Contacts of the helix formed by residues 788 - 809 (chain B) in PDB entry 3LMG
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 788 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787B LEU* 1.3 73.6 - - - +
789B PRO* 1.3 70.4 - - - +
790B GLN* 3.1 4.0 - - - -
791B LEU* 3.3 20.0 - - - +
792B LEU* 2.9 29.3 + - - +
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Residues in contact with PRO 789 (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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787B LEU 3.5 6.2 - - - +
788B GLY* 1.3 83.4 - - - +
790B GLN* 1.3 62.0 + - + +
792B LEU* 3.6 11.4 + - + -
793B LEU* 3.3 21.5 + - - +
953B PRO* 4.0 20.6 - - + +
954B PRO* 5.3 6.5 - - + -
957B LEU* 3.6 30.1 - - + +
959B ILE* 4.7 28.0 - - + -
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Residues in contact with GLN 790 (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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788B GLY* 3.1 1.5 - - - -
789B PRO* 1.3 82.2 - - + +
791B LEU* 1.3 53.6 + - - +
793B LEU* 3.4 3.9 + - - +
794B ASN* 2.7 65.3 + - - +
950B ALA* 3.9 17.4 + - - +
953B PRO* 3.7 30.0 - - + +
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Residues in contact with LEU 791 (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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779B HIS* 5.5 0.2 - - - +
787B LEU* 3.9 18.6 - - + -
788B GLY* 3.3 22.3 - - - +
790B GLN* 1.3 77.3 - - - +
792B LEU* 1.3 64.5 + - - +
794B ASN* 3.5 13.2 - - + +
795B TRP* 3.0 65.1 + - + +
826B PRO 4.4 5.8 - - - +
827B SER* 4.3 29.4 - - - +
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Residues in contact with LEU 792 (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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780B VAL* 4.7 3.8 - - + -
785B GLY* 5.8 0.4 - - - -
787B LEU* 4.0 29.6 - - + +
788B GLY 2.9 18.0 + - - +
789B PRO* 3.8 11.4 - - + +
791B LEU* 1.3 77.5 - - - +
793B LEU* 1.3 61.3 + - - +
795B TRP* 3.4 14.5 + - + +
796B GLY* 3.3 15.1 + - - -
885B LEU* 3.7 28.7 - - + +
886B MET* 4.2 15.5 - - + +
888B PHE* 3.7 15.3 - - + -
916B ILE* 3.7 30.1 - - + -
957B LEU* 3.9 13.2 - - + -
959B ILE* 5.4 4.0 - - + -
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Residues in contact with LEU 793 (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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789B PRO 3.3 15.2 + - - +
790B GLN* 3.8 4.0 - - - +
792B LEU* 1.3 75.8 - - - +
794B ASN* 1.3 63.6 + - - +
796B GLY* 3.2 10.7 + - - -
797B VAL* 3.2 17.2 + - - +
886B MET* 4.3 5.2 - - + -
921B VAL* 5.0 0.4 - - + -
946B PHE* 3.7 30.8 - - + +
949B MET* 3.6 47.1 - - + +
950B ALA* 4.3 13.0 - - + +
953B PRO* 3.8 27.4 - - + +
956B TYR* 4.2 9.0 - - + -
957B LEU* 3.7 19.7 - - + -
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Residues in contact with ASN 794 (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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790B GLN* 2.7 60.3 + - - +
791B LEU* 3.5 17.3 - - + +
793B LEU* 1.3 73.3 - - - +
795B TRP* 1.3 58.1 + - + +
797B VAL* 3.0 13.4 + - - +
798B GLN* 2.9 41.6 + - - +
950B ALA* 4.2 12.7 - - - +
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Residues in contact with TRP 795 (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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776B LEU* 3.4 25.8 - - + -
779B HIS* 3.6 23.3 - + - -
780B VAL* 4.4 2.2 - - + -
787B LEU* 3.9 22.0 - - + -
791B LEU* 3.0 52.5 + - + +
792B LEU* 3.8 14.1 - - + +
