Contacts of the helix formed by residues 604 - 626 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B THR* 3.7 12.8 - - + +
603B PRO* 1.3 73.0 - - - +
605B LEU* 1.3 62.1 + - - +
606B ALA* 3.1 8.9 + - - +
607B ASP* 2.7 40.4 + - - +
608B ARG* 2.9 28.7 + - - +
656B ALA* 4.2 9.6 - - + -
661B ASN* 3.7 9.4 - - - +
664B THR* 3.3 15.3 - - - +
758B ASN* 4.7 6.3 - - - -
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B THR* 1.3 71.8 + - - +
606B ALA* 1.3 56.8 + - - +
607B ASP 3.1 0.2 - - - -
608B ARG* 3.1 9.5 + - + +
609B PHE* 2.7 32.7 + - - +
715B ALA* 3.9 28.3 - - + -
718B ALA* 4.0 12.3 - - + -
719B PHE* 3.4 45.5 - - + +
722B LEU* 5.0 6.5 - - + -
754B PRO* 5.1 4.0 - - + -
758B ASN* 3.6 33.8 + - - +
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Residues in contact with ALA 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B THR* 3.1 6.3 + - - +
605B LEU* 1.3 79.8 - - - +
607B ASP* 1.3 65.9 + - - +
609B PHE* 3.0 3.1 + - - +
610B MET 2.9 19.1 + - - -
649B TYR* 3.3 33.3 - - + -
652B ALA* 3.7 28.3 - - + +
653B ALA* 5.5 0.2 - - - -
719B PHE* 3.9 18.3 - - + -
758B ASN* 4.9 1.0 + - - -
761B VAL* 6.0 2.0 - - + -
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Residues in contact with ASP 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B THR* 2.7 39.2 + - - +
606B ALA* 1.3 76.7 - - - +
608B ARG* 1.3 56.4 + - - +
609B PHE 2.7 12.1 + - - -
610B MET* 4.1 1.4 - - - +
611B ARG* 3.3 24.6 + - - +
649B TYR* 2.4 33.4 + - - +
653B ALA* 5.6 0.2 - - - -
663B HIS* 3.0 38.8 - - + +
664B THR* 2.8 32.3 + - - -
667B THR* 4.3 3.7 - - - +
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Residues in contact with ARG 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B PRO* 3.8 33.0 - - + +
604B THR 2.9 18.4 - - - +
605B LEU* 3.1 10.7 + - + +
607B ASP* 1.3 78.2 - - + +
609B PHE* 1.3 61.7 + - - +
611B ARG* 3.7 9.4 - - - +
612B SER* 3.5 16.6 + - - -
663B HIS* 4.9 7.5 + - + -
712B ASP* 4.4 17.5 + - + +
715B ALA* 4.2 17.3 - - + +
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Residues in contact with PHE 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU 2.7 15.1 + - - +
606B ALA* 3.2 12.1 - - - +
607B ASP 2.7 4.9 + - - -
608B ARG* 1.3 68.0 - - - +
610B MET* 1.3 74.9 + - + +
611B ARG 2.8 4.0 - - - -
612B SER* 2.6 29.1 + - - -
613B ARG* 2.9 38.3 + - + -
644B GLU* 4.3 17.7 - - + -
648B TRP* 5.2 4.3 - - + -
649B TYR* 5.4 4.0 - - + -
715B ALA* 4.4 7.9 - - + -
716B GLU* 3.7 37.9 - - + -
719B PHE* 3.5 51.1 - + + -
723B LYS* 4.5 7.4 - - - -
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Residues in contact with MET 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B ALA 2.9 7.4 + - - +
607B ASP 4.2 0.7 - - - +
609B PHE* 1.3 85.0 - - - +
611B ARG* 1.3 55.3 - - - +
613B ARG* 3.9 17.0 - - + -
614B LEU* 2.9 39.3 + - + +
640B LEU* 4.0 22.4 - - + +
644B GLU* 4.2 5.4 - - + -
645B PHE* 3.5 41.7 - - + +
649B TYR* 3.2 46.7 - - + -
667B THR* 5.4 0.2 - - + -
671B VAL* 3.9 20.2 - - + -
675B LEU* 5.5 0.9 - - + -
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ASP 3.3 15.1 + - - +
608B ARG* 3.7 13.6 - - - +
609B PHE 2.6 4.2 + - - -
610B MET* 1.3 75.0 - - - +
