Contacts of the helix formed by residues 865 - 878 (chain A) in PDB entry 2AA2
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 865 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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816A TRP* 3.7 3.6 - - - -
863A GLN 3.9 8.1 - - - +
864A LEU* 1.3 78.3 - - - +
866A PHE* 1.3 60.8 + - - +
867A GLU* 3.5 17.0 + - - +
868A GLU* 3.0 39.2 + - - +
869A TYR* 2.9 28.2 + - - +
906A MET* 5.0 1.6 - - - +
920A ARG* 4.8 1.6 - - - +
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Residues in contact with PHE 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SO4 4.2 17.5 - - - -
743A GLU* 3.8 37.0 - - + -
746A GLU* 4.0 22.4 - - + -
816A TRP* 3.5 33.2 - + + -
820A LYS* 4.8 9.6 - - - +
865A THR* 1.3 70.1 - - - +
867A GLU* 1.3 77.9 + - - +
869A TYR* 3.5 11.6 - + - +
870A THR* 3.0 49.9 + - + +
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Residues in contact with GLU 867 (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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739A VAL* 4.4 17.0 - - + -
743A GLU* 4.9 6.8 - - - +
865A THR* 3.5 18.2 + - - +
866A PHE* 1.3 91.3 + - + +
868A GLU* 1.3 63.6 + - - +
870A THR* 2.9 21.0 + - - -
871A ILE* 3.3 15.6 + - - +
906A MET* 3.4 35.2 - - + -
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Residues in contact with GLU 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A LEU* 3.4 13.7 - - + +
865A THR* 3.0 32.1 + - - +
867A GLU* 1.3 74.9 - - - +
869A TYR* 1.3 64.2 + - - +
871A ILE* 3.3 3.6 + - - +
872A MET* 2.9 29.4 + - - +
903A LEU* 4.4 9.4 - - + +
906A MET* 4.0 18.4 - - + +
907A VAL* 3.9 15.0 - - + +
920A ARG* 2.6 47.0 + - - -
924A LEU* 4.1 15.7 - - + -
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Residues in contact with TYR 869 (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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204A GOL 5.1 0.2 - - - -
746A GLU* 3.7 27.1 + - - -
812A PHE* 3.5 33.0 - + - -
813A ALA* 3.5 24.4 - - - +
816A TRP* 3.4 66.8 - + + +
859A PHE* 5.0 0.2 - + - -
864A LEU* 4.2 9.5 - - + +
865A THR 2.9 16.4 + - - +
866A PHE* 3.5 9.0 - + - +
868A GLU* 1.3 77.2 - - - +
870A THR* 1.3 69.0 + - + +
872A MET* 3.2 5.6 + - - +
873A LYS* 2.9 43.7 + - + +
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Residues in contact with THR 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A VAL* 4.6 4.7 + - - +
742A LEU* 3.8 34.3 - - + +
743A GLU 5.0 0.4 - - - +
746A GLU* 4.3 11.7 - - - +
783A TRP* 5.2 0.3 - - - -
866A PHE* 3.0 51.5 + - + +
867A GLU* 2.9 22.0 + - - -
869A TYR* 1.3 80.9 - - + +
871A ILE* 1.3 61.7 + - - +
873A LYS* 3.4 10.2 + - - +
874A VAL* 3.3 24.8 + - - +
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Residues in contact with ILE 871 (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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739A VAL* 3.7 28.5 - - + -
742A LEU* 4.1 13.5 - - + -
867A GLU 3.3 12.0 + - - +
868A GLU 3.8 5.8 - - - +
869A TYR 3.3 0.6 - - - -
870A THR* 1.3 76.9 + - - +
872A MET* 1.3 65.3 + - - +
874A VAL* 3.0 16.2 + - - +
875A LEU* 3.0 16.0 + - + +
899A TYR* 3.6 20.9 - - + +
902A GLU* 3.9 17.7 - - + +
903A LEU* 3.6 47.6 - - + +
906A MET* 4.2 11.9 - - + -
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Residues in contact with MET 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A PHE* 3.6 34.8 - - + -
864A LEU* 3.9 25.4 - - + -
868A GLU 2.9 23.0 + - - +
869A TYR 3.6 0.9 - - - +
871A ILE* 1.3 75.0 - - - +
873A LYS* 1.3 57.2 + - - +
