Contacts of the helix formed by residues 802 - 819 (chain B) in PDB entry 5MJA
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 802 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B VAL* 3.3 15.6 - - - +
769B LEU* 4.5 2.5 - - - -
776B PRO* 3.4 22.9 - - + +
777B THR* 3.5 16.6 - - + +
794B GLU* 4.8 0.9 + - - -
800B LYS* 4.5 2.4 + - + +
801B PHE* 1.3 80.6 - - - +
803B SER* 1.3 63.0 + - - +
804B ALA* 3.2 20.4 + - - +
805B SER* 2.8 28.5 + - - -
806B ASP 3.3 5.4 + - - -
865B ARG* 4.6 21.9 - - - +
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Residues in contact with SER 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B SER* 3.2 34.8 + - - -
740B TYR 4.1 6.2 + - - -
741B VAL* 5.0 0.7 - - - -
769B LEU* 4.4 12.3 - - - +
776B PRO 4.9 0.4 + - - -
802B THR* 1.3 74.0 - - - +
804B ALA* 1.4 56.3 + - - +
806B ASP* 3.2 14.1 + - - +
807B VAL* 3.0 31.7 + - - +
871B PHE* 3.9 3.7 - - - -
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Residues in contact with ALA 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B THR* 3.2 11.5 + - - +
803B SER* 1.4 77.5 - - - +
805B SER* 1.3 60.2 + - - +
807B VAL* 3.4 9.6 + - - +
808B TRP 3.3 13.3 + - - -
865B ARG* 3.6 39.0 - - + +
868B ARG* 3.0 22.4 + - + +
869B PRO 5.8 0.2 - - - -
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Residues in contact with SER 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B VAL* 4.5 1.4 - - - +
791B THR* 6.1 0.2 - - - -
792B ALA* 3.7 27.7 + - - +
794B GLU* 3.8 7.6 - - - -
795B ALA* 4.2 13.2 - - - -
800B LYS 4.9 0.7 - - - -
801B PHE* 3.5 13.9 - - - +
802B THR* 2.8 38.1 + - - -
804B ALA* 1.3 73.5 - - - +
806B ASP* 1.4 63.8 + - - +
808B TRP* 3.2 6.4 + - - +
809B SER* 3.2 22.8 + - - -
868B ARG* 3.9 0.8 - - - +
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Residues in contact with ASP 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B MET* 3.4 19.3 - - + +
736B SER* 5.8 0.7 - - - -
740B TYR 4.4 2.6 - - - +
741B VAL* 3.5 17.7 - - - +
742B HIS* 2.8 25.6 + - - +
743B ARG* 3.1 26.6 + - - -
744B ASP 4.9 0.2 + - - -
745B LEU* 3.6 7.1 - - + +
802B THR 3.3 5.0 + - - +
803B SER* 3.2 13.4 + - - +
805B SER* 1.4 75.6 + - - +
807B VAL* 1.3 53.1 + - - +
809B SER* 3.2 11.4 + - - -
810B TYR* 2.8 33.3 + - - +
871B PHE* 3.7 14.4 - - + -
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Residues in contact with VAL 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B SER 3.0 18.6 + - - +
804B ALA* 3.5 12.3 - - - +
805B SER 3.3 0.2 - - - -
806B ASP* 1.3 73.0 - - - +
808B TRP* 1.3 65.7 + - - +
810B TYR* 3.2 4.2 + - - +
811B GLY 3.0 18.2 + - - -
860B CYS* 3.5 33.1 - - - +
868B ARG* 4.0 9.9 - - + -
869B PRO* 3.3 29.2 - - + +
870B ARG* 4.5 1.8 - - - -
871B PHE* 3.6 34.1 - - + +
874B ILE* 3.9 5.6 - - + -
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Residues in contact with TRP 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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789B ARG 4.8 1.4 + - - -
790B TRP 3.6 16.5 + - - -
791B THR 3.6 9.2 + - - -
792B ALA* 3.6 20.2 - - + -
