Contacts of the helix formed by residues 813 - 830 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B GLU 5.5 0.9 - - - -
812B GLY* 1.3 76.2 - - - +
814B PRO* 1.3 76.6 - - + +
815B SER* 3.5 9.4 + - - -
816B MET* 3.1 32.7 + - + +
817B ARG* 3.0 17.5 + - - +
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Residues in contact with PRO 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B MET* 3.6 43.6 - - + +
456B LYS* 5.1 0.4 - - + -
504B GLU* 3.6 35.0 - - + +
505B LEU* 4.2 13.7 - - + +
812B GLY 4.4 1.1 - - - +
813B THR* 1.3 87.8 - - - +
815B SER* 1.3 60.9 + - - +
817B ARG* 3.3 6.1 + - - +
818B GLU* 3.1 29.9 + - - +
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Residues in contact with SER 815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLU 4.9 0.6 + - - -
506B SER* 3.8 20.2 + - - -
509B GLU* 2.8 32.3 + - - -
762B THR* 2.8 26.8 + - - -
813B THR* 3.1 9.4 + - - -
814B PRO* 1.3 81.6 - - - +
816B MET* 1.3 64.2 + - - +
818B GLU* 3.4 7.1 + - - +
819B LEU 3.1 14.0 + - - -
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Residues in contact with MET 816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B ASN* 3.4 26.7 - - - +
761B HIS* 4.5 7.9 - - + -
762B THR* 3.8 17.3 - - - +
806B GLN* 4.8 1.7 - - - +
811B GLU 5.0 1.6 - - - +
812B GLY* 4.7 6.1 - - - -
813B THR* 3.1 31.0 + - + +
815B SER* 1.3 81.9 - - - +
817B ARG* 1.3 65.7 + - - +
819B LEU* 3.4 16.2 + - + +
820B ARG* 3.1 25.2 + - - +
1P NAG 5.8 9.2 - - + +
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Residues in contact with ARG 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B SER 4.7 1.0 - - - -
452B MET* 3.9 32.2 - - + +
810B ASP* 3.2 36.6 + - - +
811B GLU 3.4 18.4 - - - +
812B GLY 3.4 15.9 + - - +
813B THR 3.0 16.7 + - - +
814B PRO* 3.6 13.1 - - + +
816B MET* 1.3 76.9 - - - +
818B GLU* 1.3 62.6 + - - +
820B ARG* 3.2 15.5 + - - +
821B SER* 3.1 23.4 + - - -
857B THR* 3.9 4.4 + - - -
858B ASP* 2.6 44.5 + - - +
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Residues in contact with GLU 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B MET* 4.4 13.5 - - + -
453B ALA* 3.9 20.9 - - + +
456B LYS* 2.7 45.2 + - - +
505B LEU 4.6 1.0 - - - +
509B GLU* 4.4 7.9 - - - +
510B ASP* 4.7 3.4 - - - +
762B THR* 4.7 10.3 - - + -
814B PRO 3.1 16.3 + - - +
815B SER* 3.8 5.5 - - - +
817B ARG* 1.3 76.7 - - - +
819B LEU* 1.3 58.2 + - - +
821B SER* 3.3 8.6 + - - -
822B ALA* 3.0 28.4 + - - +
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Residues in contact with LEU 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B ASN* 4.2 19.3 - - - +
762B THR* 3.3 31.9 + - + +
765B ILE* 3.8 43.3 - - + -
766B THR* 5.2 0.7 - - + -
802B GLN* 5.8 2.2 - - + -
806B GLN* 4.8 8.7 - - - +
815B SER 3.1 6.6 + - - +
816B MET* 3.5 21.3 - - - +
817B ARG 3.3 0.2 - - - -
818B GLU* 1.3 73.4 - - - +
820B ARG* 1.3 65.7 + - - +
822B ALA* 3.3 5.7 + - + -
823B LEU* 3.0 45.2 + - + +
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Residues in contact with ARG 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B GLN* 3.3 27.6 + - + +
807B THR* 2.8 41.7 + - - +
809B THR* 3.0 34.5 + - - +
811B GLU* 2.9 35.2 + - - +
816B MET* 3.1 13.3 + - - +
817B ARG* 3.2 19.7 + - - +
819B LEU* 1.3 75.4 - - - +
821B SER* 1.3 58.7 + - - +
823B LEU* 3.9 0.3 - - - +
824B LEU* 2.9 49.4 + - + +
858B ASP* 3.7 19.4 + - - +
859B VAL* 4.3 11.0 - - + -
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Residues in contact with SER 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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817B ARG 3.1 10.4 + - - -
818B GLU* 3.5 11.8 - - - -
820B ARG* 1.3 79.3 - - - +
822B ALA* 1.3 63.2 + - - +
824B LEU* 4.2 2.4 - - - +
825B GLU* 2.9 29.1 + - - +
858B ASP* 2.8 32.8 + - - +
862B THR* 4.7 1.9 + - - -
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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
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766B THR* 4.1 24.9 - - + -
769B LEU* 4.3 15.8 - - + +
818B GLU 3.0 16.5 + - - +
819B LEU* 3.3 8.3 + - + +
821B SER* 1.3 77.3 - - - +
823B LEU* 1.3 56.7 + - - +
