Contacts of the helix formed by residues 674 - 702 (chain D) in PDB entry 6PB4
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 THR 674 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D PHE* 4.0 5.8 - - - -
672D LEU 5.5 1.1 - - - +
673D VAL* 1.3 81.9 - - - +
675D ALA* 1.3 60.5 + - - +
676D GLY* 3.3 3.3 + - - -
677D GLU* 2.8 37.5 + - + +
678D ARG* 3.0 24.7 - - - +
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Residues in contact with ALA 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D PHE* 4.7 8.3 - - + -
674D THR* 1.3 76.5 - - - +
676D GLY* 1.3 53.6 + - - +
677D GLU 3.3 0.2 - - - -
678D ARG* 3.1 10.9 + - - +
679D TYR* 2.3 41.6 + - + +
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Residues in contact with GLY 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674D THR* 3.3 4.0 + - - -
675D ALA* 1.3 77.9 - - - +
677D GLU* 1.3 55.8 + - - +
679D TYR* 3.8 8.7 - - - -
680D ASN* 2.6 44.0 + - - +
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Residues in contact with GLU 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664D ILE* 5.8 2.0 - - + -
673D VAL* 3.3 36.1 - - + +
674D THR* 2.8 31.1 + - + +
676D GLY* 1.3 69.3 - - - +
678D ARG* 1.3 66.5 + - - +
680D ASN* 3.9 3.5 - - - +
681D LYS* 3.0 30.3 + - + +
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Residues in contact with ARG 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661D VAL 5.4 1.2 + - - -
664D ILE* 3.9 32.4 + - + +
665D GLN* 2.3 45.5 + - - +
668D PHE* 3.7 35.3 - - - +
673D VAL* 4.2 5.8 - - + -
674D THR 3.0 22.4 + - - +
675D ALA* 3.1 8.4 + - - +
677D GLU* 1.3 77.8 - - - +
679D TYR* 1.3 58.1 + - - +
681D LYS* 4.0 0.3 - - - +
682D VAL* 2.9 45.3 + - + +
756D GLU* 6.3 1.6 - - - +
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Residues in contact with TYR 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675D ALA* 2.3 32.5 + - + +
676D GLY* 3.5 9.4 - - - +
677D GLU 3.1 0.2 - - - -
678D ARG* 1.3 70.5 - - - +
680D ASN* 1.3 78.7 + - - +
682D VAL* 3.3 4.3 + - - +
683D ILE* 3.0 32.0 + - + +
753D SER* 5.1 1.6 - - - -
754D ILE* 2.4 51.6 + - + +
755D ILE 5.3 0.7 - - - -
756D GLU* 3.1 41.5 - - + -
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Residues in contact with ASN 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676D GLY* 2.6 30.2 + - - +
677D GLU* 4.1 3.7 - - - +
679D TYR* 1.3 85.9 - - - +
681D LYS* 1.3 57.7 + - - +
683D ILE* 2.9 26.3 - - - +
684D ASP* 2.9 23.2 + - - +
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Residues in contact with LYS 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664D ILE* 4.9 14.1 - - + -
677D GLU* 3.0 20.0 + - + +
678D ARG 4.2 1.6 - - - +
680D ASN* 1.3 74.3 - - - +
682D VAL* 1.3 66.3 + - - +
684D ASP* 3.2 19.7 + - + +
685D ILE* 3.0 37.5 + - + +
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Residues in contact with VAL 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661D VAL* 4.4 8.7 - - + -
664D ILE* 4.0 27.8 - - + -
678D ARG* 2.9 38.3 + - + +
679D TYR* 3.8 4.3 - - - +
681D LYS* 1.3 77.5 - - - +
683D ILE* 1.3 61.9 + - - +
685D ILE* 3.0 26.8 - - + +
686D TRP* 3.0 38.8 + - + +
756D GLU* 4.8 11.7 - - + +
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Residues in contact with ILE 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D TYR* 3.0 24.1 + - + +
680D ASN* 2.9 33.7 - - - +
682D VAL* 1.3 76.7 - - - +
684D ASP* 1.3 67.3 + - - +
686D TRP* 3.9 6.8 - - + +
687D ALA* 2.9 28.0 + - + +
746D LEU* 4.0 21.1 - - + -
754D ILE* 3.4 40.2 - - + -
755D ILE 4.8 2.2 - - - +
756D GLU* 5.8 2.9 - - - +
