Contacts of the helix formed by residues 604 - 627 (chain A) in PDB entry 1IVS
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 604 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A THR* 3.3 14.4 - - - +
603A PRO* 1.3 73.9 - - - +
605A LEU* 1.3 65.0 + - - +
606A ALA* 3.4 9.3 + - - +
607A ASP* 2.9 38.0 + - - +
608A ARG* 3.0 16.7 + - - +
656A ALA* 4.6 8.9 - - + +
661A ASN* 3.7 9.6 - - - +
663A HIS* 4.1 0.8 + - - -
664A THR* 3.1 25.2 + - - +
758A ASN* 5.2 4.5 - - - -
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO 4.4 0.2 + - - -
604A THR* 1.3 71.9 - - - +
606A ALA* 1.3 64.8 + - - +
608A ARG* 3.3 8.6 + - - +
609A PHE* 2.8 24.8 + - + +
715A ALA* 4.3 9.9 - - + +
718A ALA* 4.0 20.2 - - + -
719A PHE* 3.4 47.1 - - + +
722A LEU* 5.3 3.6 - - + -
754A PRO* 4.6 13.0 - - + -
757A GLU* 4.5 11.0 - - - +
758A ASN* 3.4 38.2 + - - +
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Residues in contact with ALA 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A THR* 3.2 8.6 + - - +
605A LEU* 1.3 80.5 - - - +
607A ASP* 1.3 62.2 + - - +
609A PHE* 3.3 3.9 + - - +
610A MET 3.0 18.9 + - - -
649A TYR* 3.2 21.1 - - + -
652A ALA* 3.7 37.9 - - + +
653A ALA* 5.4 0.7 - - - -
719A PHE* 4.0 16.6 - - + -
758A ASN* 5.0 1.4 + - - -
761A VAL* 5.8 2.7 - - + -
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Residues in contact with ASP 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A THR* 2.9 31.0 + - - +
606A ALA* 1.3 72.5 - - - +
608A ARG* 1.3 64.9 + - - +
609A PHE 2.8 4.8 + - - -
610A MET* 2.9 13.3 + - - +
611A ARG* 3.0 17.7 + - + +
649A TYR* 2.4 34.1 + - - +
653A ALA* 5.2 0.2 - - - +
663A HIS* 2.7 38.6 + - + -
664A THR* 3.0 29.4 + - - +
667A THR* 3.9 8.2 - - - +
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Residues in contact with ARG 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A PRO* 3.8 34.8 - - + +
604A THR 3.0 14.2 + - - +
605A LEU* 3.8 9.0 - - - +
607A ASP* 1.3 78.9 - - + +
609A PHE* 1.3 58.7 + - - +
611A ARG* 4.0 14.8 - - - +
612A SER* 3.4 21.8 + - - -
663A HIS* 4.9 8.8 + - + -
712A ASP* 4.1 27.2 + - - +
715A ALA* 4.4 9.0 - - + -
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Residues in contact with PHE 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 2.8 18.0 + - + +
606A ALA 3.3 8.3 - - - +
607A ASP 2.8 0.8 + - - -
608A ARG* 1.3 76.7 - - - +
610A MET* 1.3 68.5 + - + +
612A SER* 3.2 5.8 + - - -
613A ARG* 2.9 54.7 + - + +
644A GLU* 4.2 20.9 - - - -
648A TRP* 5.0 0.9 - - + -
649A TYR* 5.3 3.4 - + - -
715A ALA* 4.7 7.4 - - - +
716A GLU* 3.9 24.7 - - + +
719A PHE* 3.5 60.1 - + + -
720A GLU* 6.1 0.4 - - - -
723A LYS* 4.2 16.8 - - - -
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Residues in contact with MET 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A ALA 3.0 5.5 + - - +
607A ASP 2.9 5.6 + - - +
609A PHE* 1.3 76.5 - - + +
611A ARG* 1.3 66.0 + - - +
613A ARG* 3.7 9.1 - - + -
614A LEU* 3.0 29.5 + - + +
640A LEU* 4.1 28.5 - - + -
644A GLU* 3.3 33.9 - - + +
645A PHE* 3.9 21.8 - - + -
649A TYR* 3.1 53.2 - - + -
671A VAL* 4.0 16.6 - - + -
675A LEU* 5.4 0.7 - - + -
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Residues in contact with ARG 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A ASP 3.0 14.9 + - - +
608A ARG* 4.0 13.5 - - - +
610A MET* 1.3 77.3 - - - +
612A SER* 1.3 61.8 + - - +
614A LEU* 3.1 21.2 + - - +
