Contacts of the helix formed by residues 896 - 903 (chain A) in PDB entry 6A69
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 THR 896 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A VAL* 5.7 1.6 - - + -
169A VAL* 4.8 12.9 + - + +
170A THR* 4.1 26.0 - - + -
173A ASN* 2.7 34.4 + - - +
892A LEU* 4.4 24.5 - - + +
895A ASP* 1.3 78.7 - - + +
897A LEU* 1.3 67.9 + - + +
898A ALA 3.3 0.2 - - - -
899A SER* 2.8 21.0 + - - -
900A LEU* 3.1 11.3 + - - +
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Residues in contact with LEU 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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169A VAL* 5.9 6.5 - - + -
889A TRP* 5.8 2.9 - - + -
892A LEU* 3.2 37.0 + - + +
893A ILE* 4.6 7.0 - - + +
896A THR* 1.3 81.4 - - + +
898A ALA* 1.3 57.0 + - - +
900A LEU* 3.5 11.5 + - + -
901A ALA* 2.9 29.2 + - - +
1012A ILE* 3.7 36.3 - - + -
1016A THR* 3.8 25.6 - - + +
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Residues in contact with ALA 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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855A PHE* 4.5 3.6 - - + -
858A PHE* 3.8 23.1 - - + -
893A ILE 3.3 23.1 + - - +
894A MET 3.4 19.1 - - - +
896A THR 3.3 1.2 - - - +
897A LEU* 1.3 77.6 - - - +
899A SER* 1.3 60.9 + - - +
901A ALA* 3.4 0.2 - - - +
902A LEU* 3.0 38.6 + - + +
987A GLU* 4.0 12.1 - - - +
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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
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173A ASN* 4.7 3.8 + - - -
437A LEU 6.0 0.2 - - - -
438A ALA* 5.0 12.3 - - - -
441A ILE* 4.6 11.9 - - - +
855A PHE* 3.7 32.7 - - - -
895A ASP 3.5 11.2 + - - -
896A THR* 2.8 15.4 + - - -
898A ALA* 1.3 77.5 - - - +
900A LEU* 1.3 60.2 + - - +
903A ALA* 2.7 40.5 + - - +
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Residues in contact with LEU 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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173A ASN* 3.4 31.9 - - + +
176A SER* 6.3 0.9 - - - -
441A ILE* 4.6 10.5 - - + -
445A TYR* 3.9 25.8 - - + +
896A THR* 3.1 13.3 + - - +
897A LEU* 3.9 13.0 - - + +
899A SER* 1.3 81.7 + - - +
901A ALA* 1.3 62.7 + - - +
904A THR* 3.7 12.4 + - - -
1008A ILE* 3.5 28.9 - - + +
1012A ILE* 4.5 13.9 - - + -
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Residues in contact with ALA 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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897A LEU 2.9 19.3 + - - +
898A ALA 3.0 5.4 + - - +
900A LEU* 1.3 81.1 - - - +
902A LEU* 1.3 62.8 + - + +
903A ALA 3.5 0.6 + - - -
904A THR* 4.0 11.4 + - - +
987A GLU* 3.5 20.0 - - - +
1008A ILE* 4.6 7.2 - - - +
1009A PHE* 3.9 29.5 + - + +
1012A ILE* 3.8 21.1 - - + -
1013A VAL* 5.6 0.2 - - + -
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Residues in contact with LEU 902 (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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851A SER* 4.0 1.6 + - - +
854A LYS* 3.3 38.2 + - + +
855A PHE* 4.0 22.0 - - + -
858A PHE* 4.6 14.1 - - + -
898A ALA* 3.0 36.3 + - + +
901A ALA* 1.3 74.0 - - + +
903A ALA* 1.3 62.7 + - - +
904A THR 3.3 2.6 + - - -
905A GLU* 3.6 24.4 - - - +
987A GLU* 4.5 15.3 - - + +
990A ALA* 3.7 25.1 - - + +
991A ARG* 4.8 5.4 - - + +
1009A PHE* 4.4 15.7 - - + -
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Residues in contact with ALA 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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438A ALA* 4.8 7.4 - - + +
441A ILE* 4.8 4.3 - - + -
442A SER* 3.6 30.4 - - - +
851A SER* 2.8 28.2 + - - +
855A PHE* 4.9 9.9 - - + -
898A ALA 4.2 0.2 + - - -
899A SER* 2.7 29.8 + - - +
902A LEU* 1.3 79.1 - - - +
904A THR* 1.3 60.6 + - - +
905A GLU 3.5 2.3 + - - -
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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