Contacts of the helix formed by residues 898 - 906 (chain A) in PDB entry 6S1M
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 GLN 898 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A LYS* 4.6 9.5 + - - -
893A ASP* 4.9 8.3 + - + +
896A GLY* 3.4 20.3 + - - +
897A LYS* 1.3 78.9 + - - +
899A ALA* 1.3 64.8 + - - +
900A HIS* 3.8 20.7 - - + +
901A VAL* 3.8 29.2 - - + +
902A GLU* 3.5 17.5 + - - +
936A TYR* 3.4 15.4 - - - +
19P G 5.8 4.0 + - - +
20P A 4.0 32.1 + - - +
21P A 4.8 1.4 - - - +
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Residues in contact with ALA 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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898A GLN* 1.3 74.9 - - - +
900A HIS* 1.3 64.3 + - - +
901A VAL 3.3 0.2 - - - -
902A GLU* 3.3 4.7 + - - +
903A LEU* 3.0 22.5 + - - +
924A TYR* 4.3 26.2 - - + +
926A ILE* 5.4 0.2 - - + -
935A ALA 4.2 8.5 - - - +
936A TYR* 3.8 22.8 - - + +
939A SER* 3.6 15.1 + - - -
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Residues in contact with HIS 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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885A LYS* 3.6 44.0 - - + +
886A GLU 3.7 27.0 + - - -
887A LEU* 4.5 8.3 - - + -
893A ASP* 4.9 0.2 + - - -
898A GLN* 3.8 31.4 - - + +
899A ALA* 1.3 77.4 + - - +
901A VAL* 1.3 81.3 + - + +
903A LEU* 3.3 7.3 + - - +
904A ALA* 2.9 30.3 + - - +
922A VAL* 4.2 21.7 - - + +
924A TYR* 4.3 15.1 - - + -
21P A 3.9 13.6 + - - -
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Residues in contact with VAL 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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887A LEU* 4.2 15.9 - - + -
893A ASP* 3.8 44.0 - - + +
894A TYR* 6.2 3.1 - - + -
898A GLN* 3.8 20.2 - - + +
899A ALA 3.3 0.2 - - - -
900A HIS* 1.3 101.2 - - + +
902A GLU* 1.3 56.9 + - - +
904A ALA* 3.9 1.1 - - - -
905A GLU* 2.9 51.1 + - + +
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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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897A LYS* 3.4 29.9 + - - -
898A GLN 3.5 18.2 + - - +
899A ALA 3.3 6.1 + - - +
901A VAL* 1.3 80.3 - - - +
903A LEU* 1.3 60.6 + - - +
905A GLU* 4.6 2.9 - - - +
906A ARG* 3.2 42.4 + - - +
936A TYR* 3.6 25.4 - - + +
937A MET* 5.2 10.1 - - - +
939A SER* 5.3 0.2 - - - +
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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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899A ALA 3.0 16.0 + - - +
900A HIS* 3.8 4.9 - - - +
901A VAL 3.3 0.2 - - - -
902A GLU* 1.3 78.4 - - - +
904A ALA* 1.3 56.9 + - - +
906A ARG* 3.0 46.7 - - - +
908A ARG* 5.9 2.7 - - - +
922A VAL* 3.8 15.0 - - + -
923A PRO 3.6 24.2 - - - +
924A TYR* 3.7 17.0 - - + -
939A SER* 3.8 8.2 + - - +
940A GLU* 4.0 10.5 - - - +
941A ASP* 3.7 32.3 - - + +
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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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887A LEU* 4.1 22.0 - - + -
900A HIS 2.9 18.3 + - - +
901A VAL* 3.9 3.8 - - - +
903A LEU* 1.3 79.6 - - - +
905A GLU* 1.3 68.3 + - - +
906A ARG 3.3 5.7 + - - +
907A MET* 4.3 12.1 - - - +
915A ALA* 4.8 7.1 - - - +
916A PRO* 4.1 32.0 - - + +
922A VAL* 4.4 4.5 - - + -
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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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887A LEU* 4.7 10.3 - - - +
894A TYR* 5.2 13.4 + - + -
901A VAL* 2.9 35.8 + - + +
902A GLU* 4.6 3.1 - - - +
904A ALA* 1.3 83.2 - - - +
906A ARG* 1.3 58.5 + - - +
907A MET* 3.2 21.0 + - - +
916A PRO 5.5 1.9 - - - +
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Residues in contact with ARG 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 48.3 + - - +
903A LEU* 3.0 45.3 - - - +
904A ALA 3.2 3.8 - - - +
905A GLU* 1.3 75.6 - - - +
907A MET* 1.3 71.8 + - - +
908A ARG* 3.3 27.4 + - - +
936A TYR 4.7 5.7 + - - -
937A MET* 5.6 6.3 + - - +
939A SER* 3.8 18.4 + - - +
940A GLU* 4.3 7.5 + - - -
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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