Contacts of the helix formed by residues 888 - 908 (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 SER 888 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LEU* 4.5 0.9 - - - +
794A PRO* 3.7 29.8 - - - -
797A ASP* 2.9 8.6 + - - +
886A LEU* 4.3 1.6 - - - -
887A LYS* 1.3 74.7 - - - +
889A GLN* 1.3 65.1 + - - +
890A ALA* 3.2 3.8 - - - +
891A ALA* 3.2 16.3 + - - -
892A PHE* 3.1 21.1 + - - +
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Residues in contact with GLN 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A ILE* 3.8 15.8 - - - +
885A GLY* 3.1 13.1 - - - -
886A LEU* 2.7 49.4 + - - +
887A LYS 3.5 4.4 + - - -
888A SER* 1.3 75.2 - - - +
890A ALA* 1.3 60.1 + - - +
892A PHE* 3.4 15.5 + - - +
893A GLU* 2.8 66.7 + - + +
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Residues in contact with ALA 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A SER* 3.2 1.2 - - - -
889A GLN* 1.3 79.2 - - - +
891A ALA* 1.3 62.7 + - - +
893A GLU* 3.4 8.3 + - - +
894A GLU* 3.1 22.8 + - - +
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Residues in contact with ALA 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ASN* 5.7 3.1 - - + +
793A LEU* 3.8 18.3 - - + +
888A SER* 3.2 19.0 + - - +
890A ALA* 1.3 77.8 - - - +
892A PHE* 1.3 62.7 + - - +
894A GLU* 3.3 12.9 + - - +
895A MET* 3.0 23.7 + - - +
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Residues in contact with PHE 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A LEU* 3.9 14.1 - - + +
801A LEU* 4.0 21.3 - - + -
878A LEU* 3.4 50.9 - - + -
881A ILE* 3.5 26.2 - - + -
886A LEU* 4.3 13.5 - - + -
888A SER 3.1 12.2 + - - +
889A GLN* 3.6 29.6 - - - +
891A ALA* 1.3 78.6 - - - +
893A GLU* 1.3 66.7 + - + +
895A MET* 3.1 6.6 + - - +
896A ARG* 2.9 41.1 + - - +
979A LEU* 3.8 13.5 - - + -
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Residues in contact with GLU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A GLN* 2.8 51.1 + - - +
890A ALA* 3.8 7.0 - - - +
892A PHE* 1.3 84.9 - - + +
894A GLU* 1.3 57.8 + - - +
896A ARG* 3.8 5.3 - - - +
897A THR* 3.0 34.5 + - - +
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Residues in contact with GLU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ALA 3.1 13.3 + - - +
891A ALA* 3.5 13.5 - - - +
893A GLU* 1.3 78.1 - - - +
895A MET* 1.3 61.9 + - - +
897A THR* 3.4 5.9 + - - -
898A ASN* 3.1 44.3 + - - +
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Residues in contact with MET 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A LEU* 4.4 7.9 - - + -
788A PRO 3.5 11.0 - - - +
789A GLY* 3.7 13.9 - - - +
790A PHE* 3.1 51.4 - - + +
793A LEU* 4.2 13.2 - - + -
874A VAL* 4.9 0.4 - - + -
878A LEU* 3.8 28.0 - - + -
891A ALA 3.0 13.8 + - - +
892A PHE* 3.6 7.0 - - - +
894A GLU* 1.3 75.4 - - - +
896A ARG* 1.3 65.8 + - - +
898A ASN* 3.4 8.6 + - - +
899A TYR* 3.2 40.5 + - + -
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Residues in contact with ARG 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A LEU* 4.1 7.9 + - + +
878A LEU* 3.3 46.8 + - + +
879A SER* 5.0 4.6 + - - +
892A PHE* 2.9 32.0 + - + +
893A GLU* 3.8 6.7 - - - +
895A MET* 1.3 77.7 - - - +
897A THR* 1.3 57.6 + - - +
899A TYR* 3.3 4.4 + - - +
900A ILE* 3.0 53.9 + - + +
979A LEU* 3.8 34.0 + - - +
980A TYR 4.7 5.3 + - - -
981A PHE* 3.8 30.4 - - - -
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Residues in contact with THR 897 (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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893A GLU* 3.0 20.2 + - - +
894A GLU* 3.5 6.7 - - + -
895A MET 3.3 0.2 - - - -
896A ARG* 1.3 77.0 - - - +
898A ASN* 1.3 63.8 + - - +
900A ILE* 3.1 14.8 + - - +
901A LYS* 2.9 58.2 + - + +
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Residues in contact with ASN 898 (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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894A GLU* 3.1 33.3 + - - +
895A MET* 3.7 7.5 - - - +
896A ARG 3.3 0.2 - - - -
897A THR* 1.3 87.5 - - - +
899A TYR* 1.3 60.1 + - + +
901A LYS* 3.1 19.8 + - - +
902A GLU* 2.9 33.6 + - - +
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Residues in contact with TYR 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A PRO* 5.1 12.9 + - + +
