Contacts of the helix formed by residues 813 - 830 (chain A) in PDB entry 5MJ6
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 813 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A GLY* 1.3 73.4 - - - -
814A PRO* 1.4 67.1 - - + +
815A SER* 3.7 8.0 + - - -
816A MET* 2.8 49.0 + - + +
817A ARG* 2.8 11.5 + - - +
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Residues in contact with PRO 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A MET* 3.7 45.7 - - + +
456A LYS* 5.2 0.9 - - + -
504A GLU* 3.1 39.0 - - + +
505A LEU* 4.2 16.6 - - + +
812A GLY 3.9 2.0 - - - +
813A THR* 1.4 87.2 - - + +
815A SER* 1.3 56.9 + - - +
817A ARG* 3.1 8.2 + - + +
818A GLU* 2.9 30.8 + - - +
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Residues in contact with SER 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A SER* 3.8 20.3 + - - -
509A GLU* 3.0 26.0 + - - -
761A HIS* 6.2 0.2 - - - -
762A THR* 2.8 40.0 + - - -
813A THR* 3.2 8.8 + - - -
814A PRO* 1.3 80.6 - - - +
816A MET* 1.3 63.4 + - - +
818A GLU* 3.3 5.5 + - - +
819A LEU 3.1 16.1 + - - -
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Residues in contact with MET 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A ASN* 3.4 26.7 - - - +
761A HIS* 4.6 1.8 - - + -
762A THR* 3.6 21.8 - - - +
806A GLN* 4.7 2.3 - - - +
811A GLU 5.2 0.9 - - - +
812A GLY* 4.6 6.3 - - - -
813A THR* 2.8 34.4 + - + +
815A SER* 1.3 79.8 - - - +
817A ARG* 1.3 61.1 + - - +
819A LEU* 3.4 17.3 + - + +
820A ARG* 3.1 32.3 + - - +
1F NAG 5.8 11.9 - - + -
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Residues in contact with ARG 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A SER 5.4 0.4 + - - -
451A SER 4.7 0.4 - - - -
452A MET* 3.7 40.7 - - + +
810A ASP* 3.4 36.6 + - - +
811A GLU 3.6 17.9 - - - +
812A GLY 3.6 13.0 + - - +
813A THR 2.8 16.1 + - - +
814A PRO* 3.3 13.5 - - + +
816A MET* 1.3 78.4 - - - +
818A GLU* 1.3 62.0 + - - +
820A ARG* 3.4 9.7 + - - +
821A SER* 3.3 25.1 + - - -
857A THR* 3.6 7.7 + - - -
858A ASP* 2.7 46.5 + - - +
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Residues in contact with GLU 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A MET* 5.4 4.9 - - + -
453A ALA* 4.8 16.6 - - + +
456A LYS* 2.6 44.2 + - + +
509A GLU* 3.0 19.9 - - - +
510A ASP* 4.5 5.6 - - - +
762A THR* 4.3 9.7 - - + +
766A THR* 5.1 0.5 - - - +
814A PRO 2.9 13.6 + - - +
815A SER* 3.3 8.9 + - - +
817A ARG* 1.3 76.7 - - - +
819A LEU* 1.3 59.3 + - - +
821A SER* 3.6 6.0 + - - -
822A ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A ASN* 3.9 12.3 - - - +
762A THR* 3.7 27.3 - - + +
765A ILE* 3.8 37.5 - - + -
766A THR* 5.2 0.2 - - + -
802A GLN* 5.8 3.1 - - + -
806A GLN* 4.6 6.7 - - - +
815A SER 3.1 5.9 + - - +
816A MET* 3.7 35.4 - - + +
817A ARG 3.3 0.2 - - - -
818A GLU* 1.3 74.4 - - - +
820A ARG* 1.3 61.1 + - - +
822A ALA* 3.4 5.6 + - + -
823A LEU* 2.9 61.7 + - + +
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Residues in contact with ARG 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A GLN* 3.4 25.9 + - + +
807A THR* 3.0 43.2 + - - +
809A THR* 3.3 32.0 + - - +
811A GLU* 2.9 34.5 + - - +
816A MET* 3.1 13.9 + - - +
817A ARG* 3.6 23.2 - - - +
818A GLU 3.3 0.2 - - - -
819A LEU* 1.3 75.4 - - - +
821A SER* 1.3 59.0 + - - +
823A LEU* 3.9 0.7 - - - +
824A LEU* 2.9 44.2 + - + +
858A ASP* 3.7 10.6 + - - +
859A VAL* 4.3 9.2 - - + -
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Residues in contact with SER 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ARG 3.3 13.9 + - - -
818A GLU* 3.9 6.5 - - - -
819A LEU 3.3 0.2 - - - -
820A ARG* 1.3 79.1 - - - +
822A ALA* 1.3 63.0 + - - +
824A LEU* 4.3 3.1 - - - +
825A GLU* 2.9 29.4 + - - +
858A ASP* 2.7 34.7 + - - +
862A THR* 4.7 3.3 + - - -