793B LEU 3.3 0.2 - - - -
794B ASN* 1.3 73.5 - - + +
796B GLY* 1.3 60.3 + - - +
798B GLN* 3.1 22.0 - - - +
799B ILE* 2.9 39.4 + - + +
823B LEU* 4.1 10.3 - - + -
826B PRO 3.7 15.3 - - - -
827B SER 2.7 19.8 + - - -
829B VAL* 3.3 28.5 - - + +
885B LEU* 4.3 12.6 - - + -
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Residues in contact with GLY 796 (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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792B LEU 3.3 8.9 + - - -
793B LEU 3.2 9.6 + - - -
795B TRP* 1.3 78.3 - - - +
797B VAL* 1.3 60.3 + - - +
799B ILE* 5.0 2.5 - - - -
800B ALA* 3.3 12.8 + - - +
878B TYR* 2.7 29.5 + - - -
882B VAL* 5.1 6.3 - - - -
885B LEU* 4.7 3.7 - - - +
886B MET* 5.8 0.9 - - - -
946B PHE* 3.9 18.6 - - - -
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Residues in contact with VAL 797 (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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793B LEU 3.2 15.7 + - - +
794B ASN* 3.0 14.1 + - - +
796B GLY* 1.3 75.9 - - - +
798B GLN* 1.3 59.3 + - + +
800B ALA* 3.1 8.2 + - - +
801B LYS* 2.9 55.8 + - + +
943B ALA* 4.1 5.6 - - - +
946B PHE* 3.6 31.3 - - + +
947B THR* 3.5 25.4 - - + +
950B ALA* 4.6 4.9 - - + -
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Residues in contact with GLN 798 (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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751B HIS* 3.2 46.2 - - + +
794B ASN* 2.9 31.0 + - + +
795B TRP* 3.1 28.0 + - - +
797B VAL* 1.3 77.9 - - + +
799B ILE* 1.3 62.0 + - - +
801B LYS* 3.2 6.4 + - + +
802B GLY 3.1 18.0 + - - -
827B SER 3.4 6.7 + - - -
828B GLN* 3.3 13.0 + - - +
829B VAL* 3.1 38.3 + - + -
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Residues in contact with ILE 799 (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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751B HIS* 5.7 0.4 - - - -
776B LEU* 4.0 20.0 - - + -
795B TRP* 2.9 23.2 + - + +
796B GLY* 4.3 1.3 - - - +
798B GLN* 1.3 75.0 - - - +
800B ALA* 1.3 63.2 + - - +
802B GLY* 3.5 1.9 + - - -
803B MET* 3.1 23.5 + - + +
816B LEU* 4.2 15.7 - - + -
821B VAL* 3.9 31.6 - - + -
829B VAL* 4.4 5.2 - - + -
830B GLN 6.2 0.2 - - - -
831B VAL* 4.0 19.7 - - + +
878B TYR* 3.7 26.0 - - + -
881B THR* 4.7 9.4 - - + -
882B VAL* 5.9 2.2 - - + -
885B LEU* 4.0 14.1 - - + -
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Residues in contact with ALA 800 (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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796B GLY 3.3 13.6 + - - +
797B VAL 3.1 10.0 + - - +
799B ILE* 1.3 80.2 - - - +
801B LYS* 1.3 52.0 + - - +
803B MET* 3.2 5.8 + - - +
804B TYR* 2.8 36.1 + - - +
878B TYR* 3.7 19.3 - - + +
939B PHE* 4.0 11.0 - - + +
942B LEU* 4.3 1.6 - - + -
943B ALA* 3.8 28.9 - - - +
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Residues in contact with LYS 801 (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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749B HIS* 3.6 20.4 + - + +
751B HIS* 4.4 15.9 + - + +
797B VAL* 2.9 40.7 + - + +
798B GLN* 3.2 8.7 + - + +
800B ALA* 1.3 72.4 - - - +
802B GLY* 1.3 65.6 + - - +
804B TYR* 3.6 9.5 + - - +
805B TYR* 3.0 22.3 + - - +
943B ALA* 4.7 13.2 - - + -
947B THR* 5.2 3.4 - - - -
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Residues in contact with GLY 802 (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 HIS* 4.1 8.2 - - - -
751B HIS* 3.8 22.0 - - - +
752B ILE* 3.5 16.5 - - - +
798B GLN 3.1 10.9 + - - -
