Contacts of the helix formed by residues 894 - 906 (chain A) in PDB entry 3KSY
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 PRO 894 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A VAL* 5.9 0.4 - - + -
853A SER* 4.4 7.4 - - - +
892A GLN 4.2 3.6 - - - +
893A ILE* 1.3 93.1 - - + +
895A SER* 1.3 64.1 + - - +
896A ARG* 3.8 28.9 - - + +
897A GLN* 3.4 27.9 + - + +
898A LYS* 3.3 19.4 + - - +
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Residues in contact with SER 895 (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 ILE 4.9 1.0 + - - -
894A PRO* 1.3 71.7 - - - +
896A ARG* 1.3 63.9 + - - +
897A GLN 3.2 0.2 - - - -
898A LYS* 3.6 17.8 + - - +
899A LYS* 3.4 31.5 + - - +
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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
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857A GLU* 5.1 4.0 + - - -
894A PRO* 3.8 20.6 - - + +
895A SER* 1.3 80.2 - - - +
897A GLN* 1.3 80.1 + - + +
899A LYS* 3.7 7.9 + - - +
900A ILE* 3.3 26.9 + - + +
1041A ARG* 5.1 13.1 - - - +
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Residues in contact with GLN 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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853A SER* 2.9 41.9 + - - +
856A ILE* 3.9 26.1 - - + +
857A GLU* 3.4 26.6 + - - +
860A GLN* 4.4 9.8 + - - +
893A ILE* 4.7 2.6 - - + +
894A PRO* 3.4 27.9 + - + +
895A SER 3.2 0.4 - - - -
896A ARG* 1.3 100.1 - - + +
898A LYS* 1.3 65.5 + - - +
899A LYS 3.2 1.6 - - - -
900A ILE* 3.0 11.3 + - + +
901A LEU* 2.9 22.3 + - - +
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Residues in contact with LYS 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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856A ILE* 5.5 0.2 - - - -
890A PHE 3.3 25.9 + - - -
891A GLU* 3.8 14.1 + - - +
893A ILE* 3.2 37.8 + - + +
894A PRO 3.3 11.0 - - - +
895A SER* 3.8 17.8 + - - +
897A GLN* 1.3 77.8 - - - +
899A LYS* 1.3 59.0 + - + +
901A LEU* 3.1 8.0 + - - +
902A GLU* 2.8 46.6 + - + +
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Residues in contact with LYS 899 (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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895A SER* 3.4 18.7 + - - +
896A ARG* 3.8 10.8 - - - +
897A GLN 3.2 0.4 - - - -
898A LYS* 1.3 78.2 - - - +
900A ILE* 1.3 57.0 + - + +
902A GLU* 3.9 23.2 + - - +
903A GLU* 3.0 28.8 + - - +
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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
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856A ILE* 4.5 9.2 - - + +
859A LEU* 4.9 13.7 - - + +
860A GLN* 3.1 50.5 - - + +
863A GLN* 5.4 4.1 + - + +
896A ARG* 3.3 19.1 - - + +
897A GLN* 3.0 13.9 + - + +
899A LYS* 1.3 76.3 - - + +
901A LEU* 1.3 65.0 + - - +
903A GLU* 3.2 18.9 - - - +
904A ALA* 3.4 8.3 + - - +
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Residues in contact with LEU 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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856A ILE* 4.1 24.9 - - + +
859A LEU* 4.0 22.0 - - + -
874A VAL* 5.0 0.9 - - + -
875A VAL* 5.2 4.7 - - + -
878A MET* 3.9 23.1 - - + -
890A PHE* 4.1 28.3 - - + -
893A ILE* 5.5 2.2 - - + -
897A GLN 2.9 11.7 + - - +
898A LYS* 3.1 9.4 + - - +
900A ILE* 1.3 76.0 - - - +
902A GLU* 1.3 66.6 + - + +
904A ALA* 2.9 18.0 + - + +
905A HIS* 3.0 41.4 + - + -
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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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898A LYS* 2.8 36.1 + - + +
899A LYS* 4.0 27.5 + - - +
901A LEU* 1.3 73.8 - - + +
903A GLU* 1.3 61.1 + - - +
905A HIS* 3.3 20.9 + - + +
906A GLU* 3.2 27.7 + - - +
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Residues in contact with GLU 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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863A GLN* 5.4 10.1 - - - +
899A LYS 3.0 15.7 + - - +
900A ILE* 3.2 15.5 - - - +
901A LEU 3.1 0.2 - - - -
902A GLU* 1.3 77.4 - - - +
904A ALA* 1.3 62.5 + - - +
906A GLU* 3.3 21.4 + - - +
907A LEU* 3.9 8.3 + - + +
914A LYS* 2.9 40.3 + - - +
918A LYS* 5.4 7.2 + - - +
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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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859A LEU* 4.3 11.9 - - + -
863A GLN* 4.8 4.3 - - - +
871A VAL* 4.2 18.8 - - + -
872A LEU* 4.6 1.9 - - - +
875A VAL* 3.7 28.4 - - + +
900A ILE 3.4 7.7 + - - +
901A LEU 2.9 9.4 + - - +
903A GLU* 1.3 74.8 - - - +
905A HIS* 1.3 57.6 + - - +
906A GLU 3.0 4.9 - - - -
907A LEU* 2.9 36.3 + - + +
908A SER* 4.2 2.3 + - - -
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Residues in contact with HIS 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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875A VAL* 4.1 17.8 - - + +
878A MET* 4.5 7.2 + - + +
879A ASN* 3.0 31.3 + - - -
884A TYR* 5.4 5.5 - + - -
901A LEU* 3.0 56.8 + - + -
902A GLU* 3.5 17.2 - - + +
903A GLU 3.3 0.2 - - - -
904A ALA* 1.3 76.1 - - - +
906A GLU* 1.3 62.1 + - + +
907A LEU 3.3 0.6 + - - -
908A SER* 3.8 11.3 + - - -
909A GLU* 3.8 15.7 - - - +
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Residues in contact with GLU 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 GLU* 3.2 22.2 - - - +
903A GLU* 3.3 11.1 + - - +
904A ALA 3.0 1.2 - - - -
905A HIS* 1.3 75.7 - - + +
907A LEU* 1.3 63.5 + - - +
908A SER 3.2 2.6 + - - -
909A GLU* 3.4 37.7 + - - +
914A LYS* 2.7 50.8 + - + +
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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