612B SER* 1.3 62.1 + - - +
614B LEU* 3.2 17.6 + - - +
615B SER* 3.2 12.0 + - - -
663B HIS* 4.4 7.2 + - - -
666B ARG* 3.1 25.1 - - - +
667B THR* 3.0 38.6 + - + +
670B GLU* 2.8 29.4 + - - +
671B VAL* 4.5 10.3 - - - +
710B GLY* 4.6 11.0 + - - +
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Residues in contact with SER 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ARG 3.5 9.1 + - - -
609B PHE* 2.6 13.9 + - - -
611B ARG* 1.3 76.0 - - - +
613B ARG* 1.3 60.1 + - - -
615B SER* 3.3 16.0 + - - -
616B ARG* 3.4 11.6 + - - -
711B ARG* 3.2 17.2 - - - +
712B ASP* 2.8 31.5 + - - -
716B GLU* 2.8 34.6 + - - -
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B PHE* 2.9 37.1 + - + +
610B MET* 3.7 21.5 - - + +
612B SER* 1.3 76.8 - - - +
614B LEU* 1.3 65.2 + - - +
616B ARG* 3.1 29.9 + - - +
617B GLY* 3.0 19.9 + - - +
620B GLU* 3.8 17.6 + - - -
636B GLU* 5.2 4.9 + - - -
639B GLU* 5.6 1.8 - - - +
640B LEU* 3.0 40.9 - - - +
644B GLU* 3.2 30.7 + - - +
716B GLU* 4.2 10.3 - - - +
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Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B MET* 2.9 16.1 + - + +
611B ARG* 3.2 12.8 + - - +
613B ARG* 1.3 75.6 - - - +
615B SER* 1.3 65.7 + - - +
617B GLY* 2.8 4.1 + - - +
618B VAL* 2.7 31.9 + - + +
640B LEU* 4.1 9.0 - - + -
671B VAL* 3.7 41.1 - - + -
674B VAL* 3.7 43.5 - - + -
675B LEU* 3.7 25.6 - - + -
678B LEU* 4.5 1.1 - - + -
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ARG 3.2 4.3 + - - -
612B SER 3.3 10.5 - - - -
613B ARG 3.2 0.2 - - - -
614B LEU* 1.3 78.7 - - - +
616B ARG* 1.3 68.7 + - - +
618B VAL* 3.6 3.4 + - - +
619B GLU* 3.0 25.3 + - - +
708B PRO* 4.0 10.7 - - - +
709B GLY 3.7 16.9 + - - +
710B GLY 2.7 42.0 + - - +
711B ARG* 4.3 6.1 + - - +
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Residues in contact with ARG 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B SER* 3.4 13.5 + - - -
613B ARG* 3.1 30.6 + - - +
614B LEU 3.1 0.6 - - - -
615B SER* 1.3 81.6 + - - +
617B GLY* 1.3 58.4 - - - +
619B GLU* 2.9 6.7 + - - -
620B GLU* 2.6 52.1 + - + +
711B ARG* 3.2 53.4 + - - +
713B GLU* 5.8 3.6 - - - +
716B GLU* 3.7 28.0 + - - +
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Residues in contact with GLY 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ARG* 3.0 7.1 + - - +
614B LEU 2.8 11.5 + - - -
616B ARG* 1.3 74.3 - - - +
618B VAL* 1.3 54.0 + - - -
620B GLU* 4.1 8.7 + - - -
621B ILE* 2.8 43.6 + - - +
636B GLU* 6.3 0.4 - - - -
640B LEU* 3.4 27.8 - - - -
678B LEU* 4.5 0.4 - - - -
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Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B LEU* 2.7 24.4 + - + +
615B SER* 3.8 4.7 - - - +
617B GLY* 1.3 68.6 - - - +
619B GLU* 1.3 59.7 + - - +
621B ILE* 4.0 0.2 - - - +
622B THR* 2.8 41.8 + - - +
674B VAL* 4.0 15.9 - - + -
678B LEU* 4.1 16.9 - - + +
706B PRO* 3.6 35.0 - - + +
707B GLU 3.9 5.2 - - - +
708B PRO* 3.3 35.7 - - + -
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Residues in contact with GLU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B SER* 3.0 14.6 + - - +
616B ARG* 2.9 6.9 + - - +
618B VAL* 1.3 80.9 - - - +
620B GLU* 1.3 65.8 + - + +
