Contacts of the helix formed by residues 555 - 580 (chain D) in PDB entry 1P93
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 SER 555 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D PRO 3.8 1.1 + - - -
554D ASP* 1.3 79.0 - - - +
556D THR* 1.3 65.7 + - - +
557D TRP* 3.1 31.3 + - - -
558D ARG* 3.3 23.5 - - - +
559D ILE* 2.9 31.3 + - - +
636D LEU* 4.8 2.9 - - - +
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Residues in contact with THR 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D SER* 1.3 70.5 + - - +
557D TRP* 1.3 68.0 + - + +
559D ILE* 2.9 14.4 + - - +
560D MET* 3.1 29.3 + - + +
636D LEU* 3.8 9.1 - - - +
637D PRO* 3.1 47.7 + - - +
638D ASP* 4.7 7.2 - - + +
639D MET* 4.1 18.4 - - + -
642D GLN* 5.4 0.2 - - - +
747D ILE* 5.2 4.0 - - + -
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Residues in contact with TRP 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D SER* 3.1 25.4 + - - -
556D THR* 1.3 80.4 - - + +
558D ARG* 1.3 75.2 + - + +
559D ILE 3.3 0.3 + - - -
560D MET* 4.1 0.4 - - - -
561D THR* 2.7 44.0 + - + -
745D MET 3.5 20.6 - - - +
746D SER* 2.7 43.3 - - - -
747D ILE* 3.6 18.6 - - + +
748D GLU* 6.3 0.2 - - + -
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Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D TYR* 2.6 51.6 + - + +
549D ASP* 4.3 5.7 - - - +
550D SER 3.6 11.5 + - - +
552D VAL* 2.2 57.2 + - - +
553D PRO 3.0 20.0 + - - -
554D ASP* 3.8 4.4 + - - +
555D SER* 3.2 26.6 + - - +
556D THR 3.1 0.2 - - - -
557D TRP* 1.3 103.2 - - + +
559D ILE* 1.3 52.6 + - - +
561D THR* 3.9 4.0 - - - -
562D THR* 2.7 27.4 + - - -
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Residues in contact with ILE 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D TYR* 3.5 23.1 - - + +
554D ASP* 4.3 9.2 - - - +
555D SER 2.9 27.2 + - - +
556D THR* 2.9 8.0 + - - +
558D ARG* 1.3 74.4 - - - +
560D MET* 1.3 71.2 + - - +
561D THR 3.2 1.6 - - - -
562D THR* 2.9 19.3 + - - -
563D LEU* 3.0 33.8 + - + +
627D LEU* 5.5 9.6 - - + -
629D ILE* 5.9 5.4 - - + -
633D ARG* 4.8 9.9 - - + +
636D LEU* 3.5 30.7 - - + -
639D MET* 4.3 11.0 - - + -
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Residues in contact with MET 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D THR* 3.1 28.0 + - + +
559D ILE* 1.3 78.7 - - - +
561D THR* 1.3 53.2 + - - +
563D LEU* 2.8 22.5 + - + +
564D ASN* 2.6 38.1 + - - -
639D MET* 4.9 8.5 - - - +
642D GLN* 3.0 43.7 - - - +
739D THR* 5.6 2.0 - - + -
747D ILE* 3.3 34.5 - - + -
4999D DEX 3.1 33.4 - - - +
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Residues in contact with THR 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D TRP* 2.7 34.2 + - + -
558D ARG 3.9 6.3 - - - -
559D ILE 3.2 0.2 - - - -
560D MET* 1.3 78.1 - - - +
562D THR* 1.3 59.6 + - - +
564D ASN* 3.7 1.1 + - - +
565D MET* 3.0 38.7 + - + +
747D ILE* 3.4 5.9 - - - -
748D GLU* 3.1 52.5 + - + +
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Residues in contact with THR 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D ALA* 4.5 10.8 - - + +
547D GLY 4.7 1.6 - - - -
548D TYR* 4.0 44.0 - - + +
558D ARG 2.7 21.0 + - - -
559D ILE* 2.9 10.2 + - - -
561D THR* 1.3 75.6 - - - +
563D LEU* 1.3 54.8 + - - +
565D MET* 2.9 12.3 + - + +
566D LEU* 2.7 33.8 + - - +
627D LEU* 5.0 9.4 - - + -
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Residues in contact with LEU 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D ILE* 3.0 30.3 + - + +
560D MET* 2.8 21.7 + - + +
562D THR* 1.3 77.4 - - - +
564D ASN* 1.3 52.4 + - - +
566D LEU* 3.0 8.5 + - + +
567D GLY* 2.5 36.2 + - - -
623D PHE* 3.9 44.0 - - + -
627D LEU* 3.7 30.1 - - + -
629D ILE* 5.5 3.6 - - + -
639D MET* 6.5 0.4 - - - -
4999D DEX 3.7 25.2 + - + +
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Residues in contact with ASN 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D MET 2.6 24.2 + - - +
