Contacts of the helix formed by residues 797 - 812 (chain O) in PDB entry 6IY3
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 GLY 797 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771O GLN* 4.0 1.8 + - - -
792O ASP* 5.3 0.2 - - - -
795O GLY 3.8 0.6 - - - -
796O LEU* 1.3 81.3 - - - +
798O LYS* 1.3 62.3 + - - -
799O THR 3.5 0.4 - - - -
800O ILE* 4.2 3.8 - - - +
801O GLN* 3.2 25.9 + - - +
2000O ADP 2.9 50.7 + - - -
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Residues in contact with LYS 798 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790O LEU* 4.5 15.1 - - + +
792O ASP* 3.3 40.6 - - - +
793O GLU 2.6 22.2 + - - -
794O MET* 3.7 5.7 - - - +
796O LEU 5.2 0.2 - - - -
797O GLY* 1.3 72.5 - - - +
799O THR* 1.3 60.6 + - - +
801O GLN* 3.2 4.7 + - - +
802O THR* 3.0 32.7 + - - +
831O TRP* 5.3 1.3 - - + -
894O ASP* 5.6 3.4 - - - +
922O LEU* 5.2 18.2 - - + +
923O THR 4.1 3.6 - - - -
924O GLY* 3.7 21.3 - - - +
2000O ADP 2.5 51.5 + - - +
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Residues in contact with THR 799 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798O LYS* 1.3 73.2 - - - +
800O ILE* 1.3 59.8 + - - +
802O THR* 3.2 3.1 + - - -
803O ILE* 2.9 30.1 + - + +
830O ASN 5.9 0.2 - - - -
831O TRP* 3.2 60.2 + - + +
834O GLU* 4.4 26.0 - - + -
835O PHE* 5.9 1.6 - - + -
2000O ADP 2.6 27.7 + - - -
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Residues in contact with ILE 800 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762O LEU* 5.1 2.0 - - + -
767O LEU* 3.8 26.2 - - + -
771O GLN* 4.6 4.5 - - - +
797O GLY 4.0 4.0 + - - +
798O LYS 3.3 0.6 - - - -
799O THR* 1.3 79.3 - - + +
801O GLN* 1.3 61.1 + - - +
803O ILE* 3.3 7.8 - - + +
804O SER* 2.9 28.1 + - - -
834O GLU* 4.4 5.6 - - + +
838O TRP* 3.5 49.4 - - + +
2000O ADP 3.5 58.1 + - + +
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Residues in contact with GLN 801 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767O LEU* 6.0 1.8 - - + -
770O TYR* 4.3 1.2 - - - -
771O GLN* 3.4 51.9 - - + +
774O GLY* 4.5 1.5 - - - -
778O MET* 3.7 25.1 - - + +
790O LEU* 3.3 18.0 - - + +
792O ASP* 4.0 5.0 + - - -
796O LEU 4.1 3.8 + - - -
797O GLY 3.2 15.2 + - - +
798O LYS 3.2 8.6 + - - +
800O ILE* 1.3 78.7 - - - +
802O THR* 1.3 56.6 + - - +
804O SER* 2.5 24.5 + - - +
805O LEU* 2.9 14.7 + - - +
994O ARG* 3.1 34.2 + - - +
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Residues in contact with THR 802 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778O MET* 5.5 1.9 - - - -
790O LEU* 5.5 0.3 - - - +
798O LYS 3.0 15.1 + - - -
799O THR 3.2 8.0 + - - -
801O GLN* 1.3 76.8 - - - +
803O ILE* 1.3 58.5 + - - +
805O LEU* 3.1 12.4 + - + +
806O LEU* 2.9 38.8 + - + +
821O VAL* 5.0 2.7 - - + -
831O TRP* 4.2 20.4 - - + -
892O ILE* 3.7 31.0 - - + -
922O LEU* 3.3 24.4 - - - +
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Residues in contact with ILE 803 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762O LEU* 4.7 2.2 - - + -
799O THR* 2.9 19.6 + - + +
800O ILE* 3.3 21.8 - - + +
802O THR* 1.3 76.1 - - - +
804O SER* 1.3 55.5 - - - +
806O LEU* 4.1 12.6 - - + -
807O THR* 2.9 30.0 + - - +
831O TRP* 5.6 0.4 - - + -
834O GLU* 5.0 4.3 - - + +
835O PHE* 3.6 39.3 - - + -
838O TRP* 4.1 24.2 - - + +
839O ALA* 3.9 17.7 - - + -
842O LEU* 3.9 26.0 - - + -
868O VAL* 5.4 0.7 - - + -
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Residues in contact with SER 804 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759O PRO* 4.5 2.6 - - - +
762O LEU* 4.4 20.6 - - - -
767O LEU* 4.8 5.9 - - - +
771O GLN 5.5 0.2 + - - -
775O LEU* 3.4 30.1 - - - +
800O ILE 2.9 15.1 + - - -
801O GLN* 2.5 28.7 + - - -
803O ILE* 1.3 75.6 - - - +
805O LEU* 1.3 58.2 + - - +
