Contacts of the helix formed by residues 817 - 839 (chain B) in PDB entry 1S0V
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 ILE 817 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 3.2 31.2 - - + -
448B LYS 4.1 17.3 - - - +
449B GLY 4.2 1.8 - - - +
450B LYS* 3.7 34.3 - - + +
530B CYS 4.1 3.8 - - - +
531B SER* 3.8 22.4 - - - +
534B LEU* 5.1 0.2 - - - -
806B SER* 5.1 2.2 - - - -
816B THR* 1.3 86.2 - - + +
818B PRO* 1.3 64.7 - - + -
819B ALA* 4.3 0.9 - - + +
820B ASP* 2.4 60.7 + - + +
821B ALA* 2.8 10.3 + - - -
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Residues in contact with PRO 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ILE* 3.5 16.2 - - + -
456B GLY* 3.3 37.3 - - - +
460B LEU* 4.7 1.1 - - + -
530B CYS* 3.5 35.7 - - + +
532B LEU 2.9 20.2 - - - +
534B LEU* 4.0 25.0 - - + -
816B THR 4.1 0.4 - - - +
817B ILE* 1.3 88.2 - - + +
819B ALA* 1.3 58.4 + - - +
820B ASP 3.1 4.7 + - - -
821B ALA* 3.2 14.4 + - + +
822B ALA* 4.0 3.1 + - - +
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Residues in contact with ALA 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LYS* 3.3 45.1 - - + +
451B PRO 3.9 5.6 - - - +
452B ILE* 3.7 23.6 - - - +
456B GLY* 4.6 2.5 - - - +
530B CYS 5.2 1.1 + - - +
817B ILE* 2.8 2.5 + - + +
818B PRO* 1.3 78.3 - - - +
820B ASP* 1.3 62.2 + - - +
822B ALA* 5.1 5.7 - - - +
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Residues in contact with ASP 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LYS* 2.9 29.1 + - - -
803B GLY* 5.0 1.0 + - - -
804B ILE* 3.1 49.0 + - + +
805B GLU* 4.6 7.4 + - - +
806B SER* 5.2 1.6 + - - -
816B THR* 3.0 28.7 - - + +
817B ILE* 2.4 45.1 + - + +
819B ALA* 1.3 68.6 - - - +
821B ALA* 1.3 62.8 + - - +
822B ALA* 3.2 3.4 - - - -
823B ASN* 3.1 14.5 + - - +
824B LEU 3.3 0.2 + - - -
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Residues in contact with ALA 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TRP* 4.2 22.9 - - + -
534B LEU* 4.4 13.7 - - + +
536B PHE* 4.3 12.8 - - + -
816B THR* 4.4 4.4 - - - -
817B ILE 2.8 9.5 + - - +
818B PRO* 3.4 15.9 - - + +
820B ASP* 1.3 74.4 - - - +
822B ALA* 1.3 70.8 + - - +
823B ASN 2.8 1.7 + - - -
824B LEU* 4.5 9.2 - - - +
825B PHE* 3.2 22.0 + - - +
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Residues in contact with ALA 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLU* 3.5 34.7 - - + +
456B GLY 5.7 0.2 - - - +
459B TRP* 3.8 17.2 + - - +
818B PRO 4.0 4.1 + - - +
819B ALA 5.4 4.3 - - - +
820B ASP 4.6 3.1 - - - +
821B ALA* 1.3 80.4 - - - +
823B ASN* 1.3 72.9 + - - +
825B PHE* 3.5 14.0 - - - +
826B LYS* 4.1 3.6 + - - +
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Residues in contact with ASN 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B TYR* 3.1 46.6 - - + +
803B GLY 5.2 1.4 + - - -
804B ILE* 3.9 5.8 - - + +
820B ASP* 3.1 8.8 + - - +
821B ALA 2.8 3.8 + - - -
822B ALA* 1.3 85.9 + - - +
824B LEU* 1.3 53.5 + - - +
825B PHE 2.4 6.9 + - - -
826B LYS* 2.4 37.0 + - - +
827B ALA* 2.8 9.5 + - - -
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Residues in contact with LEU 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU 5.3 0.9 - - - +
536B PHE* 4.6 6.5 - - + -
794B THR* 4.7 3.6 - - + +
798B ALA* 4.3 8.3 - - + -
804B ILE* 3.3 14.6 - - + +
807B PHE* 4.0 31.0 - - + -
