Contacts of the helix formed by residues 912 - 933 (chain A) in PDB entry 6AH0
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 912 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A LYS 5.5 3.8 + - - -
894A VAL* 5.6 1.0 - - - +
911A VAL* 1.3 73.6 - - - +
913A PRO* 1.3 59.6 - - - +
914A LEU 3.4 2.5 - - - -
915A GLU* 3.4 5.9 + - - +
916A LYS* 3.0 23.7 + - - -
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Residues in contact with PRO 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A GLU* 5.6 11.0 - - - -
911A VAL 3.4 4.6 - - - +
912A GLU* 1.3 67.5 - - - +
914A LEU* 1.3 59.0 + - - +
916A LYS* 3.1 2.1 + - - +
917A ILE* 2.9 28.9 + - - -
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Residues in contact with LEU 914 (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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912A GLU 3.4 0.6 - - - -
913A PRO* 1.3 76.0 - - - +
915A GLU* 1.3 62.8 + - - +
917A ILE* 4.1 0.6 - - - +
918A THR* 3.3 18.7 + - - -
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Residues in contact with GLU 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A GLU* 3.4 7.1 + - - +
913A PRO 3.2 0.4 - - - -
914A LEU* 1.3 76.2 - - - +
916A LYS* 1.3 60.8 + - - +
918A THR* 3.5 0.9 + - - -
919A ASP* 3.1 20.8 + - - -
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Residues in contact with LYS 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A GLU 3.0 14.4 + - - -
913A PRO* 3.1 4.4 + - - -
915A GLU* 1.3 74.1 - - - +
917A ILE* 1.3 59.0 + - - +
919A ASP* 3.4 1.4 + - - +
920A ALA* 2.9 26.9 + - - -
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Residues in contact with ILE 917 (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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913A PRO 2.9 18.9 + - - -
914A LEU 4.1 0.7 - - - -
916A LYS* 1.3 73.1 - - - +
918A THR* 1.3 63.1 + - - +
920A ALA* 3.3 1.3 + - - +
921A TYR* 3.1 20.4 + - - -
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Residues in contact with THR 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A ILE* 5.3 13.5 - - - +
914A LEU 3.3 13.7 + - - -
915A GLU 3.9 2.5 - - - -
917A ILE* 1.3 77.1 - - - +
919A ASP* 1.3 56.6 + - - +
921A TYR* 3.5 1.6 + - - -
922A LEU* 3.0 23.9 + - - -
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Residues in contact with ASP 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A GLU 3.1 15.9 + - - -
916A LYS* 3.9 0.9 - - - +
918A THR* 1.3 73.4 - - - +
920A ALA* 1.3 60.4 + - - +
922A LEU* 3.2 2.2 + - - +
923A ASP* 2.9 26.9 + - - -
1036A PHE* 5.1 8.7 - - - -
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Residues in contact with ALA 920 (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 ALA* 4.7 16.2 - - - +
916A LYS 2.9 17.6 + - - -
917A ILE* 3.3 2.4 + - - +
919A ASP* 1.3 74.4 - - - +
921A TYR* 1.3 62.3 + - - +
923A ASP* 3.3 2.8 + - - +
924A GLN* 3.1 17.8 + - - -
1035A GLN* 5.5 13.0 - - - +
1036A PHE* 5.5 0.4 - - - +
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Residues in contact with TYR 921 (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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838A LEU 6.0 1.6 - - - -
839A LEU* 5.7 8.5 - - - +
842A ALA* 5.1 8.6 - - - +
917A ILE 3.1 12.6 + - - -
918A THR 3.9 2.9 - - - -
920A ALA* 1.3 76.5 - - - +
922A LEU* 1.3 62.1 + - - +
924A GLN* 3.1 3.9 + - - +
925A TYR* 3.0 19.1 + - - -
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Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A THR 3.0 15.2 + - - -
919A ASP* 3.2 4.0 + - - +
921A TYR* 1.3 76.7 - - - +
923A ASP* 1.3 56.1 + - - +
925A TYR* 3.2 2.8 + - - +
926A LEU* 2.9 26.9 + - - -
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Residues in contact with ASP 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ASP 2.9 14.2 + - - -
