Contacts of the helix formed by residues 807 - 821 (chain B) in PDB entry 1SO2
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 PRO 807 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784B ILE* 3.6 29.4 - - + -
785B ALA 3.6 4.9 - - - +
786B TYR* 3.4 15.6 - - + +
805B ASN 4.0 2.9 - - - +
806B ILE* 1.3 85.9 - - - +
808B ALA* 1.3 67.3 + - - +
809B LEU* 3.2 6.3 - - + +
810B GLU* 2.9 43.9 + - + +
811B LEU* 3.1 9.0 + - - +
925B ARG* 3.6 24.5 - - - +
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Residues in contact with ALA 808 (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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709B LEU* 4.0 2.1 - - - +
712B ILE* 4.2 6.7 - - + -
713B PHE* 3.8 20.9 - - + -
785B ALA* 2.8 29.8 + - + +
786B TYR* 3.9 3.5 - - - +
787B ILE* 3.8 29.6 - - + +
806B ILE 3.7 0.8 + - - -
807B PRO* 1.3 70.3 - - - +
809B LEU* 1.3 58.4 + - - +
811B LEU* 3.2 4.4 + - - +
812B MET* 2.8 32.1 + - - +
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Residues in contact with LEU 809 (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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713B PHE* 3.6 15.3 - - + -
785B ALA 4.7 0.2 + - - -
807B PRO* 3.2 6.1 - - + +
808B ALA* 1.3 78.1 - - - +
810B GLU* 1.3 60.3 + - + +
812B MET* 3.7 15.3 - - + +
813B ALA* 3.1 25.3 + - - +
874B LEU* 4.1 24.2 - - + -
878B GLU* 4.2 28.0 - - + +
881B ARG* 4.6 23.3 - - + +
882B PHE* 3.8 25.1 - - + +
885B LEU* 4.8 3.0 - - + +
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Residues in contact with GLU 810 (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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806B ILE* 3.6 11.6 - - + +
807B PRO* 2.9 25.4 + - + +
809B LEU* 1.3 78.5 - - + +
811B LEU* 1.3 65.7 + - - +
813B ALA* 3.3 4.2 + - - +
814B LEU* 3.1 20.3 + - - +
881B ARG* 2.9 20.7 + - - +
885B LEU* 3.5 28.2 - - + +
925B ARG* 2.6 57.0 + - - +
926B LEU 5.3 0.3 + - - -
929B CYS* 4.6 9.8 - - - -
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Residues in contact with LEU 811 (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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753B THR* 3.6 31.4 - - + +
787B ILE* 3.7 28.7 - - + -
802B LEU 5.4 0.2 - - - +
803B SER* 3.8 21.8 - - - +
806B ILE* 3.7 44.0 - - + +
807B PRO 3.1 6.2 + - - +
808B ALA 4.0 4.7 - - - +
810B GLU* 1.3 73.8 - - - +
812B MET* 1.3 67.2 + - - +
814B LEU* 3.1 14.1 + - + +
815B TYR* 2.9 44.9 + - + +
929B CYS* 4.8 0.4 - - - -
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Residues in contact with MET 812 (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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704B PHE* 4.0 19.5 - - + -
709B LEU* 4.0 21.0 - - + +
713B PHE* 3.5 39.9 - - + -
715B ILE* 4.0 20.9 - - - -
808B ALA 2.8 18.7 + - - +
809B LEU* 3.7 10.8 - - + +
811B LEU* 1.3 78.1 - - - +
813B ALA* 1.3 61.1 + - - +
815B TYR* 3.2 2.8 + - - +
816B VAL* 2.9 25.0 + - + +
870B PHE* 5.4 0.4 - - - -
871B LEU* 4.0 19.3 - - + -
874B LEU* 4.3 1.6 - - + -
882B PHE* 3.5 28.9 - - + -
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Residues in contact with ALA 813 (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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809B LEU 3.1 14.7 + - - +
810B GLU* 3.5 9.4 - - - +
811B LEU 3.2 0.4 - - - -
812B MET* 1.3 76.3 - - - +
814B LEU* 1.3 57.9 + - - +
816B VAL 3.3 0.2 + - - -
817B ALA* 2.9 30.9 + - - +
882B PHE* 3.4 21.7 - - + -
885B LEU* 3.6 31.2 - - + -
886B VAL* 3.6 15.9 - - + +
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Residues in contact with LEU 814 (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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749B VAL* 4.0 18.4 - - + -
753B THR* 3.9 27.8 - - + -
810B GLU 3.1 13.6 + - - +
811B LEU* 3.1 13.2 + - + +
813B ALA* 1.3 77.4 - - - +
815B TYR* 1.3 63.3 + - + +
817B ALA* 3.4 4.9 + - - +
818B ALA* 3.1 21.0 + - - +
889B ALA* 4.6 7.6 - - + -
929B CYS* 3.5 48.5 - - + +
932B CYS* 4.3 6.3 - - + -