875A LEU* 3.2 12.1 + - - +
876A LEU* 3.0 31.0 + - - +
903A LEU* 4.3 13.9 - - + -
924A LEU* 3.7 41.7 - - + +
927A LEU* 4.1 13.5 - - + -
928A LEU* 3.8 21.0 - - + +
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Residues in contact with LYS 873 (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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204A GOL 3.0 27.0 + - - +
746A GLU* 2.7 35.9 + - - -
747A PRO* 4.3 2.4 - - - +
783A TRP* 3.6 30.8 - - + -
809A LEU* 3.3 29.9 - - + +
812A PHE* 3.9 15.9 - - + -
813A ALA* 4.9 4.5 - - + -
869A TYR* 2.9 38.4 + - + +
870A THR* 3.7 7.2 - - - +
871A ILE 3.1 0.2 - - - -
872A MET* 1.3 74.4 - - - +
874A VAL* 1.3 65.1 + - - +
876A LEU* 3.3 3.8 + - + +
877A LEU* 3.2 17.2 + - - +
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Residues in contact with VAL 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A LEU* 4.0 13.5 - - + -
783A TRP* 4.1 9.9 - - + -
787A LEU* 3.9 34.1 - - + -
870A THR 3.3 14.3 + - - +
871A ILE 3.0 8.0 + - - +
873A LYS* 1.3 77.2 - - - +
875A LEU* 1.3 63.2 + - - +
877A LEU* 3.0 18.7 + - - +
878A LEU* 3.2 20.1 + - + +
895A MET* 4.9 0.7 - - + -
899A TYR* 3.6 46.7 - - + -
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Residues in contact with LEU 875 (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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871A ILE* 3.0 22.8 + - + +
872A MET* 3.2 8.9 + - - +
874A VAL* 1.3 75.8 - - - +
876A LEU* 1.3 56.0 + - - +
878A LEU* 3.0 16.3 + - + +
879A SER* 2.6 26.0 + - - +
896A ARG* 4.1 15.4 + - + +
899A TYR* 3.7 28.7 - - + +
900A ILE* 4.0 21.3 - - + -
903A LEU* 4.1 21.1 - - + -
928A LEU* 3.9 27.4 - - + -
981A PHE* 4.5 14.6 - - + -
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Residues in contact with LEU 876 (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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805A SER* 3.5 14.3 - - - -
808A SER* 3.5 29.5 + - - +
809A LEU* 4.2 7.4 - - + -
812A PHE* 3.3 53.6 - - + -
872A MET 3.0 16.0 + - - +
873A LYS* 3.6 8.1 - - - +
874A VAL 3.2 0.4 - - - -
875A LEU* 1.3 75.7 - - - +
877A LEU* 1.3 62.3 + - - +
879A SER* 3.1 27.4 + - - +
880A THR* 4.6 0.3 + - - -
928A LEU* 3.7 23.8 - - + +
931A MET* 4.2 17.5 - - + -
932A HIS* 6.4 0.4 - - + -
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Residues in contact with LEU 877 (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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780A VAL* 6.2 0.2 - - + -
783A TRP* 4.1 11.7 - - + -
784A ALA* 4.6 2.9 - - + -
787A LEU* 3.4 33.0 - - + -
790A PHE* 3.7 27.4 - - + -
801A LEU* 3.7 32.0 - - - +
802A ILE* 4.1 17.5 - - + -
805A SER* 3.4 25.9 + - - +
809A LEU* 3.9 14.7 - - + +
873A LYS 3.2 11.5 + - - +
874A VAL* 3.0 10.4 + - - +
876A LEU* 1.3 76.2 - - - +
878A LEU* 1.3 62.2 + - + +
879A SER 3.4 1.0 + - - -
880A THR 5.0 0.7 + - - +
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Residues in contact with LEU 878 (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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790A PHE* 4.6 2.0 - - + -
801A LEU* 4.2 12.6 - - + -
874A VAL* 3.4 26.2 - - + +
875A LEU* 3.0 12.9 + - + +
876A LEU 3.0 1.0 - - - -
877A LEU* 1.3 90.8 - - + +
879A SER* 1.3 55.8 + - - -
880A THR 3.6 2.2 - - - -
892A PHE* 3.4 39.3 - - + -
895A MET* 3.8 37.2 - - + +
896A ARG* 3.3 50.7 + - + -
899A TYR* 4.4 1.3 - - + -
979A LEU* 3.6 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
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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