Contacts of the helix formed by residues 802 - 819 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A VAL* 3.3 17.8 - - - +
769A LEU* 4.5 2.9 - - - -
776A PRO* 3.4 24.5 - - + +
777A THR* 3.5 17.3 - - + +
794A GLU* 4.8 0.7 + - - -
800A LYS* 4.1 4.4 + - + +
801A PHE* 1.3 78.6 - - - +
803A SER* 1.3 62.5 + - - +
804A ALA* 3.2 20.6 + - - +
805A SER* 2.8 28.5 + - - -
806A ASP 3.3 3.1 + - - -
865A ARG* 4.5 22.1 - - - +
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Residues in contact with SER 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A SER* 3.2 35.6 + - - -
740A TYR 4.1 6.2 + - - -
741A VAL* 4.5 2.0 - - - +
769A LEU* 4.4 12.1 - - - +
776A PRO 5.0 0.2 + - - -
802A THR* 1.3 74.1 - - - +
804A ALA* 1.3 55.7 + - - +
806A ASP* 3.1 13.8 + - - +
807A VAL* 3.0 31.3 + - - +
871A PHE* 3.9 3.9 - - - -
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Residues in contact with ALA 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A THR* 3.2 11.3 + - - +
803A SER* 1.3 78.1 - - - +
805A SER* 1.3 60.1 + - - +
807A VAL* 3.4 9.5 + - - +
808A TRP 3.3 13.7 + - - -
865A ARG* 3.6 39.0 - - + +
868A ARG* 3.1 22.6 + - + +
869A PRO 5.8 0.2 - - - -
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Residues in contact with SER 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A VAL* 4.4 1.4 - - - +
791A THR* 6.1 0.2 - - - -
792A ALA* 3.7 28.8 + - - +
794A GLU* 3.7 8.7 + - - -
795A ALA* 4.2 12.6 - - - -
800A LYS 4.6 0.7 - - - -
801A PHE* 3.4 14.4 - - - +
802A THR* 2.8 35.7 + - - -
804A ALA* 1.3 74.2 - - - +
806A ASP* 1.4 64.2 + - - +
808A TRP* 3.2 6.2 + - - +
809A SER* 3.2 22.6 + - - -
868A ARG* 3.9 1.1 - - - +
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Residues in contact with ASP 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A MET* 3.4 19.8 - - + +
735A LEU* 4.3 1.6 - - - +
736A SER* 5.8 0.7 - - - -
740A TYR 4.4 1.0 - - - +
741A VAL* 3.5 17.5 - - - +
742A HIS* 2.8 26.7 + - - +
743A ARG* 3.1 26.2 + - - -
745A LEU* 3.6 7.1 - - + +
802A THR 3.3 5.0 + - - +
803A SER* 3.1 12.6 + - - +
805A SER* 1.4 74.2 + - - +
807A VAL* 1.3 53.3 + - - +
809A SER* 3.2 11.5 + - - -
810A TYR* 2.8 33.4 + - - +
871A PHE* 3.7 13.7 - - + -
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A SER 3.0 20.5 + - - +
804A ALA* 3.5 11.7 - - - +
805A SER 3.3 0.2 - - - -
806A ASP* 1.3 74.3 - - - +
808A TRP* 1.4 64.6 + - - +
810A TYR* 3.2 4.5 + - - +
811A GLY 3.0 18.2 + - - -
860A CYS* 3.4 33.1 - - - +
868A ARG* 4.0 9.9 - - + -
869A PRO* 3.3 30.1 - - + +
870A ARG* 4.5 1.8 - - - -
871A PHE* 3.6 33.2 - - + +
874A ILE* 3.9 6.1 - - + -
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Residues in contact with TRP 808 (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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789A ARG 4.9 1.6 + - - -
790A TRP 3.6 16.2 + - - -
791A THR 3.6 9.1 + - - -
792A ALA* 3.6 22.2 - - + -
793A PRO* 3.4 32.5 - - + -
804A ALA 3.3 8.7 + - - +
805A SER 3.2 11.5 + - - +
807A VAL* 1.4 75.2 - - - +
809A SER* 1.4 63.2 + - - +
811A GLY 3.1 11.1 + - - -
812A ILE* 3.2 23.5 + - + +
