Contacts of the helix formed by residues 897 - 911 (chain B) in PDB entry 7AUD
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 897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896B LEU* 1.3 81.5 - - - +
898B ARG* 1.3 64.7 + - - +
899B ARG* 3.7 8.1 + - - +
900B GLU* 3.3 23.7 + - - +
901B CYS* 3.3 24.8 + - - -
946B THR* 3.9 6.5 - - - -
1000B ARG* 3.7 15.2 + - - -
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Residues in contact with ARG 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897B SER* 1.3 72.2 - - - +
899B ARG* 1.3 61.0 - - - +
901B CYS* 3.1 6.1 + - - +
902B ASP* 2.9 33.7 + - - +
919B HIS* 3.5 41.6 - - + +
920B ALA* 3.8 18.4 + - - +
921B GLY* 3.4 31.9 - - - +
946B THR* 4.4 4.3 - - + -
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Residues in contact with ARG 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B SER* 3.3 7.7 + - - +
898B ARG* 1.3 78.2 - - - +
900B GLU* 1.3 57.1 + - - +
902B ASP* 3.3 8.8 + - - +
903B THR* 2.9 40.5 + - + +
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Residues in contact with GLU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B LYS* 3.9 7.8 + - - -
874B VAL* 6.3 2.2 - - - -
895B CYS* 3.4 15.2 - - + +
896B LEU 2.9 22.5 + - - -
897B SER* 3.3 21.5 + - - +
898B ARG 3.2 0.6 - - - -
899B ARG* 1.3 77.3 - - - +
901B CYS* 1.3 55.7 + - - +
903B THR* 3.0 8.2 + - - +
904B MET* 2.9 34.7 + - + +
964B ALA* 4.6 5.9 - - - +
965B SER* 3.1 13.0 + - - -
1000B ARG* 2.7 39.1 + - - +
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Residues in contact with CYS 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895B CYS* 3.5 16.8 - - - -
897B SER 3.5 13.9 - - - -
898B ARG* 3.1 9.7 + - - +
900B GLU* 1.3 79.5 - - - +
902B ASP* 1.3 62.1 + - - +
904B MET* 3.7 1.0 - - - +
905B ALA* 2.9 26.9 + - - +
917B ALA* 3.7 4.6 - - + +
918B TYR 4.1 1.8 - - - -
919B HIS* 4.0 11.9 - - + -
944B CYS* 3.4 18.3 - - - +
945B ALA* 3.3 34.5 - - - -
946B THR* 3.4 11.7 - - - -
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Residues in contact with ASP 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B ARG* 2.9 21.4 + - - +
899B ARG* 3.3 8.1 + - - +
901B CYS* 1.3 76.3 - - - +
903B THR* 1.3 60.2 + - + +
905B ALA* 3.8 1.8 - - - +
906B ASP* 2.9 30.9 + - - +
917B ALA* 3.4 16.7 - - - +
919B HIS* 3.4 23.6 + - - -
922B LEU* 5.6 1.4 - - - +
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Residues in contact with THR 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B ALA* 5.1 4.4 - - - +
899B ARG* 2.9 25.3 + - + +
900B GLU* 3.0 14.6 + - - +
902B ASP* 1.3 74.7 - - + +
904B MET* 1.3 60.4 + - - +
906B ASP* 3.7 6.0 - - - +
907B THR* 2.9 36.1 + - - -
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Residues in contact with MET 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874B VAL* 4.5 4.7 - - + -
875B ALA* 3.6 39.3 - - + +
878B CYS* 4.1 10.3 - - - -
893B ILE* 3.9 26.2 - - + -
895B CYS* 4.4 5.4 - - - -
900B GLU* 2.9 21.9 + - + +
901B CYS 3.7 3.4 - - - +
903B THR* 1.3 77.4 + - - +
905B ALA* 1.3 62.7 + - - +
907B THR* 3.4 0.5 + - - -
908B LEU* 3.0 43.7 + - + +
944B CYS* 3.5 21.5 - - + -
964B ALA* 3.9 27.8 - - + -
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Residues in contact with ALA 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B CYS 2.9 17.7 + - - +
902B ASP 3.9 3.1 - - - +
904B MET* 1.3 76.0 - - - +
906B ASP* 1.3 57.7 + - - +
908B LEU* 3.9 0.7 - - - +
909B GLN* 2.9 32.2 + - - +
915B ALA* 4.0 14.5 - - - +
916B LEU 3.9 5.8 - - - -
917B ALA* 3.6 29.6 - - + +
944B CYS* 3.7 11.3 - - - -
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Residues in contact with ASP 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B ASP 2.9 18.5 + - - +
903B THR* 3.7 8.0 - - - +
904B MET 3.3 0.2 - - - -
905B ALA* 1.3 76.9 - - - +
907B THR* 1.3 61.4 + - - +
909B GLN* 3.8 4.0 - - - +
910B ARG* 2.8 68.4 + - - +
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Residues in contact with THR 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B ALA* 3.8 27.0 - - + +
876B PHE* 3.8 40.0 - - + -
879B LEU* 4.2 11.0 - - + -
903B THR* 2.9 19.8 + - - -
904B MET 3.8 3.4 - - - -
906B ASP* 1.3 79.9 + - - +
908B LEU* 1.3 63.7 + - - +
910B ARG* 3.1 10.2 + - + +
911B ASP* 3.0 21.7 + - - +
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Residues in contact with LEU 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B ALA 4.1 14.1 - - - +
879B LEU* 3.9 26.9 - - + +
882B ILE* 4.1 10.3 - - + -
893B ILE* 4.1 11.2 - - + -
904B MET* 3.0 44.8 + - + +
905B ALA 3.9 0.2 - - - +
907B THR* 1.3 77.8 - - - +
909B GLN* 1.3 56.4 + - - +
911B ASP* 3.1 10.0 + - - +
912B GLY 3.1 0.2 + - - -
913B LEU* 2.7 41.2 + - + +
915B ALA* 3.5 28.0 - - + -
942B VAL* 4.0 24.0 - - + -
944B CYS* 4.6 1.3 - - - -
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Residues in contact with GLN 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B ALA 2.9 17.5 + - - +
906B ASP* 4.0 4.7 - - - +
908B LEU* 1.3 77.0 - - - +
910B ARG* 1.3 62.2 + - - +
912B GLY* 3.1 16.1 + - - -
913B LEU 3.2 23.5 + - - +
914B ALA* 4.5 5.5 - - - +
915B ALA 4.1 17.1 + - - +
916B LEU* 5.1 7.5 - - - +
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Residues in contact with ARG 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B PHE* 6.4 1.8 - - + -
906B ASP* 2.8 54.4 + - - +
907B THR* 3.1 11.9 + - + +
909B GLN* 1.3 77.1 - - - +
911B ASP* 1.3 57.9 + - + +
912B GLY 3.3 0.4 + - - -
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Residues in contact with ASP 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879B LEU* 3.1 49.1 - - + +
883B ARG* 2.4 46.5 + - - +
907B THR 3.0 6.3 + - - +
908B LEU 3.1 1.9 + - - -
910B ARG* 1.3 75.5 - - - +
912B GLY* 1.3 50.9 + - - +
913B LEU 3.5 0.4 - - - -
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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