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Residues in contact with ASP 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680D ASN* 2.9 32.5 + - - +
681D LYS* 3.4 29.0 + - + +
682D VAL 3.2 0.2 - - - -
683D ILE* 1.3 81.1 - - - +
685D ILE* 1.3 59.5 + - + +
687D ALA* 3.4 4.4 + - - +
688D ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D ALA* 4.8 15.0 - - + +
660D GLU* 5.0 8.7 - - + +
661D VAL* 3.7 36.1 - - + +
664D ILE* 5.8 1.8 - - + -
681D LYS* 3.0 26.8 + - + +
682D VAL* 3.0 29.6 - - + +
684D ASP* 1.3 76.8 - - + +
686D TRP* 1.3 61.4 + - + +
688D ALA* 3.3 7.6 + - - +
689D ALA* 2.9 28.2 + - - +
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Residues in contact with TRP 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D ILE* 5.8 12.1 - - + -
657D ALA* 5.3 9.4 - - + -
658D GLU* 5.4 10.8 - - + -
661D VAL* 3.4 30.9 - - + +
682D VAL* 3.0 51.0 + - + +
683D ILE* 4.0 5.6 - - - +
685D ILE* 1.3 80.8 - - + +
687D ALA* 1.3 57.4 + - - +
689D ALA* 3.2 12.1 + - + +
690D ASN* 2.9 26.7 + - - +
743D MET* 4.7 10.7 - - + +
746D LEU* 5.4 5.1 - - + +
756D GLU 4.1 10.6 + - - +
757D THR* 5.3 10.3 - - + -
758D PRO* 3.4 41.7 - - + -
759D ILE 6.0 0.9 - - - -
760D THR* 5.6 10.3 - - + -
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Residues in contact with ALA 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D ILE* 2.9 22.6 + - + +
684D ASP* 3.8 5.4 - - - +
686D TRP* 1.3 75.4 - - - +
688D ALA* 1.3 59.2 + - - +
690D ASN* 3.2 9.9 + - - +
691D ASP* 2.9 36.3 + - - +
746D LEU* 5.3 10.9 - - + +
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Residues in contact with ALA 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP 3.0 17.4 + - - +
685D ILE* 3.6 8.5 - - - +
687D ALA* 1.3 78.5 - - - +
689D ALA* 1.3 56.1 + - - +
691D ASP* 3.1 12.7 + - - +
692D ARG* 2.9 39.1 + - - +
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Residues in contact with ALA 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653D ILE* 4.1 24.8 - - + +
654D ILE* 6.3 0.9 - - - -
657D ALA* 4.9 12.3 - - + -
685D ILE 2.9 14.2 + - - +
686D TRP* 3.2 17.0 + - + +
688D ALA* 1.3 72.9 - - - +
690D ASN* 1.3 64.8 + - - +
692D ARG* 3.3 6.5 + - - +
693D VAL* 2.9 29.9 + - + +
743D MET* 4.2 5.8 - - + -
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Residues in contact with ASN 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686D TRP 2.9 10.6 + - - +
687D ALA* 3.3 13.6 - - - +
689D ALA* 1.3 76.3 - - - +
691D ASP* 1.3 67.0 + - - +
693D VAL* 3.2 3.6 + - - +
694D SER* 2.9 20.4 + - - -
738D ARG* 3.9 21.4 - - - +
743D MET* 3.0 44.9 + - - +
745D GLY* 3.8 27.3 - - - +
746D LEU* 5.4 5.6 - - + +
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Residues in contact with ASP 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687D ALA* 2.9 26.7 + - - +
688D ALA* 3.1 11.3 + - - +
690D ASN* 1.3 81.3 + - - +
692D ARG* 1.3 59.3 + - + +
694D SER* 3.3 8.3 + - - -
695D LYS* 2.9 28.5 + - - +
738D ARG* 5.4 6.1 + - - -
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Residues in contact with ARG 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D ILE* 4.1 43.2 - - + +
656D GLU* 4.5 12.5 + - - -
688D ALA* 2.9 26.8 + - + +
689D ALA* 3.6 8.7 - - - +
691D ASP* 1.3 76.4 - - + +
693D VAL* 1.3 55.8 + - - +
695D LYS* 3.3 25.8 + - - +
696D ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D PRO* 4.7 7.0 - - + +
649D LYS 5.3 0.4 - - - -
650D LYS* 4.2 43.7 - - + +
653D ILE* 4.8 17.3 - - + -
654D ILE* 5.8 1.8 - - + -
689D ALA* 2.9 19.0 + - + +
690D ASN* 3.5 7.6 - - - +
692D ARG* 1.3 76.9 - - - +
694D SER* 1.3 63.5 + - - +
696D ALA* 3.2 7.0 + - - +
697D MET* 3.0 25.1 + - - +
738D ARG* 6.3 0.7 - - + -