825A TYR* 4.4 3.7 + - - -
837A ILE* 3.9 28.0 - - + -
842A ARG* 3.7 29.2 - - - -
860A CYS 3.4 11.9 - - - +
861A TRP* 3.1 50.8 + + + -
862A GLN 4.0 4.5 - - - -
868A ARG* 3.6 13.5 - - - +
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Residues in contact with SER 809 (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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743A ARG* 5.4 4.3 + - - -
745A LEU* 3.3 35.9 + - - +
790A TRP* 2.7 26.6 + - - +
791A THR* 4.6 2.3 - - - -
805A SER 3.2 10.7 + - - -
806A ASP* 3.2 13.9 + - - -
808A TRP* 1.4 76.5 - - - +
810A TYR* 1.4 57.2 + - - +
812A ILE* 3.0 8.3 + - - +
813A VAL* 3.0 29.4 + - - +
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Residues in contact with TYR 810 (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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725A LEU* 2.6 35.8 + - + +
728A ILE* 3.8 21.5 - - + -
729A ALA* 3.6 25.1 - - + -
732A MET* 4.9 0.4 - - + -
745A LEU* 3.7 10.0 - - + +
806A ASP 2.8 8.8 + - - +
807A VAL 3.2 8.2 + - - +
809A SER* 1.4 74.9 - - - +
811A GLY* 1.3 57.4 + - - +
813A VAL* 3.0 9.1 + - + +
814A MET* 2.9 54.5 + - + +
860A CYS* 4.2 10.1 - - - -
871A PHE* 3.6 27.8 - + + -
874A ILE* 3.5 24.0 - - + -
878A LEU* 3.3 15.8 - - + +
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Residues in contact with GLY 811 (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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807A VAL 3.0 10.9 + - - -
808A TRP 3.1 5.3 + - - -
810A TYR* 1.3 75.2 - - - +
812A ILE* 1.3 59.7 + - - +
814A MET* 3.4 12.8 - - - +
815A TRP 3.2 16.6 + - - -
857A MET* 3.8 3.9 - - - +
860A CYS* 3.7 20.0 - - - -
861A TRP* 3.3 24.5 - - - -
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Residues in contact with ILE 812 (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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789A ARG 3.7 15.7 - - - +
790A TRP* 3.4 29.2 - - + +
808A TRP* 3.2 22.2 + - + +
809A SER 3.0 8.3 + - - +
811A GLY* 1.3 73.1 - - - +
813A VAL* 1.4 57.7 + - - +
815A TRP* 3.1 6.0 + - - +
816A GLU* 2.9 25.7 + - - +
824A PRO* 3.5 25.8 - - + -
825A TYR* 3.4 25.4 - - - +
843A LEU* 4.0 9.2 - - + -
861A TRP* 3.5 30.1 - - + +
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Residues in contact with VAL 813 (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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725A LEU* 4.5 3.1 - - + -
728A ILE* 4.0 20.4 - - + -
745A LEU* 3.9 12.8 - - + +
746A ALA* 3.7 35.0 - - - +
747A ALA* 3.8 9.0 - - - +
750A ILE* 3.9 20.0 - - + -
790A TRP* 4.7 0.4 - - + -
809A SER 3.0 17.9 + - - +
810A TYR* 3.0 10.7 + - + +
812A ILE* 1.4 71.8 - - - +
814A MET* 1.3 58.3 + - - +
816A GLU* 3.1 11.0 + - - +
817A VAL* 2.9 35.5 + - + +
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Residues in contact with MET 814 (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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725A LEU* 3.6 20.0 - - + -
810A TYR* 2.9 49.9 + - + +
811A GLY* 3.4 10.5 - - - +
812A ILE 3.3 0.2 - - - -
813A VAL* 1.3 73.7 - - - +