615A SER* 3.3 11.3 + - - -
663A HIS* 5.1 7.6 + - - -
666A ARG* 4.4 7.5 - - - +
667A THR* 3.4 46.0 + - + +
670A GLU* 2.7 44.3 + - - +
671A VAL* 4.4 8.9 - - + +
710A GLY 6.1 0.4 - - - -
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ARG 3.4 13.0 + - - -
609A PHE 3.2 7.7 + - - -
611A ARG* 1.3 74.7 - - - +
613A ARG* 1.3 58.8 + - - +
614A LEU 2.9 10.8 + - - -
615A SER* 3.1 14.0 + - - -
616A ARG* 3.2 12.3 + - - +
710A GLY 5.1 0.7 - - - -
711A ARG* 3.4 13.4 - - - +
712A ASP* 2.7 33.5 + - - -
716A GLU* 2.6 34.2 + - - +
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Residues in contact with ARG 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A PHE* 2.9 47.6 + - + +
610A MET* 3.7 15.9 - - + +
611A ARG 3.4 0.2 - - - -
612A SER* 1.3 76.3 - - - +
614A LEU* 1.3 56.2 + - - +
616A ARG* 3.6 24.0 - - - +
617A GLY* 3.4 16.1 + - - +
620A GLU* 4.6 6.9 + - - -
636A GLU 5.8 0.2 + - - -
639A GLU* 4.9 6.9 - - - +
640A LEU* 3.1 41.3 - - - +
644A GLU* 3.2 35.7 + - + +
716A GLU* 3.8 17.9 - - - +
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Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A MET* 3.0 14.5 + - + +
611A ARG* 3.2 12.3 - - - +
612A SER 2.9 0.6 - - - -
613A ARG* 1.3 77.9 - - - +
615A SER* 1.3 55.9 + - - +
616A ARG 3.1 1.1 - - - -
617A GLY* 2.8 3.3 + - - -
618A VAL* 2.7 35.9 + - + +
640A LEU* 3.6 27.1 - - + -
671A VAL* 3.6 40.4 - - + -
674A VAL* 3.9 31.0 - - + -
675A LEU* 3.8 14.1 - - + -
678A LEU* 4.7 2.9 - - + -
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ARG 3.3 7.1 + - - -
612A SER 3.1 6.4 + - - -
614A LEU* 1.3 77.7 - - - +
616A ARG* 1.3 67.2 + - - +
618A VAL* 4.3 1.6 - - - +
619A GLU* 2.8 31.2 + - - +
708A PRO* 3.8 16.4 - - - +
709A GLY* 3.0 23.8 + - - +
710A GLY 2.7 36.3 + - - -
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Residues in contact with ARG 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A SER* 3.2 16.4 + - - +
613A ARG* 3.6 29.4 - - - +
615A SER* 1.3 80.5 - - - +
617A GLY* 1.3 60.2 + - - +
619A GLU* 3.8 10.7 + - - +
620A GLU* 3.1 49.1 + - - +
710A GLY 4.7 0.2 + - - -
711A ARG* 3.3 36.0 - - - +
712A ASP 5.0 1.0 + - - +
713A GLU* 4.2 16.8 + - - -
716A GLU* 3.1 34.4 + - - +
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Residues in contact with GLY 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ARG* 3.4 8.5 + - - -
614A LEU 2.8 10.6 + - - -
616A ARG* 1.3 79.6 - - - +
618A VAL* 1.3 63.6 + - - -
619A GLU 3.3 0.2 + - - -
620A GLU* 3.4 6.0 + - - -
621A ILE* 2.8 36.4 + - - +
636A GLU* 6.1 0.4 - - - -
640A LEU* 4.4 17.9 - - - -
678A LEU* 4.9 1.1 - - - -
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Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU* 2.7 22.3 + - + +
615A SER* 3.8 3.4 - - - +
617A GLY* 1.3 70.5 - - - +
619A GLU* 1.3 68.1 + - - +
621A ILE* 4.2 0.2 - - - +
622A THR* 2.8 32.0 + - - +
674A VAL* 3.6 31.0 - - + -
678A LEU* 3.9 17.6 - - + +
706A PRO* 3.7 24.0 - - + +
707A GLU 3.9 1.3 - - - +
708A PRO* 3.4 39.3 - - + -
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Residues in contact with GLU 619 (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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615A SER* 2.8 23.3 + - - +
616A ARG* 3.8 11.3 + - - +
618A VAL* 1.3 79.8 - - - +
620A GLU* 1.3 67.8 + - + +
622A THR* 3.0 11.0 + - - -
623A ALA* 3.2 15.6 + - + +