742D GLY* 4.3 17.0 - - - -
743D MET* 3.8 20.0 - - + +
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Residues in contact with SER 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690D ASN* 2.9 12.5 + - - -
691D ASP* 3.5 10.8 - - - -
693D VAL* 1.3 76.8 - - - +
695D LYS* 1.3 58.4 + - - +
697D MET* 3.0 14.7 - - - +
698D MET* 2.9 31.5 + - - +
738D ARG* 2.9 47.2 + - - +
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Residues in contact with LYS 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D ASP 2.9 13.4 + - - +
692D ARG* 3.6 33.3 + - - +
694D SER* 1.3 76.0 - - - +
696D ALA* 1.3 64.6 + - - +
698D MET* 3.2 5.9 + - + +
699D ASP* 2.9 40.4 + - - +
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Residues in contact with ALA 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D PRO* 4.5 12.6 - - + -
649D LYS* 4.5 29.4 - - + +
653D ILE* 5.6 2.0 - - + -
692D ARG 2.9 16.9 + - - +
693D VAL* 3.6 7.9 - - - +
695D LYS* 1.3 79.1 - - - +
697D MET* 1.3 57.8 + - - +
699D ASP* 3.3 5.1 + - - +
700D ASN* 2.9 31.1 + - - +
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Residues in contact with MET 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D PRO* 3.7 27.5 - - + +
693D VAL* 3.0 14.6 + - - +
694D SER* 3.0 27.4 - - - +
696D ALA* 1.3 77.1 - - - +
698D MET* 1.3 60.1 + - + +
700D ASN* 4.1 4.3 - - - -
701D LEU* 2.9 57.2 + - + +
737D ILE* 4.2 20.0 - - + +
738D ARG* 4.4 11.2 - - - -
741D ALA* 3.3 34.5 - - + -
742D GLY* 4.0 14.4 - - - -
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Residues in contact with MET 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694D SER* 2.9 20.5 + - - +
695D LYS* 3.6 7.9 - - - +
696D ALA 3.2 0.2 - - - -
697D MET* 1.3 80.2 - - + +
699D ASP* 1.3 63.2 + - - +
701D LEU* 5.0 2.0 - - - -
702D GLN* 2.8 66.0 + - + +
723D TYR* 4.6 18.6 - - + -
734D ALA* 5.0 16.8 - - + -
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Residues in contact with ASP 699 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D LYS* 2.9 36.1 + - - +
696D ALA* 3.9 4.6 - - - +
698D MET* 1.3 81.4 - - - +
700D ASN* 1.3 59.1 + - - +
701D LEU 3.4 0.2 - - - -
702D GLN* 4.9 3.0 - - - +
703D THR* 4.1 22.7 + - + +
704D GLU* 3.5 10.0 - - - +
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Residues in contact with ASN 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D VAL* 5.9 1.9 - - - +
646D ILE 4.7 1.6 + - - -
647D PRO* 3.5 29.7 - - + +
648D GLU 4.4 1.6 - - - +
649D LYS* 4.0 20.1 - - - +
696D ALA 2.9 18.0 + - - +
697D MET* 3.8 7.4 - - - +
698D MET 3.1 0.4 - - - -
699D ASP* 1.3 77.1 - - - +
701D LEU* 1.3 69.7 + - + +
704D GLU* 3.1 40.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D VAL* 3.6 45.8 - - + +
646D ILE 5.9 1.1 - - - -
647D PRO* 5.6 0.9 - - + -
697D MET* 2.9 50.0 + - + +
698D MET* 4.4 2.2 - - - +
700D ASN* 1.3 90.2 - - + +
702D GLN* 1.3 65.0 + - - +
703D THR 3.5 1.3 + - - -
704D GLU* 4.3 6.0 + - - +
705D THR* 5.5 3.1 - - - +
718D SER* 3.1 15.4 + - - -
720D ASN* 3.3 34.9 - - + +
723D TYR* 6.4 0.2 - - - -
737D ILE* 5.8 2.9 - - + -
741D ALA* 5.3 0.2 - - + -
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Residues in contact with GLN 702 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D MET* 2.8 41.3 + - + +
699D ASP* 4.9 0.7 - - - +
701D LEU* 1.3 72.2 - - - +
703D THR* 1.3 69.1 + - + +
704D GLU 3.7 0.4 + - - -
705D THR* 6.1 0.2 - - - +
716D GLN 4.2 2.6 - - - +
717D VAL* 5.3 1.7 - - - -
718D SER* 2.0 41.6 + - - -
723D TYR* 3.3 53.5 + - - -
724D MET* 4.6 6.2 - - - +
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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