Contacts of the helix formed by residues 905 - 917 (chain A) in PDB entry 1X86
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 ASP 905 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822A ILE* 3.8 16.8 - - - +
901A ARG* 3.1 41.0 + - - +
902A GLN 3.8 2.4 + - - +
903A LYS 3.4 3.8 + - - -
904A LYS* 1.3 77.3 - - - +
906A SER* 1.3 68.8 + - - +
907A ARG* 2.8 49.3 + - - +
908A PHE* 3.2 14.4 + - + -
909A GLN* 3.0 23.8 + - - +
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Residues in contact with SER 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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905A ASP* 1.3 70.6 + - - +
907A ARG* 1.3 68.9 + - - +
909A GLN* 4.0 2.8 - - - +
910A THR* 2.9 32.6 + - - -
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Residues in contact with ARG 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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821A GLY 4.9 1.8 + - - -
822A ILE* 3.3 45.7 + - + +
905A ASP* 2.8 24.3 + - - +
906A SER* 1.3 80.7 - - - +
908A PHE* 1.3 61.6 + - - +
909A GLN 3.1 1.1 - - - -
910A THR* 3.4 10.8 - - + +
911A PHE* 2.8 30.5 + - - +
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Residues in contact with PHE 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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817A VAL* 4.2 11.9 - - + -
822A ILE* 3.6 28.9 - - + +
823A LEU* 3.9 26.5 - - + -
831A ILE* 4.1 15.9 - - + -
832A PHE* 6.3 1.6 - + - -
898A ILE* 3.8 29.8 - - + -
901A ARG* 3.6 28.5 - - + +
902A GLN* 3.7 6.5 - - + -
905A ASP* 3.1 25.5 + - + +
907A ARG* 1.3 79.8 - - - +
909A GLN* 1.3 59.2 + - - +
911A PHE* 3.4 6.0 + + - +
912A VAL* 3.1 50.0 + - + +
926A LEU* 5.2 3.6 - - + -
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Residues in contact with GLN 909 (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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902A GLN* 3.5 56.0 - - + +
905A ASP 3.0 11.2 + - - +
906A SER 4.1 2.1 - - - +
908A PHE* 1.3 75.5 - - - +
910A THR* 1.3 69.2 + - - +
911A PHE 3.0 1.1 + - - -
912A VAL* 3.1 0.9 + - - +
913A GLN* 2.9 56.5 + - - +
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Residues in contact with THR 910 (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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906A SER* 2.9 20.8 + - - -
907A ARG* 3.4 13.2 - - + +
909A GLN* 1.3 80.4 + - - +
911A PHE* 1.3 66.8 + - + +
913A GLN* 3.3 6.9 + - - +
914A ASP* 3.0 26.5 + - + +
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Residues in contact with PHE 911 (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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812A VAL 4.1 1.8 - - - -
813A PHE* 3.4 42.8 - + + -
816A ARG* 3.7 28.9 - - + +
817A VAL* 3.5 39.3 - - + -
820A GLU* 3.5 20.6 - - - -
822A ILE* 3.6 10.3 - - + -
832A PHE* 5.8 1.1 - + - -
907A ARG 2.8 21.6 + - - +
908A PHE* 3.5 9.4 - + - +
909A GLN 3.0 0.4 - - - -
910A THR* 1.3 76.2 - - + +
912A VAL* 1.3 82.4 + - + +
914A ASP* 3.6 4.8 + - - +
915A ALA* 3.1 24.4 + - + +
926A LEU* 5.6 2.0 - - + -
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Residues in contact with VAL 912 (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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813A PHE* 4.7 2.0 - - + -
898A ILE* 4.9 0.7 - - + -
902A GLN* 3.9 23.1 - - - +
908A PHE* 3.1 48.2 + - + +
909A GLN 3.1 0.8 + - - +
911A PHE* 1.3 85.4 - - + +
913A GLN* 1.3 67.4 + - - +
915A ALA* 3.4 3.6 + - - +
916A GLU* 2.9 46.7 + - + +
926A LEU* 4.0 24.0 - - + -
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Residues in contact with GLN 913 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909A GLN* 2.9 42.5 + - - +
910A THR* 3.5 6.1 - - - +
912A VAL* 1.3 77.6 - - - +
914A ASP* 1.3 58.7 + - - +
916A GLU* 2.9 33.9 + - - +
917A SER* 3.3 8.4 + - - -
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Residues in contact with ASP 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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816A ARG* 3.6 25.9 + - - +
910A THR* 3.0 17.0 + - + +
911A PHE* 4.0 4.3 - - - +
913A GLN* 1.3 79.1 - - - +
915A ALA* 1.3 63.8 + - - +
917A SER* 2.8 28.9 + - - -
918A ASN* 3.8 2.9 + - - +
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Residues in contact with ALA 915 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812A VAL* 3.5 14.3 - - + +
813A PHE* 3.3 31.4 - - + -
816A ARG* 3.9 18.8 - - - +
911A PHE* 3.1 21.7 + - + +
912A VAL 3.6 1.6 - - - +
914A ASP* 1.3 81.4 + - - +
916A GLU* 1.3 60.5 + - - +
918A ASN* 3.1 13.6 + - - +
921A CYS* 3.3 12.6 - - - -
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Residues in contact with GLU 916 (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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813A PHE* 4.2 7.0 - - + -
902A GLN* 5.0 4.4 + - - -
912A VAL* 2.9 37.3 + - + +
913A GLN* 2.9 20.0 + - - +
915A ALA* 1.3 78.8 - - - +
917A SER* 1.3 55.3 + - - +
918A ASN 3.2 4.4 + - - +
921A CYS* 3.5 22.6 - - - +
923A ARG* 4.5 8.3 - - - -
924A LEU 4.1 5.4 - - - +
925A GLN* 2.9 37.1 - - + +
926A LEU* 2.6 28.9 + - - +
927A LYS* 4.6 0.7 + - - +
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Residues in contact with SER 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 GLN 3.3 7.8 + - - -
914A ASP* 2.8 21.0 + - - -
915A ALA 3.1 0.6 - - - -
916A GLU* 1.3 77.2 - - - +
918A ASN* 1.3 60.2 + - - -
919A PRO* 3.6 9.1 - - - +
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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