814B PHE* 3.0 54.3 - - + +
815B GLY* 3.9 1.8 - - - +
816B THR* 3.7 19.3 - - - +
820B ASP 3.3 2.8 + - - +
821B ALA* 4.0 8.7 - - - +
823B ASN* 1.3 78.0 - - - +
825B PHE* 1.3 53.2 + - - +
827B ALA* 3.6 7.2 - - + -
828B VAL* 2.8 44.4 + - + +
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Residues in contact with PHE 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TRP* 3.0 39.9 - + + -
475B PHE* 4.2 11.0 - + - -
536B PHE* 3.1 29.1 - + + -
821B ALA 3.2 4.2 + - - +
822B ALA 3.5 16.4 - - - +
823B ASN 2.4 10.1 + - - -
824B LEU* 1.3 73.6 - - - +
826B LYS* 1.3 63.1 + - + +
828B VAL* 4.5 0.2 - - - -
829B ARG* 2.3 73.0 + - - +
876B LEU 5.9 0.7 - - - -
877B GLU 6.5 0.2 - - - -
878B SER 4.4 3.4 - - - -
879B ASP* 3.7 24.0 - - - -
882B PHE* 4.5 3.1 - + - -
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Residues in contact with LYS 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B TYR* 3.2 22.4 - - + +
822B ALA 4.8 1.8 - - - +
823B ASN* 2.4 28.5 + - - +
825B PHE* 1.3 75.5 - - + +
827B ALA* 1.3 52.8 + - - +
829B ARG* 3.3 7.2 + - - +
830B GLU* 2.7 67.6 + - + +
876B LEU* 4.8 23.1 + - + +
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Residues in contact with ALA 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B THR* 3.6 12.8 - - + -
797B TRP* 3.5 28.0 - - + +
798B ALA* 4.5 9.2 - - + -
802B TYR* 4.5 10.2 - - + -
804B ILE* 5.8 0.2 - - + -
823B ASN 2.8 8.2 + - - +
824B LEU* 3.4 14.8 - - - +
826B LYS* 1.3 74.1 - - - +
828B VAL* 1.3 72.8 + - - +
830B GLU* 2.6 15.8 + - - +
831B THR* 2.8 11.7 + - - -
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Residues in contact with VAL 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 5.4 1.6 - - + -
790B HIS* 3.5 15.8 - - + +
794B THR* 3.1 11.5 - - + +
814B PHE* 3.2 48.0 - - + -
824B LEU* 2.8 24.3 + - + +
825B PHE* 4.1 6.1 - - - +
827B ALA* 1.3 73.9 - - - +
829B ARG* 1.3 64.2 + - - +
831B THR* 2.7 21.9 - - - +
832B MET* 2.8 6.8 + - - +
883B ALA* 3.2 37.9 - - + +
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Residues in contact with ARG 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 4.9 0.8 - - - -
825B PHE* 2.3 82.9 + - - +
826B LYS* 3.3 7.3 + - - +
827B ALA 2.9 1.8 + - - -
828B VAL* 1.3 75.6 - - - +
830B GLU* 1.3 66.4 + - - +
832B MET* 3.3 4.9 + - - +
833B VAL* 3.2 19.9 + - - +
875B ILE* 3.9 30.3 - - + +
876B LEU* 3.4 28.2 - - + +
877B GLU* 5.6 0.2 - - - +
878B SER 3.2 17.2 + - - -
879B ASP 3.6 3.0 + - - -
881B ALA* 3.3 4.2 + - + +
882B PHE* 2.5 42.1 - - - +
883B ALA* 3.8 18.4 - - - +
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Residues in contact with GLU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B TRP* 2.6 42.6 + - + +
802B TYR* 3.0 20.4 + - - -
826B LYS* 2.7 50.8 + - + +
827B ALA* 2.6 12.4 + - - +
829B ARG* 1.3 75.2 - - - +
831B THR* 1.3 65.9 + - - +
833B VAL* 3.2 3.3 + - - +
834B ASP* 3.0 20.0 + - - +
876B LEU* 3.4 20.5 - - + +
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Residues in contact with THR 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B HIS* 3.0 8.2 + - + -
793B LYS* 3.0 36.2 + - - +
794B THR* 2.8 36.1 - - + +
797B TRP* 4.7 9.3 - - - -
827B ALA 2.8 15.7 + - - +
828B VAL* 2.7 25.1 - - - +
830B GLU* 1.3 72.4 - - - +
832B MET* 1.3 70.7 + - - +
834B ASP* 3.0 16.2 + - - +
835B THR* 3.2 13.0 + - - -