561D THR 3.9 1.3 - - - +
563D LEU* 1.3 70.9 - - - +
565D MET* 1.3 56.4 + - - +
568D GLY 2.9 21.8 + - - -
747D ILE* 3.4 21.2 - - - +
748D GLU 3.0 28.3 + - - +
749D PHE* 3.8 13.2 - - + -
750D PRO* 3.0 26.5 - - + +
753D LEU* 3.4 2.7 - - + +
4999D DEX 2.9 48.1 + - - +
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Residues in contact with MET 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D ALA 6.1 0.9 - - - +
561D THR* 3.0 35.4 + - + +
562D THR* 2.9 16.9 + - + +
564D ASN* 1.3 77.7 - - - +
566D LEU* 1.3 59.9 + - - +
568D GLY* 3.7 1.4 + - - -
569D ARG* 3.2 31.0 + - - +
748D GLU* 4.5 5.2 - - + +
749D PHE 3.6 7.2 - - - +
750D PRO* 3.1 49.4 - - + +
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Residues in contact with LEU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D LEU* 3.6 25.6 - - + +
545D TYR 4.1 7.4 - - - +
546D ALA* 4.5 10.5 + - + +
562D THR 2.7 11.3 + - - +
563D LEU* 3.4 15.0 - - + +
565D MET* 1.3 75.1 - - - +
567D GLY* 1.3 69.1 + - - +
569D ARG* 2.8 41.7 + - - +
570D GLN* 2.9 25.2 + - - +
623D PHE* 3.8 32.8 - - + +
624D ALA* 3.9 13.9 - - + -
627D LEU* 6.2 0.2 - - + -
4999D DEX 4.5 7.6 - - + -
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Residues in contact with GLY 567 (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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563D LEU 2.5 20.2 + - - -
564D ASN 4.1 0.9 - - - -
566D LEU* 1.3 71.5 - - - +
568D GLY* 1.3 53.4 + - - +
570D GLN* 2.6 28.5 + - - +
571D VAL* 2.9 18.0 + - - +
604D MET* 4.6 0.7 - - - +
753D LEU* 4.5 2.2 - - - -
4999D DEX 3.4 35.4 - - - -
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Residues in contact with GLY 568 (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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564D ASN 2.9 20.5 + - - -
565D MET 4.0 1.8 - - - -
566D LEU 3.1 0.4 - - - -
567D GLY* 1.3 76.1 - - - +
569D ARG* 1.3 58.9 + - - +
571D VAL* 3.6 8.2 + - - +
572D ILE* 3.3 22.0 + - - +
750D PRO* 3.8 17.7 - - - -
752D MET* 3.9 7.5 - - - +
753D LEU* 3.9 15.0 - - - +
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Residues in contact with ARG 569 (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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544D LEU* 3.2 47.0 - - + +
545D TYR 3.1 27.1 + - - +
546D ALA 3.7 9.3 + - - -
565D MET* 3.2 17.8 + - - +
566D LEU* 2.8 28.6 + - - +
568D GLY* 1.3 72.6 - - - +
570D GLN* 1.3 62.9 + - - +
571D VAL 3.3 0.2 - - - -
572D ILE* 3.5 17.5 - - + +
573D ALA* 3.2 19.1 + - - +
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Residues in contact with GLN 570 (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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543D VAL* 5.3 1.4 - - - -
544D LEU* 4.0 26.7 + - + +
566D LEU* 3.1 30.3 - - + +
567D GLY 2.6 9.4 + - - +
569D ARG* 1.3 78.4 - - - +
571D VAL* 1.3 57.6 + - - -
573D ALA* 3.3 8.9 + - - +
574D ALA* 2.9 27.5 + - - +
604D MET* 3.9 22.0 - - + +
607D ALA* 6.2 0.6 - - - +
611D ARG* 4.3 16.6 + - - +
623D PHE 4.4 1.9 - - - +
4999D DEX 3.0 42.6 + - - -
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Residues in contact with VAL 571 (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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567D GLY 2.9 13.1 + - - +
568D GLY 3.7 8.7 - - - +
569D ARG 3.3 0.4 - - - -
570D GLN* 1.3 70.9 - - - +
572D ILE* 1.3 55.9 + - - +
574D ALA* 2.7 30.1 + - + +
575D VAL* 2.7 28.0 + - + +
600D TRP* 4.1 25.6 - - + -
604D MET* 4.9 5.6 - - - -
752D MET* 4.3 12.8 - - + -
753D LEU* 3.5 31.9 - - + -
756D ILE* 4.3 17.3 - - + -
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Residues in contact with ILE 572 (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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631A GLU* 6.4 3.1 - - + -