793B PRO* 3.5 31.9 - - + -
804B ALA 3.3 9.8 + - - +
805B SER 3.2 11.3 + - - +
807B VAL* 1.3 75.7 - - - +
809B SER* 1.4 63.5 + - - +
811B GLY 3.1 11.1 + - - -
812B ILE* 3.2 24.1 + - + +
825B TYR* 4.4 4.1 + - - -
837B ILE* 3.8 28.7 - - + -
842B ARG* 3.7 23.1 - - - -
860B CYS 3.4 11.2 - - - +
861B TRP* 3.1 55.4 + + + -
862B GLN 4.0 4.5 - - - -
868B ARG* 3.7 13.5 - - - +
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Residues in contact with SER 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B ARG 5.5 3.3 + - - -
745B LEU* 3.3 35.2 + - - +
790B TRP* 2.7 26.3 + - - +
791B THR* 4.6 2.1 - - - -
805B SER 3.2 10.3 + - - -
806B ASP* 3.2 14.2 + - - -
808B TRP* 1.4 76.6 - - - +
810B TYR* 1.4 58.3 + - - +
812B ILE* 3.1 8.2 + - - +
813B VAL* 3.0 29.4 + - - +
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Residues in contact with TYR 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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725B LEU* 2.6 34.9 + - + +
728B ILE* 3.8 21.5 - - + -
729B ALA* 3.6 25.8 - - + -
732B MET* 4.9 0.2 - - + -
745B LEU* 3.7 10.2 - - + +
806B ASP 2.8 9.5 + - - +
807B VAL 3.2 8.0 + - - +
809B SER* 1.4 74.9 - - - +
811B GLY* 1.3 56.6 + - - +
813B VAL* 3.0 9.0 + - + +
814B MET* 2.9 54.9 + - + +
860B CYS* 4.2 8.5 - - - -
871B PHE* 3.5 27.8 - + + -
874B ILE* 3.5 25.6 - - + -
878B LEU* 3.3 16.8 - - - +
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Residues in contact with GLY 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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807B VAL 3.0 11.1 + - - -
808B TRP 3.1 5.7 + - - -
810B TYR* 1.3 75.1 - - - +
812B ILE* 1.3 60.6 + - - +
814B MET* 3.3 12.7 - - - +
815B TRP 3.2 16.3 + - - -
857B MET* 3.9 3.2 - - - +
860B CYS* 3.7 20.0 - - - -
861B TRP* 3.2 24.3 - - - -
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Residues in contact with ILE 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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789B ARG 3.7 15.3 - - - +
790B TRP* 3.4 28.7 - - + -
808B TRP* 3.2 22.6 + - + +
809B SER* 3.1 8.4 + - - +
811B GLY* 1.3 73.5 - - - +
813B VAL* 1.3 57.6 + - - +
815B TRP* 3.1 6.5 + - - +
816B GLU* 2.9 25.3 + - - +
824B PRO* 3.5 26.0 - - + -
825B TYR* 3.4 29.8 - - + +
843B LEU* 4.0 4.7 - - + -
861B TRP* 3.4 30.1 - - + +
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Residues in contact with VAL 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B LEU* 4.3 3.6 - - + -
728B ILE* 4.1 19.7 - - + -
745B LEU* 4.0 12.6 - - + +
746B ALA* 3.7 36.8 - - - +
747B ALA* 3.8 7.0 - - + +
750B ILE* 3.9 20.4 - - + -
790B TRP* 4.7 0.2 - - + -
809B SER 3.0 17.9 + - - +
810B TYR* 3.4 10.5 - - + +
812B ILE* 1.3 72.4 - - - +
814B MET* 1.4 58.9 + - - +
816B GLU* 3.1 9.4 + - - +
817B VAL* 2.9 36.4 + - + +
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Residues in contact with MET 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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725B LEU* 3.6 19.3 - - + -
810B TYR* 2.9 50.6 + - + +