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Residues in contact with ALA 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766A THR* 3.8 26.2 - - + -
769A LEU* 3.9 13.7 - - + +
818A GLU 3.0 20.2 + - - +
819A LEU* 3.8 6.3 - - + +
820A ARG 3.3 0.2 - - - -
821A SER* 1.3 77.0 - - - +
823A LEU* 1.3 57.6 + - - +
825A GLU* 3.8 4.0 - - - +
826A PHE* 3.1 27.5 + - - +
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Residues in contact with LEU 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A ILE* 4.1 21.5 - - + -
769A LEU* 4.1 10.3 - - + -
799A LEU* 4.5 11.9 - - + -
802A GLN* 3.8 34.1 - - + +
803A ILE* 3.8 27.7 - - + +
806A GLN* 3.9 25.1 - - + +
819A LEU* 2.9 37.2 + - + +
820A ARG 3.9 1.8 - - - +
822A ALA* 1.3 74.9 - - - +
824A LEU* 1.3 66.4 + - - +
826A PHE* 3.2 6.0 + - + +
827A ALA* 3.1 22.3 + - - +
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Residues in contact with LEU 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ILE* 4.8 5.6 - - + +
806A GLN* 4.2 20.4 - - + +
807A THR 4.1 6.1 - - - +
808A TRP* 3.7 48.7 - - + +
820A ARG* 2.9 31.7 + - + +
821A SER* 4.3 2.7 - - - +
823A LEU* 1.3 77.3 - - - +
825A GLU* 1.3 57.3 + - - +
827A ALA* 3.3 3.2 + - - +
828A CYS* 2.9 34.5 + - - +
835A CYS* 4.2 16.2 - - - -
859A VAL* 3.8 25.8 - - + -
862A THR* 4.4 9.4 - - - +
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Residues in contact with GLU 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A SER 2.9 22.2 + - - +
822A ALA* 3.8 4.9 - - - +
824A LEU* 1.3 78.2 - - - +
826A PHE* 1.3 61.5 + - - +
828A CYS* 4.8 2.6 - - - +
829A THR* 3.0 37.2 + - - +
861A THR* 3.5 22.5 - - - +
862A THR* 3.8 24.6 + - - +
865A LYS* 3.2 41.9 + - - +
895A GLU* 4.3 1.0 - - - +
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Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A LEU* 3.7 31.0 - - + -
772A THR* 4.0 11.4 - - + -
773A ASP* 3.7 29.2 - - - +
792A VAL* 4.0 26.0 - - + -
795A VAL* 4.0 17.9 - - + -
796A PHE* 4.4 12.6 - + + -
799A LEU* 5.8 1.1 - - + -
803A ILE* 4.4 13.9 - - + -
822A ALA 3.1 19.4 + - - +
823A LEU* 3.2 5.8 + - + +
825A GLU* 1.3 79.2 - - - +
827A ALA* 1.3 64.9 + - - +
829A THR* 4.8 0.7 - - - -
830A HIS* 2.9 42.4 + + - +
832A LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A PHE* 4.6 6.3 - - + -
803A ILE* 4.4 13.9 - - + -
823A LEU 3.1 16.2 + - - +
824A LEU 3.9 1.8 - - - +
826A PHE* 1.3 83.4 - - - +
828A CYS* 1.3 62.8 + - - +
830A HIS 3.6 0.3 + - - -
831A ASN* 3.0 3.8 + - - -
832A LEU* 2.9 40.4 + - - +
835A CYS* 3.5 30.3 - - - -
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Residues in contact with CYS 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808A TRP* 4.3 2.2 - - - -
824A LEU 2.9 15.2 + - - +
825A GLU* 4.2 4.3 - - - +
827A ALA* 1.3 74.1 - - - +
829A THR* 1.3 66.6 + - - +
831A ASN* 3.3 18.4 + - - +
835A CYS* 3.5 38.6 - - - -
836A SER* 3.6 12.7 - - - +
839A ALA* 4.2 5.6 - - - -
862A THR* 3.4 31.2 - - + -
865A LYS* 6.4 0.7 - - + -
866A VAL* 4.3 15.3 - - + +
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Residues in contact with THR 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A TYR* 6.0 0.7 - - + -
825A GLU* 3.0 36.2 + - - +
826A PHE* 4.1 3.8 - - - -
828A CYS* 1.3 78.5 - - - +
830A HIS* 1.3 82.4 + - + +
831A ASN* 3.7 8.1 + - - -
865A LYS* 4.3 10.7 + - - +
934A HIS* 4.7 21.4 + - + +
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Residues in contact with HIS 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ASP* 3.3 26.4 + - - -
776A TYR* 3.5 52.3 - + + +
792A VAL* 3.9 14.8 - - + +
826A PHE* 2.9 40.6 + + - +
828A CYS 3.3 0.4 - - - -
829A THR* 1.3 95.0 - - + +
831A ASN* 1.3 72.9 + - - +
832A LEU* 3.3 20.2 + - + +
1031A GLN* 3.5 15.2 - - - +
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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