825B GLU* 3.7 4.9 - - - +
826B PHE* 3.0 29.8 + - - +
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Residues in contact with LEU 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B ILE* 4.3 21.1 - - + -
769B LEU* 4.4 8.5 - - + -
799B LEU* 4.6 11.7 - - + -
802B GLN* 3.8 38.4 - - + +
803B ILE* 3.9 24.3 - - + +
806B GLN* 3.9 21.8 - - + +
819B LEU* 3.0 34.9 + - + +
820B ARG 3.9 3.1 - - - +
822B ALA* 1.3 76.9 - - - +
824B LEU* 1.3 58.3 + - - +
826B PHE* 3.4 7.3 + - + +
827B ALA* 3.1 27.4 + - - +
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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
----------------------------------------------------------
803B ILE* 4.7 5.4 - - + +
806B GLN* 4.1 21.3 - - + +
807B THR 4.8 1.3 - - - +
808B TRP* 3.7 58.1 - - + +
820B ARG* 2.9 36.0 + - + +
821B SER* 4.2 2.5 - - - +
823B LEU* 1.3 73.3 - - - +
825B GLU* 1.3 66.3 + - - +
827B ALA* 4.0 1.5 - - - +
828B CYS* 3.0 31.2 + - - -
835B CYS* 4.7 14.4 - - + -
858B ASP 5.9 0.2 - - - +
859B VAL* 4.0 16.4 - - + -
862B THR* 4.0 10.1 - - + +
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Residues in contact with GLU 825 (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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821B SER 2.9 19.8 + - - +
822B ALA* 3.7 5.2 - - - +
824B LEU* 1.3 77.9 - - - +
826B PHE* 1.3 55.4 + - - +
828B CYS* 4.9 2.0 - - - +
829B THR* 2.7 44.7 + - - +
861B THR* 3.2 19.6 - - - +
862B THR* 3.0 27.4 + - - +
865B LYS* 2.9 41.8 + - - +
895B GLU* 3.9 1.9 - - - +
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Residues in contact with PHE 826 (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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769B LEU* 4.0 29.4 - - + -
772B THR* 4.3 5.6 - - + -
773B ASP* 3.9 20.9 - - - +
792B VAL* 4.0 25.8 - - + -
795B VAL* 4.0 21.5 - - + -
796B PHE* 4.3 16.4 - + + -
799B LEU* 5.7 1.1 - - + -
803B ILE* 4.5 11.7 - - + -
822B ALA 3.0 18.6 + - - +
823B LEU* 3.6 8.5 - - + +
824B LEU 3.2 0.2 - - - -
825B GLU* 1.3 73.7 - - - +
827B ALA* 1.3 69.7 + - - +
829B THR* 4.8 0.9 - - - -
830B HIS* 3.2 55.7 + + - +
832B LEU* 4.2 14.4 - - + -
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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
----------------------------------------------------------
796B PHE* 4.6 5.4 - - + -
803B ILE* 4.2 12.1 - - + -
823B LEU 3.1 13.3 + - - +
824B LEU* 4.1 2.0 - - - +
826B PHE* 1.3 86.2 - - + +
828B CYS* 1.3 57.8 + - - +
830B HIS 3.6 0.3 - - - -
831B ASN 2.9 7.6 + - - -
832B LEU* 2.8 42.6 + - - +
835B CYS* 3.7 29.8 - - + -
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Residues in contact with CYS 828 (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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808B TRP* 4.2 4.7 - - - -
824B LEU 3.0 21.3 + - - +
825B GLU* 4.2 2.9 - - - +
827B ALA* 1.3 74.3 - - - +
829B THR* 1.3 67.5 + - - +
830B HIS 3.1 1.6 - - - -
831B ASN* 2.9 23.7 + - - +
835B CYS* 3.7 35.7 - - - -
836B SER* 3.8 10.6 - - - +
839B ALA* 4.5 2.7 - - - -
862B THR* 3.5 26.9 - - + -
866B VAL* 4.4 12.2 - - + +
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Residues in contact with THR 829 (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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825B GLU* 2.7 39.7 + - - +
826B PHE* 4.1 3.4 - - - -
828B CYS* 1.3 77.6 - - - +
830B HIS* 1.3 76.5 + - + +
831B ASN* 3.7 7.8 + - - -
865B LYS* 4.7 7.8 + - - +
934B HIS* 4.6 22.0 - - + +
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Residues in contact with HIS 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ASP* 2.8 24.1 + - - -
776B TYR* 3.3 52.8 + + - -
777B ASN* 5.4 0.9 - - - -
792B VAL* 3.9 13.9 - - + +
826B PHE* 3.2 46.2 + + - +
828B CYS 3.1 0.4 - - - -
829B THR* 1.3 92.3 + - + +
831B ASN* 1.3 72.5 + - - +
832B LEU* 3.4 24.5 - - + +
1031B GLN* 5.6 2.3 - - - +
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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
------------------------------------------------------------
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