632A GLN* 5.6 7.0 - - + -
635A THR* 3.8 33.7 - - + +
568D GLY 3.3 19.1 - - - +
569D ARG* 3.5 18.2 - - + +
571D VAL* 1.3 76.9 - - - +
573D ALA* 1.3 63.2 + - - +
575D VAL* 3.1 20.4 + - + +
576D LYS* 3.2 13.9 + - + +
752D MET* 3.9 18.8 - - + -
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Residues in contact with ALA 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D PRO* 4.3 22.7 - - + +
542D GLU 6.0 0.2 - - - +
544D LEU* 5.3 11.0 - - + -
569D ARG 3.2 11.3 + - - +
570D GLN* 3.5 12.3 - - - +
571D VAL 3.2 0.4 - - - -
572D ILE* 1.3 80.5 - - - +
574D ALA* 1.3 56.9 + - - +
576D LYS* 3.6 8.6 + - - +
577D TRP* 2.8 29.7 + - - +
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Residues in contact with ALA 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D PRO* 5.6 1.8 - - - +
570D GLN 2.9 13.1 + - - +
571D VAL* 2.7 23.9 + - + +
573D ALA* 1.3 68.4 - - - +
575D VAL* 1.3 68.8 + - + +
577D TRP* 3.0 19.5 + - + +
578D ALA* 2.7 20.7 + - - +
596D LEU* 5.1 5.4 - - + -
603D LEU* 5.5 9.6 - - + -
604D MET* 4.8 12.8 - - + -
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Residues in contact with VAL 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D VAL* 2.7 31.7 + - + +
572D ILE* 3.3 13.0 - - + +
574D ALA* 1.3 70.6 - - - +
576D LYS* 1.3 57.3 + - - +
578D ALA* 2.5 32.8 + - - +
579D LYS* 3.0 21.5 + - + +
596D LEU* 4.5 25.1 - - + -
752D MET* 6.1 2.2 - - - -
944H LEU* 5.6 4.9 - - + +
947H LEU* 4.1 37.2 - - + +
948H LEU* 4.7 3.8 - - + +
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Residues in contact with LYS 576 (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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538C VAL 5.3 6.1 + - - -
540C GLU 5.6 3.6 + - - -
542C GLU* 3.4 43.4 - - - +
572D ILE* 3.2 7.8 + - + +
573D ALA* 3.7 10.3 - - - +
575D VAL* 1.3 81.6 - - - +
577D TRP* 1.3 62.3 - - - +
579D LYS* 3.3 14.1 + - + +
580D ALA* 3.1 25.7 + - - +
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Residues in contact with TRP 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D LEU* 4.3 0.8 + - + +
539D ILE* 3.0 54.0 - - + +
540D GLU* 3.5 12.0 + - - -
541D PRO* 3.3 17.9 - - + -
573D ALA 2.8 16.6 + - - +
574D ALA* 3.0 25.8 - - + +
575D VAL 2.8 3.2 + - - -
576D LYS* 1.3 74.3 - - - +
578D ALA* 1.3 73.1 + - + +
580D ALA* 3.1 20.2 + - - +
581D ILE* 3.3 25.2 - - + +
596D LEU* 6.1 1.1 - - + -
603D LEU* 4.0 20.2 - - + -
667D LYS* 2.6 55.7 - - + +
668D THR* 4.1 13.7 - - - -
671D LEU* 4.2 10.5 - - + -
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Residues in contact with ALA 578 (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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574D ALA 2.7 10.4 + - - +
575D VAL* 2.5 14.8 + - - +
577D TRP* 1.3 73.6 - - + +
579D LYS* 1.3 53.1 + - - +
581D ILE* 2.5 52.6 + - + +
584D PHE* 3.6 22.7 - - + +
596D LEU* 3.6 26.2 - - + -
671D LEU* 4.3 4.3 - - + -
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Residues in contact with LYS 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D VAL* 3.0 22.1 + - + +
576D LYS* 3.6 14.4 - - + +
578D ALA* 1.3 77.4 - - - +
580D ALA* 1.3 58.8 + - - +
581D ILE 3.1 1.1 - - - +
584D PHE* 3.8 19.9 - - + -
585D ARG* 2.7 58.4 - - + +
592D GLN* 5.5 1.8 - - - +
596D LEU* 6.2 0.2 - - + -
947H LEU 3.4 20.1 + - - +
948H LEU* 2.8 25.9 + - + +
950H LYS 2.7 31.9 + - - -
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Residues in contact with ALA 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C VAL* 4.8 22.9 - - + +
535D LEU* 5.2 3.5 - - - +
539D ILE* 3.8 31.1 - - + +
576D LYS* 3.1 16.3 + - - +
577D TRP* 3.1 15.2 + - - +
578D ALA 2.8 0.8 + - - -
579D LYS* 1.3 76.6 - - - +
581D ILE* 1.3 60.7 + - - +
582D PRO* 3.7 7.3 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il