708A PRO* 4.2 17.7 - - + +
711A ARG* 5.4 6.9 + - - -
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Residues in contact with GLU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ARG* 4.6 6.4 + - - -
616A ARG* 3.1 40.2 + - + +
617A GLY* 3.7 4.7 - - - +
619A GLU* 1.3 83.6 - - + +
621A ILE* 1.3 64.0 + - + +
623A ALA* 3.5 6.6 + - - +
624A LEU* 3.1 28.1 + - + +
636A GLU* 2.9 40.0 - - - +
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Residues in contact with ILE 621 (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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617A GLY* 2.8 27.3 + - - +
618A VAL 4.2 1.6 - - - +
620A GLU* 1.3 70.7 - - + +
622A THR* 1.3 67.0 + - - +
624A LEU* 3.1 9.6 + - - +
625A TYR* 3.0 45.2 + - + -
633A ALA* 4.1 9.4 - - + +
636A GLU* 4.7 17.3 - - + +
637A VAL* 3.7 39.9 - - + -
640A LEU* 4.8 4.5 - - + -
678A LEU* 4.0 32.3 - - + +
705A TRP* 4.7 0.2 - - + -
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Residues in contact with THR 622 (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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66A TYR* 3.3 21.5 - - - +
70A ARG* 3.4 20.6 - - - +
618A VAL* 2.8 28.7 + - - +
619A GLU* 3.6 3.5 - - - -
621A ILE* 1.3 75.7 - - - +
623A ALA* 1.3 53.3 + - - +
625A TYR* 2.6 30.3 + - - +
626A GLU* 2.7 20.5 + - + -
678A LEU* 5.3 0.2 - - - +
705A TRP* 3.0 27.5 + - + +
706A PRO 4.8 0.2 + - - -
708A PRO* 5.6 0.7 - - - +
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Residues in contact with ALA 623 (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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619A GLU* 3.2 10.5 + - + +
620A GLU* 3.7 10.3 - - - +
622A THR* 1.3 79.8 - - - +
624A LEU* 1.3 59.4 + - + +
626A GLU* 3.1 12.9 + - - +
627A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A GLU* 3.1 17.8 + - + +
621A ILE* 3.3 11.9 - - - +
622A THR 3.0 0.6 - - - -
623A ALA* 1.3 76.2 - - + +
625A TYR* 1.3 62.7 + - - +
627A ALA* 3.3 7.6 + - + -
629A ASP* 2.9 43.7 + - + +
632A GLN* 3.5 28.9 - - + -
633A ALA* 3.2 39.7 - - + +
636A GLU* 3.8 17.5 - - + -
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Residues in contact with TYR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 4.0 5.6 - - + -
63A LEU* 5.0 3.7 - - + +
66A TYR* 3.7 44.8 - + + -
621A ILE* 3.0 44.1 + - + -
622A THR 2.6 13.4 + - - +
624A LEU* 1.3 71.9 - - - +
626A GLU* 1.3 57.3 + - - +
628A LEU* 2.8 28.1 + - - +
630A LEU* 3.4 29.2 - - + +
633A ALA* 4.0 11.4 - - + -
678A LEU 3.8 6.6 + - - -
681A PRO* 3.2 38.1 - - + +
682A MET* 3.7 27.2 - - + +
705A TRP* 4.2 13.5 - + - -
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Residues in contact with GLU 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 2.6 29.9 + - - +
67A LYS* 4.0 12.6 + - - -
70A ARG* 3.1 10.7 + - - +
622A THR* 2.7 22.9 + - + +
623A ALA* 3.2 16.2 - - - +
625A TYR* 1.3 78.2 - - - +
627A ALA* 1.3 54.4 + - - +
628A LEU* 3.2 6.3 + - - +
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Residues in contact with ALA 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A VAL* 5.5 1.2 - - - +
623A ALA 2.9 14.0 + - - +
624A LEU* 3.3 8.5 + - + +
625A TYR 3.1 0.6 - - - -
626A GLU* 1.3 76.0 - - - +
628A LEU* 1.3 72.4 + - - +
629A ASP* 3.0 11.7 + - + +
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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