Contacts of the helix formed by residues 840 - 854 (chain A) in PDB entry 2HHT
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 GLU 840 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819A ARG 4.9 0.3 - - - +
820A LEU* 3.4 29.0 - - + +
821A GLN* 2.8 30.3 + - - +
822A ALA* 2.9 32.4 + - - +
836A ALA* 4.3 5.4 - - + -
837A PRO* 3.0 29.4 + - + +
839A GLU* 1.3 82.3 - - + +
841A MET* 1.3 63.8 + - - +
842A GLU 3.4 2.2 - - - -
843A ARG* 3.3 13.4 + - - +
844A LEU* 3.0 26.7 + - + +
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Residues in contact with MET 841 (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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648A LEU* 3.8 29.8 - - + +
650A PHE* 4.1 13.0 - - + -
836A ALA* 3.9 14.8 - - + +
837A PRO 3.6 14.4 - - - +
838A LYS 3.4 17.8 + - - +
839A GLU 3.5 0.2 - - - -
840A GLU* 1.3 76.9 - - - +
842A GLU* 1.3 67.3 + - + +
844A LEU* 3.1 28.2 + - + +
845A CYS* 2.9 29.2 + - - -
868A TYR* 3.7 51.6 - - + +
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Residues in contact with GLU 842 (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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839A GLU 5.0 3.4 + - - +
840A GLU 3.4 0.4 - - - -
841A MET* 1.3 80.1 - - + +
843A ARG* 1.3 64.3 + - + +
845A CYS* 3.4 19.5 + - - +
846A ARG* 3.7 12.0 + - - +
868A TYR* 5.9 2.7 - - - +
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Residues in contact with ARG 843 (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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818A GLU* 3.7 36.8 + - - +
819A ARG 5.4 1.0 + - - -
820A LEU* 3.2 40.0 - - + +
839A GLU 5.5 2.8 + - - +
840A GLU* 3.3 16.2 + - - +
841A MET 3.2 0.6 - - - -
842A GLU* 1.3 78.7 - - + +
844A LEU* 1.3 58.6 + - - +
846A ARG* 3.3 6.3 + - - +
847A LEU* 2.9 31.2 + - + +
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Residues in contact with LEU 844 (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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650A PHE* 3.6 25.5 - - + -
815A LEU* 4.1 16.6 - - + -
820A LEU* 4.2 10.5 - - + -
822A ALA* 3.9 18.4 - - + -
834A LEU* 4.8 6.3 - - + -
836A ALA* 3.7 18.8 - - + -
840A GLU* 3.0 18.8 + - + +
841A MET* 3.1 33.0 + - + +
843A ARG* 1.3 72.2 - - - +
845A CYS* 1.3 64.7 + - - +
846A ARG 3.0 2.5 - - - -
847A LEU* 4.4 3.4 - - + +
848A VAL* 3.0 42.5 + - + +
849A PRO* 3.4 4.5 - - - +
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Residues in contact with CYS 845 (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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650A PHE* 4.0 14.1 - - - -
841A MET 2.9 22.8 + - - -
842A GLU* 3.5 13.2 - - - +
843A ARG 3.3 0.2 - - - -
844A LEU* 1.3 76.8 - - - +
846A ARG* 1.3 59.9 + - + +
849A PRO* 3.3 19.4 - - - +
866A TYR* 3.6 34.7 + - + +
868A TYR* 3.9 26.5 - - - -
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Residues in contact with ARG 846 (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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842A GLU 3.7 9.5 + - - +
843A ARG* 3.3 8.5 + - - +
844A LEU 3.0 0.2 - - - -
845A CYS* 1.3 83.7 - - + +
847A LEU* 1.3 63.8 + - - +
849A PRO* 3.6 2.0 - - - +
850A GLU* 3.4 24.4 + - - +
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Residues in contact with LEU 847 (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 LEU* 4.8 3.6 - - + -
814A ARG* 3.3 50.9 - - + +
815A LEU* 4.0 15.5 - - + -
