Contacts of the helix formed by residues 669 - 692 (chain A) in PDB entry 1JB0
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 669 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 6.1 1.8 - - + -
660A GLN* 6.1 0.9 - - + -
664A SER* 3.0 23.2 + - - -
667A SER* 3.1 11.2 + - - +
668A ALA* 1.3 83.6 - - + +
670A SER* 1.3 55.7 + - - +
671A ALA 3.0 6.3 - - - -
672A TYR* 2.9 51.5 + - + +
749A ALA* 4.2 22.2 - - + +
752A ILE* 4.1 28.3 - - + -
753A SER* 4.2 11.9 - - - +
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Residues in contact with SER 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.4 0.2 - - - +
126A LEU* 3.8 10.6 - - - +
664A SER* 3.2 26.5 + - - -
665A TYR* 3.9 6.9 - - - +
667A SER 3.0 15.1 + - - -
668A ALA 3.2 0.2 - - - -
669A LEU* 1.3 78.8 - - - +
671A ALA* 1.3 63.3 + - - +
673A GLY* 3.3 1.5 + - - -
674A LEU* 3.0 27.4 + - - +
448B ALA* 3.4 28.2 + - - -
449B PHE* 3.8 12.1 - - - -
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Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.6 23.2 - - + +
668A ALA 4.8 0.4 - - - +
669A LEU 3.0 1.2 - - - +
670A SER* 1.3 81.6 + - - +
672A TYR* 1.3 56.9 + - - +
674A LEU* 3.3 4.6 + - - +
675A LEU* 2.8 34.2 + - - +
1106A CLA 3.6 32.5 - - + -
1107A CLA 4.0 24.3 - - + +
449B PHE* 5.5 0.2 - - - -
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Residues in contact with TYR 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 4.9 0.5 - - - +
138A GLN 4.4 2.1 + - - -
661A VAL* 3.7 2.7 - - - -
669A LEU* 2.9 41.1 + - + +
671A ALA* 1.3 75.2 - - - +
673A GLY* 1.3 56.8 + - - +
675A LEU* 3.2 1.7 + - - +
676A PHE* 2.7 36.4 + - - +
744A TRP* 3.6 27.8 - + - -
745A ALA* 3.4 22.4 - - + +
748A LEU* 3.4 35.4 - - + +
749A ALA* 3.9 24.5 - - + -
752A ILE* 4.2 11.6 - - + +
1106A CLA 3.5 51.8 - - + +
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Residues in contact with GLY 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 3.3 28.5 - - - +
664A SER* 3.2 14.1 + - - -
665A TYR* 4.1 4.9 - - - -
670A SER 3.3 3.2 + - - -
672A TYR* 1.3 77.9 - - - +
674A LEU* 1.3 59.9 + - - +
676A PHE* 3.3 9.7 - - - +
677A LEU* 3.5 6.1 + - - +
623B MET* 3.2 26.2 - - - +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TYR* 3.4 25.1 - - + +
670A SER 3.0 17.9 + - - +
671A ALA* 3.5 6.5 - - - +
673A GLY* 1.3 72.8 - - - +
675A LEU* 1.3 61.2 + - - +
676A PHE 3.1 1.3 - - - -
677A LEU* 3.2 3.9 + - - +
678A GLY 2.9 22.2 + - - -
1107A CLA 4.0 36.6 - - + -
444B ASP 3.9 13.0 - - - +
445B VAL* 4.0 9.9 - - + +
448B ALA* 3.9 20.6 - - + -
449B PHE* 4.2 10.3 - - + -
1012B CLA 3.1 36.7 - - + +
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Residues in contact with LEU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA 2.8 22.4 + - - +
672A TYR* 3.9 2.5 - - - +
674A LEU* 1.3 71.5 - - - +
676A PHE* 1.3 56.5 + - - +
678A GLY* 4.2 1.3 - - - +
679A ALA* 2.7 37.9 + - - +
741A ALA* 5.3 1.7 - - + +
744A TRP* 3.7 34.1 - - + -
745A ALA* 4.3 3.8 - - + -
1106A CLA 3.9 13.5 - - + -
1107A CLA 4.3 2.0 - - + -
1126A CLA 3.5 43.3 - - + -
4011A BCR 4.8 26.0 - - + +
1012B CLA 3.8 21.1 - - + -
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Residues in contact with PHE 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A ALA* 4.9 1.1 - - + -
661A VAL* 3.7 31.6 - - + -
662A ILE* 3.9 10.3 - - + -
672A TYR 2.7 21.7 + - - +
673A GLY 3.3 6.5 - - - +
675A LEU* 1.3 72.5 - - - +
677A LEU* 1.3 61.5 + - + +
679A ALA* 3.9 4.3 - - - +
680A HIS* 2.9 45.5 + + - -
742A THR* 3.6 31.9 - - + -
745A ALA* 3.6 10.0 - - + +
746A PHE* 3.8 19.5 - - + -
1011A CLA 3.7 26.7 - + + -
623B MET* 4.6 5.2 - - + -
