Contacts of the helix formed by residues 60 - 68 (chain O) in PDB entry 6XXD
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 ASN 60 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58O THR* 3.6 20.8 + - - +
59O SER* 1.3 82.1 + - - +
61O GLN* 1.3 60.8 + - - +
62O ALA* 3.8 12.4 - - + +
63O ALA* 3.3 34.9 + - - +
64O LEU* 4.3 1.0 + - - +
80O ILE* 3.9 2.6 - - - +
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Residues in contact with GLN 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O TYR* 3.1 21.1 + - - +
59O SER 4.1 1.0 + - - -
60O ASN* 1.3 70.2 - - - +
62O ALA* 1.3 60.3 + - - +
63O ALA 3.2 2.5 - - - -
64O LEU* 3.0 24.6 + - + +
65O ILE* 3.1 32.3 + - + +
69O LEU* 5.3 1.6 - - + -
72O THR* 2.7 31.1 + - - +
78O PHE* 3.6 38.9 - - + +
80O ILE* 4.3 7.5 - - + +
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Residues in contact with ALA 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ASN* 3.5 12.7 - - + +
61O GLN* 1.3 78.3 - - - +
63O ALA* 1.3 56.8 + - - +
65O ILE* 3.9 13.3 - - + +
66O SER* 3.0 28.9 + - - -
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Residues in contact with ALA 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O TYR* 3.8 15.7 - - + +
58O THR* 3.5 22.9 - - + -
60O ASN* 3.3 28.4 - - - +
61O GLN 3.2 0.6 - - - -
62O ALA* 1.3 79.0 - - - +
64O LEU* 1.3 60.9 + - - +
66O SER* 3.5 5.8 + - - -
67O LEU* 3.3 29.9 + - - +
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Residues in contact with LEU 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ALA* 4.5 4.5 - - + +
46O PHE* 3.4 38.0 - - + +
47O GLN* 3.7 18.2 - - + +
50O TYR* 4.7 0.9 - - + -
58O THR* 3.2 34.5 - - + +
60O ASN 4.4 1.3 - - - +
61O GLN* 3.0 9.2 + - - +
63O ALA* 1.3 74.4 - - - +
65O ILE* 1.3 63.6 + - - +
67O LEU* 3.5 12.6 + - - +
68O GLY 3.5 0.9 + - - -
69O LEU* 3.3 44.7 + - + +
78O PHE* 4.6 10.1 - - + -
80O ILE* 3.8 22.2 - - + -
90O MET* 4.6 0.9 - - - -
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Residues in contact with ILE 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O GLN* 3.1 44.1 + - + +
62O ALA* 3.9 10.8 - - - +
63O ALA 3.3 0.2 - - - -
64O LEU* 1.3 75.1 - - - +
66O SER* 1.3 65.2 + - - +
68O GLY* 3.3 11.3 + - - -
69O LEU* 3.5 22.0 - - + +
70O LYS 3.9 20.4 - - - +
71O SER* 4.7 13.0 - - - +
72O THR 5.4 0.2 - - - +
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Residues in contact with SER 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62O ALA 3.0 18.2 + - - -
63O ALA* 3.7 7.9 - - - -
64O LEU 3.4 0.4 - - - -
65O ILE* 1.3 77.6 - - - +
67O LEU* 1.3 65.1 + - - +
68O GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ALA* 4.4 7.8 - - - +
29L LYS* 5.5 4.5 + - - +
30L ARG* 4.2 13.0 - - - +
46O PHE* 3.9 21.5 - - + +
49O MET* 3.6 23.2 - - + +
50O TYR* 3.4 51.8 - - + +
53O ASP* 4.6 8.5 - - - +
54O ASN* 5.7 0.7 - - - +
63O ALA 3.3 15.4 + - - +
64O LEU* 3.8 9.6 - - - +
65O ILE 3.3 0.6 - - - -
66O SER* 1.3 82.9 - - - +
68O GLY* 1.3 55.5 + - - +
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Residues in contact with GLY 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ASN* 2.8 25.4 + - - -
26L ALA* 4.9 1.3 - - - -
46O PHE* 3.4 14.6 - - - -
65O ILE 3.3 8.3 + - - -
66O SER 3.3 0.8 - - - -
67O LEU* 1.3 79.7 - - - +
69O LEU* 1.3 68.6 + - - +
70O LYS* 3.6 3.1 + - - +
106P ASP 4.8 0.3 - - - +
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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