818A GLU* 4.6 8.3 - - + -
820A LEU* 3.9 27.6 - - + -
843A ARG* 2.9 18.2 + - + +
844A LEU* 4.4 4.3 - - + +
846A ARG* 1.3 75.3 - - - +
848A VAL* 1.3 66.9 + - - +
850A GLU* 3.5 5.2 + - + +
851A VAL* 3.0 39.8 + - + +
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Residues in contact with VAL 848 (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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650A PHE* 3.8 18.8 - - + -
652A ALA* 3.7 16.2 - - + -
811A LEU* 4.2 24.0 - - + -
832A LEU* 5.4 0.4 - - + -
834A LEU* 4.7 16.2 - - + -
844A LEU* 3.0 39.9 + - + +
847A LEU* 1.3 72.8 - - + +
849A PRO* 1.3 69.2 - - + +
851A VAL* 3.3 1.2 + - - +
852A MET* 3.0 45.3 + - + +
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Residues in contact with PRO 849 (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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650A PHE* 4.9 0.4 - - + -
844A LEU 3.4 3.1 - - - +
845A CYS* 3.3 27.8 - - - +
846A ARG 3.6 5.2 - - - +
848A VAL* 1.3 94.4 - - + +
850A GLU* 1.3 50.0 + - - +
852A MET* 3.3 1.6 + - - +
853A GLU* 2.7 48.3 + - - +
864A VAL* 4.0 26.2 - - + +
866A TYR* 3.3 34.5 - - + -
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Residues in contact with GLU 850 (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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846A ARG 3.4 19.0 + - - +
847A LEU* 3.5 6.7 + - + +
848A VAL 3.3 0.6 - - - -
849A PRO* 1.3 78.1 - - - +
851A VAL* 1.3 61.0 + - + +
853A GLU* 3.2 10.0 + - - +
854A GLN* 2.8 71.1 + - + +
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Residues in contact with VAL 851 (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 ALA 3.8 8.1 - - - +
810A ASP* 3.7 13.8 - - + +
811A LEU* 3.4 38.8 - - + +
814A ARG* 3.6 30.7 - - + +
847A LEU* 3.0 32.9 + - + +
848A VAL 3.8 2.9 - - - +
850A GLU* 1.3 78.6 - - + +
852A MET* 1.3 65.0 + - + +
854A GLN* 3.4 3.8 + - - -
855A ALA* 3.2 22.9 + - - +
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Residues in contact with MET 852 (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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652A ALA* 3.7 44.2 - - - +
653A ASP* 4.6 0.2 - - - -
654A TYR* 2.6 62.5 + - + +
804A ILE* 4.8 0.4 - - + -
807A ALA* 4.1 10.1 - - + +
811A LEU* 5.7 1.6 - - + -
830A ASP 4.8 0.7 - - - +
832A LEU* 3.9 33.4 - - + +
848A VAL* 3.0 29.3 + - + +
849A PRO 3.7 3.4 - - - +
851A VAL* 1.3 78.9 - - + +
853A GLU* 1.3 60.9 + - - +
855A ALA* 3.7 7.8 + - - +
862A LEU* 4.3 2.4 - - - +
864A VAL* 3.7 15.7 - - + -
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Residues in contact with GLU 853 (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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849A PRO* 2.7 36.1 + - - +
850A GLU* 3.7 13.0 + - - +
852A MET* 1.3 72.5 - - - +
854A GLN* 1.3 75.0 + - - +
855A ALA 3.4 0.7 + - - -
856A VAL 3.7 10.9 - - - +
862A LEU* 3.4 41.8 + - - +
863A LYS* 3.9 2.6 - - - +
864A VAL* 3.3 37.4 + - + +
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Residues in contact with GLN 854 (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 LYS* 4.8 1.6 + - - -
810A ASP* 5.1 0.4 - - - +
850A GLU* 2.8 48.0 + - + +
851A VAL* 3.8 3.8 - - - +
853A GLU* 1.3 89.9 + - - +
855A ALA* 1.3 64.8 + - - +
856A VAL* 3.1 10.0 + - - +
857A THR* 5.0 8.1 + - - -
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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