - - +
1019B LYS* 1.3 81.2 + - + +
1021B LEU* 3.5 3.9 - - + +
1022B THR* 2.9 32.1 + - - +
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Residues in contact with LYS1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B TYR* 4.8 10.7 + - - -
1015B GLU 5.6 1.9 + - - +
1016B LYS 5.3 1.2 + - - -
1017B ASN 3.3 0.2 - - - -
1018B LEU* 1.3 101.6 - - + +
1020B SER* 1.3 60.9 + - - +
1022B THR* 3.4 23.9 + - + +
1023B TRP* 3.0 27.2 + - - +
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Residues in contact with SER1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B LEU* 4.0 20.6 + - - +
747B LYS* 4.9 6.8 + - - -
1016B LYS 4.8 3.8 + - - -
1017B ASN* 3.4 15.3 + - - +
1018B LEU 3.4 0.2 - - - -
1019B LYS* 1.3 78.2 - - - +
1021B LEU* 1.3 60.7 + - - +
1023B TRP* 3.5 7.0 - - - +
1024B TRP* 3.0 29.5 + - - +
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Residues in contact with LEU1021 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B LEU* 3.9 5.6 - - + -
750B PHE* 3.6 34.5 - - + -
775B ILE* 4.0 26.5 - - + -
779B LEU* 4.1 20.4 - - + -
787B LEU* 4.6 5.2 - - + -
791B LEU* 4.8 2.7 - - + -
1013B TRP* 4.0 17.0 - - + -
1017B ASN 3.0 18.6 + - - +
1018B LEU* 3.5 6.1 - - + +
1020B SER* 1.3 77.5 + - - +
1022B THR* 1.3 64.5 + - - +
1024B TRP* 3.6 7.3 + - + -
1025B LEU* 3.3 42.1 + - + +
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Residues in contact with THR1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B TYR* 6.1 0.2 - - - -
787B LEU* 3.3 29.5 - - + +
1018B LEU* 2.9 24.2 + - - +
1019B LYS* 3.7 28.8 + - + +
1020B SER 3.3 0.2 - - - -
1021B LEU* 1.3 77.0 - - - +
1023B TRP* 1.3 63.2 + - - +
1025B LEU* 3.6 2.6 + - - +
1026B ARG* 3.4 18.2 + - - +
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Residues in contact with TRP1023 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B LYS 3.0 17.0 + - - +
1020B SER* 3.5 9.0 - - - +
1021B LEU 3.2 0.2 - - - -
1022B THR* 1.3 72.9 - - - +
1024B TRP* 1.3 61.3 + - + +
1025B LEU 3.0 4.7 - - - -
1026B ARG* 2.8 83.3 + - + +
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Residues in contact with TRP1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B LYS* 5.8 5.8 - - + -
750B PHE* 3.4 75.1 - + + +
753B ILE* 5.3 4.3 - - + -
754B ASN* 5.4 5.4 - - - -
791B LEU* 4.6 5.6 - - + -
794B ARG* 3.1 55.6 + - + +
795B VAL* 6.0 1.6 - - + -
798B LEU* 6.5 0.4 - - + -
1020B SER 3.0 17.4 + - - +
1021B LEU* 3.6 6.3 + - + +
1023B TRP* 1.3 80.5 - - + +
1025B LEU* 1.3 89.3 + - + +
1026B ARG* 3.4 6.7 + - - +
1027B THR* 5.3 0.5 + - - -
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Residues in contact with LEU1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787B LEU* 3.5 33.7 - - + +
790B ARG* 3.3 37.9 + - + +
791B LEU* 3.8 25.6 - - + +
794B ARG* 4.0 16.6 - - + +
1021B LEU* 3.3 29.7 + - + +
1022B THR 3.9 2.5 - - - +
1023B TRP 3.0 1.0 - - - -
1024B TRP* 1.3 105.6 - - + +
1026B ARG* 1.3 64.3 + - - +
1027B THR 3.2 3.4 - - - -
1028B GLU* 3.0 18.3 + - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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).
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