799B ILE 3.9 2.9 - - - -
800B ALA 3.3 0.2 - - - -
801B LYS* 1.3 75.1 - - - +
803B MET* 1.3 57.6 + - - +
805B TYR* 3.1 5.7 + - - +
806B LEU* 2.9 26.6 + - - +
831B VAL* 4.7 2.5 - - - -
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Residues in contact with MET 803 (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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799B ILE* 3.1 23.3 + - + +
800B ALA 3.6 0.7 - - - +
802B GLY* 1.3 72.9 - - - +
804B TYR* 1.3 59.2 + - - +
806B LEU* 3.4 14.5 + - + +
807B GLU* 2.9 28.9 + - - +
813B HIS* 3.1 42.4 - - + -
816B LEU* 3.6 32.8 - - + -
831B VAL* 3.2 22.9 - - + +
874B ASP* 4.9 3.6 - - - +
939B PHE* 3.4 47.0 - - + -
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Residues in contact with TYR 804 (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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800B ALA 2.8 21.0 + - - +
801B LYS* 3.8 9.6 - - - +
803B MET* 1.3 69.5 - - - +
805B TYR* 1.3 63.9 + - + +
807B GLU* 3.3 14.1 + - + +
808B GLU* 2.9 69.5 + - + +
939B PHE* 3.8 13.6 - - + +
940B LYS* 3.7 36.8 - - + +
943B ALA* 5.8 2.0 - - + -
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Residues in contact with TYR 805 (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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746B SER 4.6 1.4 + - - -
747B LEU* 3.6 25.6 - - + +
748B ASP* 2.8 48.7 + - - +
749B HIS* 3.5 29.6 - + + -
752B ILE* 3.1 23.3 - - + -
801B LYS 3.0 14.4 + - - +
802B GLY 3.1 8.3 + - - +
804B TYR* 1.3 79.8 - - + +
806B LEU* 1.3 62.0 + - - +
808B GLU* 3.1 21.9 + - - +
809B HIS* 3.2 48.6 + + - -
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Residues in contact with LEU 806 (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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747B LEU* 3.7 28.7 - - + -
752B ILE* 3.4 21.5 - - + -
802B GLY 2.9 15.4 + - - +
803B MET* 3.6 39.0 - - + +
805B TYR* 1.3 76.2 - - + +
807B GLU* 1.3 58.7 + - - +
809B HIS* 3.3 5.0 + - - -
810B GLY 3.1 4.0 + - - -
811B MET* 2.8 49.7 + - + +
813B HIS* 4.1 3.6 - - + -
831B VAL* 4.2 7.0 - - + -
834B PHE* 4.0 28.0 - - + -
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Residues in contact with GLU 807 (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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803B MET 2.9 18.0 + - - +
804B TYR* 3.5 17.3 - - + +
806B LEU* 1.3 75.6 - - - +
808B GLU* 1.3 58.7 + - - +
810B GLY* 3.0 18.7 + - - -
811B MET 4.2 0.6 + - - -
871B HIS* 3.4 50.4 + - + +
872B GLN* 5.9 1.1 + - - -
938B THR* 4.7 10.1 - - - +
939B PHE* 3.9 28.6 + - + +
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Residues in contact with GLU 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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804B TYR* 2.9 56.8 + - + +
805B TYR* 3.1 15.8 + - - +
807B GLU* 1.3 78.5 - - - +
809B HIS* 1.3 70.1 + - + +
810B GLY 3.3 0.6 + - - -
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Residues in contact with HIS 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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747B LEU* 3.5 27.2 - - + +
805B TYR* 3.2 54.0 + + - +
806B LEU 3.3 1.1 + - - +
807B GLU 3.2 0.2 - - - -
808B GLU* 1.3 86.6 + - + +
810B GLY* 1.3 60.0 + - - +
811B MET* 3.4 3.8 + - - +
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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
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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