622B THR* 4.0 2.5 - - - -
623B ALA* 3.0 29.8 + - + +
708B PRO* 3.9 25.3 - - + +
711B ARG* 4.2 16.0 + - - -
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Residues in contact with GLU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ARG* 3.8 20.1 + - - -
616B ARG* 2.6 40.9 + - + +
617B GLY* 4.1 5.0 + - - +
619B GLU* 1.3 76.5 - - + +
621B ILE* 1.3 60.9 + - - +
623B ALA* 3.5 5.6 + - - +
624B LEU* 3.2 29.5 + - + +
636B GLU* 3.3 32.6 - - + +
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Residues in contact with ILE 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B GLY* 2.8 35.8 + - - +
618B VAL 4.0 1.3 - - - +
620B GLU* 1.3 70.2 - - - +
622B THR* 1.3 65.2 + - - +
624B LEU* 3.1 8.5 + - - +
625B TYR* 3.1 44.9 + - + -
633B ALA* 4.1 10.5 - - + +
636B GLU* 4.3 19.5 - - + +
637B VAL* 3.4 42.6 - - + -
640B LEU* 4.4 5.4 - - + -
678B LEU* 4.2 26.2 - - + +
682B MET* 5.5 1.3 - - + -
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Residues in contact with THR 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.7 4.7 - - - +
70B ARG* 3.6 33.7 - - - +
618B VAL* 2.8 31.1 + - - +
619B GLU* 4.0 3.1 - - - -
621B ILE* 1.3 73.0 - - - +
623B ALA* 1.3 59.3 + - - +
625B TYR* 3.0 8.7 + - - +
626B GLU* 2.8 31.5 + - + +
678B LEU* 4.7 0.2 - - - +
705B TRP* 2.7 32.4 + - + +
706B PRO 4.5 0.3 + - - -
708B PRO* 5.7 1.5 - - - +
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Residues in contact with ALA 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B GLU* 3.0 21.4 + - + +
620B GLU* 3.6 7.4 - - - +
622B THR* 1.3 79.0 - - - +
624B LEU* 1.3 59.7 + - + +
626B GLU* 3.0 30.7 - - - +
627B ALA* 3.5 5.4 - - - +
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Residues in contact with LEU 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B GLU* 3.2 16.4 + - + +
621B ILE* 3.1 7.9 + - - +
623B ALA* 1.3 77.3 - - + +
625B TYR* 1.3 67.8 + - - +
627B ALA* 3.1 10.6 + - + +
629B ASP* 3.1 44.2 + - + +
630B LEU* 5.0 0.2 - - - -
632B GLN* 3.5 25.1 - - + -
633B ALA* 3.2 36.8 - - + +
636B GLU* 4.2 13.0 - - + +
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Residues in contact with TYR 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ALA* 4.4 2.9 - - + -
63B LEU* 4.9 4.6 - - + +
66B TYR* 3.6 49.9 - + + -
621B ILE* 3.1 45.4 + - + -
622B THR 3.0 6.8 + - - +
624B LEU* 1.3 76.1 - - - +
626B GLU* 1.3 53.9 + - - +
627B ALA 2.5 15.2 + - - -
628B LEU* 2.8 17.8 + - - +
630B LEU* 3.3 41.7 - - + +
633B ALA* 4.2 9.6 - - + -
678B LEU 3.8 1.5 + - - -
681B PRO* 3.2 27.8 - - + +
682B MET* 2.9 31.3 - - + +
705B TRP* 4.0 17.5 - + - -
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Residues in contact with GLU 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 2.5 30.6 + - - +
67B LYS* 3.0 29.3 + - - -
70B ARG* 3.1 14.5 + - - +
622B THR* 2.8 19.0 + - + +
623B ALA* 3.0 11.8 - - - +
625B TYR* 1.3 71.6 - - - +
627B ALA* 1.3 62.8 + - - +
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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) + - + + + + + -
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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