815A TRP* 1.3 58.8 + - - +
817A VAL* 3.3 1.7 + - - +
818A MET* 2.9 34.1 + - - +
853A LEU* 3.4 44.0 - - + +
856A LEU* 3.8 31.0 - - + -
857A MET* 3.7 23.1 - - + -
860A CYS* 4.5 1.1 - - - -
878A LEU* 5.1 1.1 - - + -
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Residues in contact with TRP 815 (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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811A GLY 3.2 8.5 + - - +
812A ILE* 3.1 10.2 + - - +
814A MET* 1.3 80.4 - - - +
816A GLU* 1.4 62.0 + - - +
818A MET 3.5 0.2 + - - -
819A SER* 2.7 45.6 + - - -
822A GLU* 3.5 44.4 - - + -
823A ARG 3.7 6.5 - - - -
824A PRO* 3.7 25.6 - - + -
826A TRP* 3.7 30.1 - + - -
843A LEU* 3.5 31.5 - - + +
844A PRO* 2.8 28.6 + - + -
846A PRO* 3.7 19.8 - - + +
854A HIS* 5.4 0.2 - + - -
857A MET* 3.9 17.4 - - - -
861A TRP* 4.1 7.9 - + + -
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Residues in contact with GLU 816 (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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706A ASP* 4.4 8.3 - - - +
709A LEU* 4.8 1.3 - - - -
747A ALA* 3.0 40.2 + - + +
748A ARG 4.7 1.0 + - - -
790A TRP* 2.8 43.0 + - - -
812A ILE 2.9 14.2 + - - +
813A VAL* 3.1 16.1 + - - +
815A TRP* 1.4 80.1 - - + +
817A VAL* 1.4 57.6 + - - +
819A SER* 3.4 2.3 + - - -
820A PHE 3.2 3.8 + - - -
821A GLY* 2.7 34.0 + - - -
822A GLU 4.0 12.3 - - - +
824A PRO* 3.8 19.3 - - + +
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Residues in contact with VAL 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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705A LEU* 3.6 31.6 - - + -
709A LEU* 3.7 15.1 - - + +
721A LEU* 3.9 52.1 - - + +
724A MET* 4.8 6.3 - - + -
725A LEU* 3.7 25.4 - - + -
728A ILE* 4.7 0.7 - - + -
813A VAL* 2.9 22.1 + - + +
814A MET 3.8 1.1 - - - +
816A GLU* 1.4 72.7 - - + +
818A MET* 1.3 57.7 + - - +
819A SER 3.1 4.3 - - - -
820A PHE* 3.1 19.1 + - - -
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Residues in contact with MET 818 (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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718A VAL* 4.4 15.3 - - + +
721A LEU* 3.8 39.4 - - + +
722A VAL* 5.0 0.2 - - - -
725A LEU* 4.0 19.7 - - + -
814A MET 2.9 21.1 + - - +
815A TRP 3.5 0.2 + - - -
817A VAL* 1.3 74.2 - - - +
819A SER* 1.4 55.3 + - - +
820A PHE* 3.5 10.1 + - - -
846A PRO* 3.6 28.2 - - + +
847A MET 4.4 8.1 + - - +
849A CYS* 4.2 11.1 - - + +
850A PRO* 4.4 12.1 - - + -
853A LEU* 3.9 26.0 - - + -
857A MET* 3.9 15.7 - - + -
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Residues in contact with SER 819 (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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713A ASP* 5.2 0.3 - - - +
815A TRP* 2.7 35.4 + - - -
816A GLU 3.7 4.3 - - - -
817A VAL 3.1 0.8 - - - -
818A MET* 1.4 72.6 - - - +
820A PHE* 1.3 72.1 + - - +
821A GLY 3.3 0.4 + - - -
822A GLU* 3.4 30.3 + - - +
846A PRO* 3.2 20.6 - - - +
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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