811B GLY* 3.3 10.8 - - - +
812B ILE 3.3 0.2 - - - -
813B VAL* 1.4 74.7 - - - +
815B TRP* 1.3 57.9 + - - +
817B VAL* 3.3 1.0 + - - +
818B MET* 2.9 34.5 + - - +
853B LEU* 3.4 52.3 - - + +
856B LEU* 3.7 25.1 - - + -
857B MET* 3.7 23.3 - - + -
860B CYS* 4.5 1.1 - - - -
878B LEU* 5.0 1.3 - - + -
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Residues in contact with TRP 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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811B GLY 3.2 8.6 + - - +
812B ILE 3.1 8.8 + - - +
814B MET* 1.3 79.4 - - - +
816B GLU* 1.4 56.3 + - - +
818B MET 3.5 0.2 + - - -
819B SER* 2.8 43.9 + - - -
822B GLU* 3.6 44.6 - - + -
823B ARG 3.6 5.8 - - - -
824B PRO* 3.6 26.0 - - + -
826B TRP* 3.7 30.3 - + - -
843B LEU* 3.5 32.6 - - + +
844B PRO* 2.8 29.0 + - + -
845B PRO 4.8 0.2 - - - -
846B PRO* 3.7 23.4 - - + +
857B MET* 3.9 17.4 - - - -
861B TRP* 4.2 8.5 - + + -
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Residues in contact with GLU 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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706B ASP* 4.5 8.1 - - - +
709B LEU* 4.2 1.5 - - - +
747B ALA* 3.0 38.6 + - + +
748B ARG 4.7 1.0 + - - -
790B TRP* 2.8 43.1 + - - -
812B ILE 2.9 13.8 + - - +
813B VAL* 3.1 15.6 + - - +
815B TRP* 1.4 77.6 - - - +
817B VAL* 1.3 58.7 + - - +
819B SER* 3.3 9.5 + - - -
821B GLY* 2.7 34.3 + - - -
822B GLU 4.0 11.0 - - - +
824B PRO* 3.8 18.5 - - + +
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Residues in contact with VAL 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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705B LEU* 3.6 30.7 - - + -
709B LEU* 3.6 15.6 - - + +
721B LEU* 3.9 51.2 - - + +
724B MET* 4.7 7.4 - - + -
725B LEU* 3.6 24.9 - - + -
728B ILE* 4.7 0.9 - - + -
747B ALA* 5.2 0.7 - - + -
813B VAL* 2.9 23.5 + - + +
814B MET 3.8 1.1 - - - +
816B GLU* 1.3 77.5 - - + +
818B MET* 1.4 61.8 + - - +
820B PHE* 3.1 14.6 + - - -
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Residues in contact with MET 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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718B VAL* 4.4 17.3 - - + +
721B LEU* 3.8 40.7 - - + +
722B VAL 4.9 0.2 - - - -
725B LEU* 3.9 13.7 - - + -
814B MET 2.9 20.3 + - - +
817B VAL* 1.4 75.8 - - - +
819B SER* 1.3 57.1 + - - +
820B PHE* 3.3 9.8 + - - -
846B PRO* 3.6 26.9 - - + +
847B MET 4.2 9.6 - - - +
848B ASP 5.3 0.7 - - - +
849B CYS* 4.2 8.3 - - + -
850B PRO* 4.4 13.5 - - + -
853B LEU* 3.6 31.9 - - + -
857B MET* 3.8 15.9 - - + -
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Residues in contact with SER 819 (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 ASP* 4.9 1.0 - - - +
815B TRP* 2.8 31.6 + - - -
816B GLU* 3.3 9.4 + - - -
817B VAL 3.2 0.2 - - - -
818B MET* 1.3 76.5 - - - +
820B PHE* 1.3 67.1 + - - +
821B GLY 3.6 0.2 + - - -
822B GLU* 3.3 33.2 + - - +
846B PRO* 3.9 17.0 - - - -
847B MET 5.7 0.4 - - - +
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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