Contacts of the helix formed by residues 897 - 911 (chain A) in PDB entry 3PT6
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 CYS 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ZN 2.3 36.3 - - - -
783A THR* 3.6 18.8 - - - +
796A HIS* 3.5 7.9 - - + -
798A HIS* 4.2 12.3 - - - -
823A CYS* 4.0 2.9 - - - -
895A LYS 3.3 6.0 + - - +
896A PHE* 1.3 77.2 - - - +
898A LEU* 1.3 65.7 + - - +
899A SER* 3.6 10.5 - - - -
900A CYS* 3.4 14.5 + - + +
901A ILE* 3.2 26.3 + - - +
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Residues in contact with LEU 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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798A HIS* 3.9 10.7 + - + -
819A LEU* 5.1 5.8 - - + -
872A TRP* 3.6 17.5 - - + -
883A PRO* 5.7 1.3 - - + -
884A PRO* 3.5 51.1 - - + +
886A THR* 4.9 9.9 - - - +
896A PHE* 3.2 35.4 - - + -
897A CYS* 1.3 70.8 - - - +
899A SER* 1.3 68.7 + - - +
900A CYS 3.2 0.3 + - - -
901A ILE* 3.2 7.6 + - + +
902A ARG* 2.8 25.3 + - - +
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Residues in contact with SER 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A HIS* 3.6 33.0 - - - -
820A VAL 4.0 0.9 - - - -
821A GLY* 3.0 8.7 + - - +
822A GLU* 2.9 24.9 + - - -
823A CYS* 3.3 23.6 - - - -
872A TRP* 4.5 5.8 - - - -
897A CYS* 3.4 2.1 - - - -
898A LEU* 1.3 78.2 - - - +
900A CYS* 1.3 62.8 + - - +
902A ARG* 3.7 4.8 - - - +
903A LEU* 3.2 23.2 + - - +
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Residues in contact with CYS 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ZN 2.3 35.1 - - - -
796A HIS* 3.5 11.4 - - - -
823A CYS* 3.6 6.1 - - - -
897A CYS* 3.4 13.2 + - + +
898A LEU 3.2 0.4 - - - -
899A SER* 1.3 79.1 - - - +
901A ILE* 1.3 53.0 + - + +
903A LEU* 3.2 7.4 + - - +
904A ALA* 2.8 35.0 + - - +
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Residues in contact with ILE 901 (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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886A THR* 5.0 16.2 - - - -
887A GLN 5.8 0.4 - - - +
892A ASN* 3.8 15.7 - - - +
896A PHE* 3.2 39.3 - - + -
897A CYS 3.2 15.5 - - - +
898A LEU* 3.2 6.7 + - + +
900A CYS* 1.3 73.8 - - + +
902A ARG* 1.3 68.7 + - - +
904A ALA* 2.8 9.7 + - + +
905A GLU* 2.8 30.1 + - + +
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Residues in contact with ARG 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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821A GLY* 5.7 2.7 - - - -
872A TRP* 4.8 13.5 - - + -
884A PRO* 6.4 1.6 - - + -
898A LEU 2.8 21.4 + - - +
899A SER* 3.7 7.6 - - - +
901A ILE* 1.3 74.4 - - - +
903A LEU* 1.3 64.4 + - - +
905A GLU* 3.3 5.2 + - - +
906A LEU* 2.9 31.4 + - + +
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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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821A GLY 6.1 1.1 - - - +
899A SER 3.2 11.3 + - - +
900A CYS* 3.5 9.0 - - - +
902A ARG* 1.3 77.9 - - - +
904A ALA* 1.3 62.9 + - - +
906A LEU* 3.2 10.6 + - - +
907A ARG* 3.0 23.9 + - - +
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Residues in contact with ALA 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 CYS 2.8 17.9 + - - +
901A ILE* 2.8 16.9 + - + +
903A LEU* 1.3 74.3 - - - +
905A GLU* 1.3 62.9 + - - +
907A ARG* 3.2 5.1 + - - +
908A GLN* 3.1 31.1 + - + +
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Residues in contact with GLU 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 ILE* 2.8 22.5 + - + +
902A ARG* 3.8 5.4 - - - +
904A ALA* 1.3 70.5 - - - +
906A LEU* 1.3 69.8 + - + +
908A GLN* 4.0 6.8 - - - +
909A LYS* 3.2 22.5 + - - +
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Residues in contact with LEU 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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902A ARG* 2.9 25.5 + - + +
903A LEU* 3.2 14.6 - - - +
905A GLU* 1.3 77.7 - - + +
907A ARG* 1.3 58.2 + - - +
909A LYS* 3.0 10.5 + - + +
910A GLU* 2.8 56.8 + - + +
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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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903A LEU 3.0 8.7 + - - +
904A ALA* 3.2 8.7 + - - +
906A LEU* 1.3 78.4 - - - +
908A GLN* 1.3 65.5 + - - +
910A GLU* 3.0 8.4 + - - +
911A MET* 2.9 41.3 + - + +
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Residues in contact with GLN 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 ALA* 3.1 21.3 + - + +
905A GLU* 4.1 7.2 - - - +
907A ARG* 1.3 81.6 - - - +
909A LYS* 1.3 60.2 + - - +
911A MET* 3.9 31.9 - - - +
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Residues in contact with LYS 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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905A GLU 3.2 13.0 + - - +
906A LEU* 3.0 13.3 + - + +
908A GLN* 1.3 78.6 - - - +
910A GLU* 1.3 67.3 + - - +
911A MET 3.5 2.1 + - - +
933A ASN* 2.7 68.0 + - - +
934A GLY* 3.9 9.4 + - - +
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Residues in contact with GLU 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A LEU* 2.8 54.5 + - + +
907A ARG* 3.0 7.6 + - - +
909A LYS* 1.3 85.8 - - - +
911A MET* 1.3 61.0 + - - +
912A PRO* 3.7 2.8 - - - +
932A LYS* 4.0 15.1 - - - +
933A ASN* 3.5 22.9 + - - +
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Residues in contact with MET 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A ARG* 2.9 29.3 + - - +
908A GLN* 3.9 36.2 - - - +
909A LYS 4.0 3.5 - - - +
910A GLU* 1.3 75.9 - - + +
912A PRO* 1.3 83.4 - - + +
913A LYS* 3.5 6.0 + - + +
931A THR* 4.5 2.6 - - - +
932A LYS* 4.7 1.7 - - - -
1014A GLU* 4.9 8.3 - - + +
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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