807O THR* 3.3 11.1 - - - +
808O TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 805 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775O LEU* 4.2 10.1 - - + -
778O MET* 3.6 47.8 - - + +
779O VAL* 5.7 1.8 - - + +
782O PHE* 6.1 3.8 - - + -
801O GLN 2.9 7.1 + - - +
802O THR* 3.1 13.2 + - + +
804O SER* 1.3 82.1 + - - +
806O LEU* 1.3 64.9 + - + +
808O TYR* 3.3 6.5 + - + +
809O LEU* 2.9 36.8 + - + +
890O HIS* 3.6 32.1 - - + +
892O ILE* 4.6 5.2 - - + -
920O LEU* 4.3 15.5 - - + -
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Residues in contact with LEU 806 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802O THR* 2.9 32.9 + - + +
803O ILE* 3.7 23.8 - - + +
804O SER 3.3 0.4 - - - -
805O LEU* 1.3 83.1 - - + +
807O THR* 1.3 58.2 + - - +
809O LEU* 3.3 3.2 + - + -
810O TYR* 2.9 27.1 + - - +
819O TYR* 3.6 49.7 - - + -
821O VAL* 4.4 17.5 - - + -
831O TRP* 6.4 0.2 - - + -
835O PHE* 5.1 4.9 - - + -
842O LEU* 4.9 4.7 - - + -
868O VAL* 4.7 7.6 - - + -
892O ILE* 3.8 24.5 - - + -
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Residues in contact with THR 807 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759O PRO* 3.7 20.9 - - + -
761O ILE* 3.3 34.6 - - + +
762O LEU* 4.5 13.7 - - + +
803O ILE* 2.9 21.5 + - + +
804O SER* 3.3 15.0 - - - +
806O LEU* 1.3 73.9 - - - +
808O TYR* 1.3 61.0 + - - +
810O TYR* 3.6 6.5 - - - +
811O GLU* 2.9 31.5 + - - +
838O TRP 5.4 0.9 - - - +
839O ALA* 5.0 5.8 - - - -
842O LEU* 4.8 11.6 - - - +
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Residues in contact with TYR 808 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755O ILE* 3.4 35.1 - - + +
759O PRO* 4.9 17.0 - - + -
775O LEU* 4.7 8.5 - - + -
779O VAL* 3.6 41.0 - - + +
782O PHE* 5.8 0.9 - + + -
804O SER 2.9 18.4 + - - +
805O LEU* 3.6 7.2 - - + +
807O THR* 1.3 78.9 - - - +
809O LEU* 1.3 61.2 + - + +
811O GLU* 4.8 1.6 - - - -
812O MET* 3.0 57.6 + - + +
813O LYS* 3.4 40.8 + - + -
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Residues in contact with LEU 809 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782O PHE* 3.6 40.6 - - + -
805O LEU* 2.9 23.1 + - + +
806O LEU* 3.3 4.2 + - + +
808O TYR* 1.3 78.9 - - + +
810O TYR* 1.3 60.7 + - - +
813O LYS* 3.6 22.9 - - + +
814O ASN 3.3 15.8 + - - -
815O ILE* 3.6 18.1 + - + -
819O TYR* 3.2 36.0 + - + +
889O VAL* 5.6 0.2 - - + -
890O HIS* 3.5 32.1 - - + +
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Residues in contact with TYR 810 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761O ILE* 4.3 24.9 - - + -
806O LEU 2.9 17.0 + - - +
807O THR* 3.6 7.9 - - - +
809O LEU* 1.3 77.4 - - - +
811O GLU* 1.3 71.1 + - + +
814O ASN* 3.4 20.1 + - - +
816O ARG* 3.5 45.9 + - + +
819O TYR* 3.3 7.3 + + + +
841O THR* 4.5 15.1 + - - -
842O LEU* 3.7 27.4 - - + -
867O ASP* 4.5 9.2 - - - -
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Residues in contact with GLU 811 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759O PRO* 3.3 27.8 - - - +
760O SER* 3.1 31.4 + - - -
761O ILE* 4.5 11.1 + - + +
807O THR* 2.9 20.4 + - - +
808O TYR* 4.2 1.1 - - - +
810O TYR* 1.3 83.1 - - + +
812O MET* 1.3 86.7 + - + +
814O ASN* 2.9 23.6 + - - +
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Residues in contact with MET 812 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755O ILE* 4.6 12.8 - - + -
759O PRO* 6.4 0.9 - - + -
808O TYR* 3.0 49.8 + - + +
811O GLU* 1.3 111.0 - - + +
813O LYS* 1.3 67.0 + - + +
814O ASN* 3.3 13.9 + - - -
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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
------------------------------------------------------------
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