920A ALA 3.3 3.6 + - - -
921A TYR 3.2 0.4 - - - -
922A LEU* 1.3 74.7 - - - +
924A GLN* 1.3 61.1 + - - +
926A LEU* 3.2 1.7 + - - +
927A TRP* 3.1 20.6 + - - -
1036A PHE* 5.2 13.0 - - - +
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Residues in contact with GLN 924 (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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838A LEU* 6.2 5.4 - - - +
842A ALA* 6.5 0.9 - - - +
920A ALA 3.1 10.0 + - - -
921A TYR 3.1 8.0 + - - -
923A ASP* 1.3 76.2 - - - +
925A TYR* 1.3 61.3 + - - +
927A TRP* 3.5 0.7 + - - +
928A TYR* 3.1 20.1 + - - -
1432A TYR 5.4 7.1 - - - +
1434A LYS 6.0 1.8 - - - -
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Residues in contact with TYR 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A ASP* 6.2 3.4 - - - +
921A TYR 3.0 12.8 + - - -
922A LEU* 3.6 4.0 - - - +
924A GLN* 1.3 76.8 - - - +
926A LEU* 1.3 52.1 + - - +
928A TYR* 3.2 2.1 + - - +
929A GLU* 2.7 33.1 + - - -
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Residues in contact with LEU 926 (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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922A LEU 2.9 14.7 + - - -
923A ASP* 3.2 1.8 + - - +
925A TYR* 1.3 76.2 - - - +
927A TRP* 1.3 58.2 + - - +
929A GLU* 3.2 3.0 + - - +
930A ALA* 2.7 25.5 + - - -
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Residues in contact with TRP 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A ASP 3.1 14.5 + - - -
924A GLN 4.1 0.9 - - - -
926A LEU* 1.3 73.7 - - - +
928A TYR* 1.3 56.5 + - - +
930A ALA* 3.5 2.1 - - - +
931A ASP* 2.6 31.9 + - - -
1434A LYS 6.5 0.9 - - - -
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Residues in contact with TYR 928 (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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924A GLN 3.1 15.2 + - - -
925A TYR* 3.6 3.8 - - - +
927A TRP* 1.3 75.4 - - - +
929A GLU* 1.3 53.0 + - - +
931A ASP* 3.2 1.2 + - - +
932A LYS* 2.6 34.3 + - - -
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Residues in contact with GLU 929 (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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925A TYR 2.7 14.7 + - - -
926A LEU* 3.5 4.7 - - - +
928A TYR* 1.3 76.8 - - - +
930A ALA* 1.3 48.8 + - - +
932A LYS* 4.8 0.9 - - - +
933A ARG* 2.1 44.1 + - - +
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Residues in contact with ALA 930 (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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926A LEU 2.7 18.7 + - - -
927A TRP* 3.1 4.2 + - - +
929A GLU* 1.3 73.8 - - - +
931A ASP* 1.3 52.9 + - - +
933A ARG 4.3 0.2 - - - -
934A ARG* 2.1 53.5 + - - +
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Residues in contact with ASP 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A TRP 2.6 19.8 + - - -
928A TYR* 3.6 2.0 - - - +
930A ALA* 1.3 76.9 - - - +
932A LYS* 1.3 59.9 + - - +
934A ARG* 3.6 5.8 + - - +
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Residues in contact with LYS 932 (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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928A TYR 2.6 20.3 + - - -
929A GLU* 3.7 0.9 - - - +
931A ASP* 1.3 73.4 - - - +
933A ARG* 1.3 57.3 + - - +
934A ARG 3.2 1.0 + - - -
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Residues in contact with ARG 933 (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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822A PHE* 5.6 2.9 - - - -
823A SER 5.0 10.9 + - - +
929A GLU* 2.1 29.5 + - - +
930A ALA* 3.2 1.1 - - - -
932A LYS* 1.3 66.9 - - - +
934A ARG* 1.3 64.5 + - - +
935A LEU* 3.1 4.9 + - - -
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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