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Residues in contact with MET 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B GLN* 3.9 29.2 - - + +
545B HIS* 4.0 20.6 - - + -
548B ALA* 5.0 7.4 - - + -
561B LEU* 4.0 11.0 - - + -
790B HIS* 3.7 24.5 - - - +
828B VAL 2.8 17.6 + - - +
829B ARG* 3.5 11.0 - - - +
830B GLU 3.1 0.2 + - - -
831B THR* 1.3 77.3 - - - +
833B VAL* 1.3 65.6 + - - +
834B ASP 3.0 0.2 + - - -
835B THR* 3.1 12.3 + - - -
836B TYR* 3.3 27.1 + - + +
872B LEU* 6.3 0.7 - - + -
875B ILE* 3.4 31.9 - - + -
881B ALA* 6.4 0.2 - - + -
883B ALA* 4.4 11.7 - - - +
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Residues in contact with VAL 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829B ARG 3.2 4.7 + - - +
830B GLU 3.7 6.3 - - - +
832B MET* 1.3 80.1 - - - +
834B ASP* 1.3 68.8 + - - +
836B TYR* 3.7 0.4 + - - -
837B GLU* 3.2 42.6 + - - +
872B LEU* 3.6 33.3 - - + +
873B ARG* 4.2 18.8 - - - +
875B ILE* 3.5 32.8 - - + -
876B LEU* 4.2 14.4 - - + -
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Residues in contact with ASP 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B LYS* 4.7 11.1 + - - -
830B GLU 3.0 11.7 + - - +
831B THR* 3.0 14.1 + - - +
833B VAL* 1.3 84.1 - - - +
835B THR* 1.3 65.9 + - - +
837B GLU* 2.9 21.2 + - - +
838B SER* 3.0 24.6 + - - -
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Residues in contact with THR 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B PRO* 3.3 36.8 - - + -
789B SER* 5.6 0.4 - - - +
793B LYS* 3.0 37.4 + - + +
831B THR 3.2 5.3 + - - -
832B MET* 3.1 9.6 + - - -
834B ASP* 1.3 83.0 - - - +
836B TYR* 1.3 73.2 + - + +
838B SER* 3.0 4.8 + - - +
839B CYS* 2.8 32.3 + - + +
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Residues in contact with TYR 836 (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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545B HIS* 3.7 24.6 + + + +
548B ALA* 3.1 18.4 - - + -
549B MET* 3.1 58.1 - - + +
551B ARG* 2.9 26.8 + - - +
730B PRO* 5.7 0.9 - - + -
786B GLN* 3.4 28.0 - - + +
832B MET* 3.3 25.8 + - + +
835B THR* 1.3 91.1 - - + +
837B GLU* 1.3 58.5 + - - +
839B CYS 3.1 13.3 - - - +
841B VAL* 4.6 8.5 - - + -
872B LEU* 3.2 27.1 - - + -
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Residues in contact with GLU 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ARG* 5.6 1.3 - - - +
833B VAL* 3.2 24.2 + - - +
834B ASP* 2.9 14.9 + - - +
836B TYR* 1.3 79.8 - - - +
838B SER* 1.3 58.6 + - - +
839B CYS 3.5 0.4 - - - -
872B LEU* 3.5 14.0 - - + +
873B ARG* 3.2 42.9 + - - +
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Residues in contact with SER 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B ASP* 3.0 27.2 + - - -
835B THR* 3.0 4.0 + - - -
837B GLU* 1.3 81.8 + - - +
839B CYS* 1.3 73.6 + - - +
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Residues in contact with CYS 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 6.2 0.2 - - - -
551B ARG* 4.1 5.4 + - - -
730B PRO* 4.4 34.8 - - + -
835B THR* 2.8 15.1 + - + +
836B TYR* 3.1 22.5 - - - +
837B GLU 3.5 1.4 - - - -
838B SER* 1.3 97.3 - - - +
840B ASP* 1.3 61.0 + - - +
841B VAL* 3.5 7.9 + - + +
844B ASP* 4.2 11.4 - - - +
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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