626B LEU* 3.9 28.5 - - + -
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Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TYR* 3.7 11.2 - - - +
673A GLY 3.5 8.9 + - - +
674A LEU 3.2 8.3 + - - +
676A PHE* 1.3 77.8 - - + +
678A GLY* 1.3 67.3 + - - +
680A HIS* 3.2 3.3 + - + -
681A PHE* 3.0 18.7 + - - +
444B ASP* 3.8 3.1 - - - +
622B LEU* 4.1 2.0 - - + +
623B MET* 3.5 43.1 - - + +
626B LEU* 3.6 35.7 - - + -
1012B CLA 3.3 56.6 - - + +
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Residues in contact with GLY 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU 2.9 13.2 + - - -
675A LEU* 3.1 5.6 + - - -
677A LEU* 1.3 77.0 - - - +
679A ALA* 1.3 55.9 + - - +
681A PHE* 3.1 6.4 + - - +
682A ILE* 3.0 23.6 + - - +
4011A BCR 3.6 28.5 - - - +
1012B CLA 3.5 19.9 - - - +
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Residues in contact with ALA 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A LEU 2.7 18.6 + - - +
676A PHE 3.9 0.7 - - - +
678A GLY* 1.3 70.7 - - - +
680A HIS* 1.3 64.1 + - - +
682A ILE* 3.3 1.4 + - - +
683A TRP* 3.0 20.4 + - - +
738A GLY* 3.2 17.1 - - - +
741A ALA* 3.4 15.0 - - + -
742A THR* 2.9 42.2 - - - +
4011A BCR 4.0 8.3 - - + +
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Residues in contact with HIS 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A PHE* 2.9 46.1 + + - +
677A LEU* 3.2 12.1 + - + +
679A ALA* 1.3 76.0 - - - +
681A PHE* 1.3 62.0 + - - +
683A TRP* 3.4 2.4 + - - +
684A ALA* 3.1 18.0 + - - +
742A THR* 3.1 31.4 + - + +
1011A CLA 2.3 66.8 + + + -
626B LEU* 5.4 2.8 - - + +
1012B CLA 2.9 45.5 - - + +
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Residues in contact with PHE 681 (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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677A LEU 3.0 6.0 + - - +
678A GLY 3.2 9.6 - - - +
679A ALA 3.1 0.2 - - - -
680A HIS* 1.3 75.5 - - - +
682A ILE* 1.3 67.4 + - + +
684A ALA* 3.2 4.8 + - - +
685A PHE* 2.9 40.9 + + + +
1013A CLA 3.5 45.2 - - + +
1140A CLA 4.7 11.4 - - + -
4011A BCR 3.3 32.3 - - + -
437B LEU* 3.9 20.4 - - + -
1012B CLA 3.4 62.3 - + + +
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Residues in contact with ILE 682 (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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678A GLY 3.0 11.3 + - - +
679A ALA 3.3 4.7 + - - +
681A PHE* 1.3 86.4 - - + +
683A TRP* 1.3 61.2 + - - +
685A PHE* 3.3 9.5 - - + +
686A SER 3.1 17.8 + - - -
734A HIS* 3.3 40.9 - - + +
737A LEU* 4.1 9.4 - - + -
738A GLY* 3.8 11.0 - - - +
1140A CLA 3.3 42.2 - - + -
4011A BCR 3.4 33.9 - - + -
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Residues in contact with TRP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ALA 3.0 17.2 + - - +
680A HIS 3.5 3.1 - - - +
681A PHE 3.1 0.2 - - - -
682A ILE* 1.3 77.7 - - - +
684A ALA* 1.3 73.2 + - - +
686A SER* 2.7 23.1 + - - -
687A LEU* 3.7 7.7 - - + +
734A HIS 3.9 8.1 - - - -
735A TYR* 3.1 62.5 - + - -
738A GLY* 3.9 4.9 - - - -
739A GLY* 3.9 6.3 - - - -
1011A CLA 3.2 60.4 - + + +
1022A CLA 3.6 13.2 - - + -
663B TRP* 3.7 22.9 - + - -
667B PHE* 3.8 10.8 - + - -
1012B CLA 3.6 35.9 - - + -
1021B CLA 4.5 1.1 - - + -
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Residues in contact with ALA 684 (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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680A HIS 3.1 11.6 + - - +
681A PHE 3.8 1.1 - - - +
683A TRP* 1.3 80.9 - - - +
685A PHE* 1.3 66.6 + - - +
687A LEU* 3.0 24.4 + - - +
688A MET 3.9 1.7 + - - -
1013A CLA 3.4 21.3 - - + +
1012B CLA 3.4 50.6 - - + +