933B ILE* 3.6 24.5 - - + -
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Residues in contact with TYR 815 (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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700B MET* 4.0 7.5 - - - +
703B LEU* 5.7 2.9 - - + -
704B PHE* 4.1 17.5 - + + -
707B THR* 4.2 15.7 - - + -
709B LEU* 3.8 28.0 - - + -
746B LEU* 4.1 15.0 - - + -
749B VAL* 3.7 21.8 - - + -
750B TRP* 3.7 24.1 + + + -
753B THR* 2.6 32.2 + - - -
754B THR* 4.2 3.8 - - - +
787B ILE* 3.7 19.8 - - + +
811B LEU* 2.9 30.2 + - + +
812B MET 3.8 3.4 - - - +
814B LEU* 1.3 79.1 - - + +
816B VAL* 1.3 66.5 + - - +
818B ALA* 3.2 4.2 + - - +
819B ALA* 3.1 20.6 + - - +
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Residues in contact with VAL 816 (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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700B MET* 5.0 0.9 - - - -
704B PHE* 3.9 21.3 - - + -
724B PHE* 4.2 22.0 - - + -
812B MET* 2.9 22.1 + - + +
813B ALA 3.9 1.3 - - - +
815B TYR* 1.3 77.2 - - - +
817B ALA* 1.3 57.9 + - - +
819B ALA* 3.0 10.1 - - - +
820B MET* 3.0 54.4 + - + +
870B PHE* 4.6 9.2 - - + -
882B PHE* 3.7 28.5 - - + -
886B VAL* 4.5 2.2 - - + -
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Residues in contact with ALA 817 (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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813B ALA 2.9 17.9 + - - +
814B LEU 3.7 3.4 - - - +
815B TYR 3.1 0.2 - - - -
816B VAL* 1.3 73.8 - - - +
818B ALA* 1.3 58.4 + - - +
819B ALA 3.0 1.3 - - - -
820B MET 4.3 0.4 - - - +
821B HIS* 2.6 39.8 + - - +
886B VAL* 3.8 13.0 - - + +
889B ALA* 3.7 24.5 - - + -
890B ILE* 3.7 23.8 - - + -
933B ILE* 4.1 3.4 - - + -
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Residues in contact with ALA 818 (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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742B ALA* 3.9 10.8 - - - +
745B VAL* 3.9 8.5 - - + -
746B LEU* 3.6 30.5 - - - +
749B VAL* 3.9 11.4 - - + -
814B LEU 3.1 12.7 + - - +
815B TYR 3.2 8.9 + - - +
817B ALA* 1.3 76.2 - - - +
819B ALA* 1.3 65.7 + - - +
821B HIS* 2.9 25.4 + - - -
933B ILE* 3.9 12.7 - - + +
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Residues in contact with ALA 819 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696B LEU* 3.8 22.0 - - + +
700B MET* 3.9 21.5 - - - -
724B PHE* 4.1 5.6 - - + -
727B LEU* 3.7 18.9 - - + +
731B TYR* 2.5 32.9 + - - -
742B ALA* 3.9 0.3 - - - +
746B LEU* 5.0 1.3 - - - +
815B TYR 3.1 12.4 + - - +
816B VAL* 3.0 16.4 - - - +
818B ALA* 1.3 77.0 - - - +
820B MET* 1.3 49.3 + - - +
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Residues in contact with MET 820 (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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723B TYR* 3.4 25.8 - - + +
727B LEU* 3.8 20.0 - - + -
731B TYR* 3.5 2.2 - - - -
816B VAL* 3.0 34.8 + - + +
817B ALA 3.2 0.2 + - - -
819B ALA* 1.3 74.4 - - - +
821B HIS* 1.3 63.9 + - - +
822B ASP 3.0 4.3 + - - -
823B TYR* 3.1 17.7 + - - +
854B HIS* 3.9 6.8 - - - +
858B ALA* 3.7 27.1 - - + +
859B TRP* 4.3 29.8 - - + -
862B TYR* 5.4 1.3 - - + -
886B VAL* 3.7 23.8 - - - -
890B ILE* 4.2 9.6 - - + -
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Residues in contact with HIS 821 (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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473B MG 2.4 25.4 - - - -
474B MG 4.2 0.9 - - - -
731B TYR* 4.5 0.6 + - - -
741B HIS* 4.0 5.4 - + - -
742B ALA* 4.5 6.1 - - - -
745B VAL* 3.5 28.5 - - + -
817B ALA 2.6 22.6 + - - +
818B ALA* 2.9 24.5 + - - -
819B ALA 3.5 2.2 - - - -
820B MET* 1.3 71.5 - - - +
822B ASP* 1.3 78.4 + - + +
854B HIS* 2.9 23.3 - - - +
890B ILE* 3.8 26.5 - - + +
893B THR* 4.0 22.2 + - + -
933B ILE* 4.6 7.2 - - + -
937B ASP* 2.8 10.3 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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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