742A LEU* 4.4 13.7 - - + -
787A LEU* 4.1 3.5 - - + +
788A PRO* 2.7 49.6 + - + +
789A GLY* 5.4 0.2 - - - -
871A ILE* 3.6 18.0 - - + +
874A VAL* 3.6 41.3 - - + -
875A LEU* 3.7 22.2 - - + -
878A LEU* 4.4 1.3 - - + -
895A MET* 3.2 38.4 + - + +
896A ARG* 3.8 3.6 - - - +
898A ASN* 1.3 79.6 - - + +
900A ILE* 1.3 62.6 + - - +
902A GLU* 3.2 13.0 - - + +
903A LEU* 3.1 19.2 + - - +
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Residues in contact with ILE 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A LEU* 4.0 18.4 - - + -
896A ARG* 3.0 47.4 + - + +
897A THR* 3.3 12.3 - - - +
899A TYR* 1.3 77.8 - - - +
901A LYS* 1.3 62.7 + - + +
903A LEU* 3.5 5.1 + - + +
904A ARG* 3.1 21.5 + - + +
921A PHE* 3.8 22.4 - - + -
981A PHE* 3.6 29.4 - - + -
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Residues in contact with LYS 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A THR* 2.9 40.2 + - + +
898A ASN* 3.1 19.5 + - - +
900A ILE* 1.3 76.3 - - + +
902A GLU* 1.3 60.7 + - - +
904A ARG* 3.2 11.3 + - - +
905A LYS* 2.8 28.6 + - - +
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Residues in contact with GLU 902 (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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737A SER* 5.9 0.3 - - - -
738A PRO* 3.2 38.4 - - + +
739A VAL* 5.1 7.4 - - + +
742A LEU* 6.3 0.4 - - + -
871A ILE* 3.9 21.2 - - + +
898A ASN* 2.9 16.3 + - - +
899A TYR* 3.2 20.1 - - + +
901A LYS* 1.3 75.2 - - - +
903A LEU* 1.3 65.5 + - - +
905A LYS* 3.0 13.0 + - - +
906A MET* 2.9 26.0 + - + +
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Residues in contact with LEU 903 (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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868A GLU* 4.4 17.5 - - + +
871A ILE* 3.6 25.5 - - + +
872A MET* 4.3 17.7 - - + -
875A LEU* 4.1 19.5 - - + -
899A TYR 3.1 5.2 + - - +
900A ILE* 3.8 6.5 - - + +
902A GLU* 1.3 78.8 - - - +
904A ARG* 1.3 61.0 + - - +
906A MET* 4.3 1.6 - - + -
907A VAL* 3.1 24.1 + - + +
921A PHE* 4.0 21.5 - - + -
924A LEU* 3.7 39.3 - - + -
925A THR* 4.6 9.0 - - + -
928A LEU* 4.8 1.8 - - + -
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Residues in contact with ARG 904 (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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900A ILE* 3.1 15.3 + - + +
901A LYS* 3.3 14.8 - - - +
902A GLU 3.1 0.2 - - - -
903A LEU* 1.3 79.7 - - - +
905A LYS* 1.3 52.7 + - - +
907A VAL* 3.8 3.5 + - - +
908A THR* 2.8 47.7 + - - +
914A SER 4.2 4.4 - - - +
917A SER* 3.4 45.7 + - - -
918A TRP* 3.3 52.7 - - + +
921A PHE* 3.8 25.4 - - + +
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Residues in contact with LYS 905 (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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901A LYS 2.8 13.2 + - - +
902A GLU* 3.0 17.0 + - - +
904A ARG* 1.3 76.9 - - - +
906A MET* 1.3 66.5 + - + +
908A THR* 3.0 24.3 + - - +
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Residues in contact with MET 906 (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* 3.9 28.3 - - + -
865A THR* 5.0 0.7 - - - +
867A GLU* 3.4 30.5 - - + -
868A GLU* 4.0 27.3 - - + +
871A ILE* 4.2 10.3 - - + -
902A GLU* 2.9 15.7 + - + +
903A LEU* 3.7 6.3 - - + +
905A LYS* 1.3 78.2 - - + +
907A VAL* 1.3 62.5 + - - +
908A THR 3.2 8.5 + - - +
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Residues in contact with VAL 907 (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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868A GLU* 3.9 8.7 - - - +
903A LEU* 3.1 17.9 + - + +
904A ARG* 4.1 7.0 - - - +
906A MET* 1.3 74.3 - - - +
908A THR* 1.3 69.6 + - - +
917A SER* 2.7 41.1 - - - +
920A ARG* 3.2 35.3 - - + +
921A PHE* 3.7 11.7 - - + +
924A LEU* 3.6 22.2 - - + -
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Residues in contact with THR 908 (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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904A ARG* 2.8 35.9 + - - +
905A LYS* 3.0 19.2 + - - +
906A MET 3.1 9.1 - - - +
907A VAL* 1.3 86.6 - - - +
914A SER* 4.8 20.6 - - - +
917A SER* 4.1 13.5 - - - -
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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