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Residues in contact with PHE 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE* 2.9 27.1 + + + +
682A ILE* 3.3 9.2 - - + +
684A ALA* 1.3 79.2 - - - +
686A SER* 1.3 61.6 + - - +
688A MET* 3.1 39.8 + - + +
689A PHE* 3.6 22.1 - + - -
734A HIS* 3.3 35.4 - + - -
1013A CLA 3.3 47.1 - + + +
1140A CLA 3.5 55.0 - + + -
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Residues in contact with SER 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ILE 3.1 6.1 + - - -
683A TRP 2.7 19.4 + - - -
685A PHE* 1.3 77.7 - - - +
687A LEU* 1.3 61.4 + - - +
689A PHE* 3.1 20.9 + - - +
690A LEU* 3.1 15.6 + - - +
731A GLY 3.1 24.2 - - - -
734A HIS* 3.2 22.9 - - - -
735A TYR* 3.3 25.9 - - - +
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Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A TRP* 3.7 14.1 - - + +
684A ALA* 3.0 16.3 + - - +
686A SER* 1.3 78.6 + - - +
688A MET* 1.3 56.3 + - - +
690A LEU* 3.8 6.3 - - + +
691A PHE* 2.9 53.5 + - + +
735A TYR* 3.9 25.8 - - + -
1013A CLA 3.8 15.5 - - + -
667B PHE* 3.7 41.1 - - + -
671B ILE* 5.0 0.2 - - + -
719B PHE* 5.5 2.0 - - + -
1012B CLA 4.1 24.0 - - + -
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Residues in contact with MET 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A ALA 3.9 1.2 + - - -
685A PHE* 3.1 41.2 + - + +
686A SER 3.0 0.6 - - - -
687A LEU* 1.3 80.7 - - - +
689A PHE* 1.3 69.2 + - + +
692A SER* 2.6 34.3 + - - -
697A TRP* 3.7 20.6 - - + -
1013A CLA 2.6 79.9 - - + +
1140A CLA 4.9 2.7 - - + -
2001A PQN 3.0 21.2 + - + +
4014B BCR 5.4 0.7 - - + -
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Residues in contact with PHE 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A PHE* 3.6 43.3 - + - -
686A SER* 3.1 11.0 + - - +
688A MET* 1.3 100.3 - - + +
690A LEU* 1.3 62.1 + - - +
691A PHE 3.6 0.3 + - - -
692A SER 3.6 8.1 - - - +
722A LEU* 4.0 14.1 - - + -
727A GLY 3.5 21.8 - - - +
728A ARG* 6.1 0.3 - - - +
730A VAL* 3.5 32.5 - - + -
731A GLY* 3.8 5.4 - - - -
734A HIS* 5.0 0.7 - + - -
1140A CLA 4.3 13.0 - - + -
2001A PQN 3.2 63.2 - + + -
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Residues in contact with LEU 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 3.6 32.3 - - + -
600A PHE* 3.8 25.8 - - + -
686A SER* 3.1 18.9 + - - +
687A LEU* 3.4 5.1 + - + +
689A PHE* 1.3 78.5 - - - +
691A PHE* 1.3 68.7 + - + +
728A ARG* 4.1 5.6 - - + +
731A GLY* 3.6 31.9 - - - +
732A VAL 3.7 2.5 - - - +
735A TYR* 3.9 15.3 - - + -
670B LEU 3.2 15.4 - - - +
671B ILE* 4.1 17.2 - - + +
673B TRP* 4.1 11.4 + - - -
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Residues in contact with PHE 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LEU* 2.9 36.3 + - + +
690A LEU* 1.3 82.2 - - + +
692A SER* 1.3 60.8 + - - +
1013A CLA 3.3 25.4 - - + -
575B ASP* 4.3 1.0 - - - +
583B TYR* 2.5 39.5 + - - +
587B PHE* 3.7 32.8 - + + -
667B PHE* 4.0 28.3 - + - -
670B LEU* 3.6 31.4 - - + +
671B ILE* 3.7 28.3 - - + -
673B TRP* 5.1 3.3 - - - -
719B PHE* 4.0 11.2 - + - -
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Residues in contact with SER 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A MET 2.6 23.8 + - - -
689A PHE 3.6 10.1 + - - +
690A LEU 3.5 0.6 - - - -
691A PHE* 1.3 79.2 - - - +
693A GLY* 1.3 59.0 + - - +
697A TRP* 3.0 29.8 + - - -
1013A CLA 4.4 1.6 - - - -
2001A PQN 3.3 6.5 + - - -
575B ASP* 3.2 11.8 - - - +
584B LEU* 3.4 30.1 - - - -
673B TRP* 3.6 16.6 - - - -
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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