Contacts of the helix formed by residues 60 - 68 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G THR* 3.6 20.6 + - - -
59G SER* 1.3 83.6 + - - +
61G GLN* 1.3 61.3 + - - +
62G ALA* 3.8 13.2 - - + +
63G ALA* 3.3 35.2 + - - +
64G LEU* 4.3 0.9 + - - +
80G ILE* 3.9 3.0 - - - +
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Residues in contact with GLN 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G TYR* 3.1 21.3 + - - +
59G SER 4.1 0.8 + - - -
60G ASN* 1.3 70.4 - - - +
62G ALA* 1.3 60.3 + - - +
63G ALA 3.2 2.2 - - - -
64G LEU* 3.0 24.3 + - + +
65G ILE* 3.1 32.5 + - + +
69G LEU* 5.3 1.3 - - + -
72G THR* 2.7 30.6 + - - +
78G PHE* 3.6 38.0 - - + +
80G ILE* 4.3 7.3 - - + +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G ASN* 3.5 13.1 - - + +
61G GLN* 1.3 78.5 - - - +
63G ALA* 1.3 56.5 + - - +
65G ILE* 3.8 13.9 - - + +
66G SER* 3.0 29.1 + - - -
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Residues in contact with ALA 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G TYR* 3.8 15.0 - - + +
58G THR* 3.5 22.9 - - + -
60G ASN* 3.3 30.0 - - - +
61G GLN 3.2 0.8 - - - -
62G ALA* 1.3 78.3 - - - +
64G LEU* 1.3 61.2 + - - +
66G SER* 3.5 5.6 + - - -
67G LEU* 3.3 30.1 + - - +
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ALA* 4.5 3.8 - - + +
46G PHE* 3.4 36.4 - - + +
47G GLN* 3.7 20.0 - - + +
50G TYR* 4.7 1.1 - - + -
58G THR* 3.2 32.8 - - + +
60G ASN 4.4 1.6 - - - +
61G GLN* 3.0 9.4 + - - +
63G ALA* 1.3 74.0 - - - +
65G ILE* 1.3 63.6 + - - +
67G LEU* 3.5 12.3 + - + +
68G GLY 3.5 1.2 + - - -
69G LEU* 3.3 43.5 + - + +
78G PHE* 4.6 11.9 - - + -
80G ILE* 3.8 21.8 - - + -
90G MET* 4.6 0.7 - - - -
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Residues in contact with ILE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G GLN* 3.1 46.7 + - + +
62G ALA* 3.9 11.4 - - - +
63G ALA 3.3 0.2 - - - -
64G LEU* 1.3 74.1 - - - +
66G SER* 1.3 65.2 + - - +
68G GLY* 3.3 11.4 + - - -
69G LEU* 3.5 22.5 - - + +
70G LYS 3.9 20.4 - - - +
71G SER* 4.7 13.2 - - - +
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Residues in contact with SER 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ALA 3.0 18.5 + - - -
63G ALA* 3.7 8.1 - - - -
64G LEU 3.4 0.2 - - - -
65G ILE* 1.3 77.5 - - - +
67G LEU* 1.3 64.5 + - - +
68G GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ALA* 4.4 7.6 - - - +
29D LYS* 5.5 4.5 + - - +
30D ARG* 4.2 13.4 + - - +
46G PHE* 3.9 21.7 - - + +
49G MET* 3.6 23.8 - - + +
50G TYR* 3.4 52.5 - - + +
53G ASP* 4.6 8.5 - - - +
54G ASN* 5.7 0.4 - - - +
63G ALA 3.3 15.8 + - - +
64G LEU* 3.8 9.6 - - - +
65G ILE 3.3 0.6 - - - -
66G SER* 1.3 84.2 - - - +
68G GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASN* 2.8 25.0 + - - -
26D ALA* 4.9 1.3 - - - -
46G PHE* 3.4 15.7 - - - -
65G ILE 3.3 8.3 + - - -
66G SER 3.3 0.6 - - - -
67G LEU* 1.3 79.4 - - - +
69G LEU* 1.3 69.0 + - - +
70G LYS* 3.6 3.1 + - - +
106H ASP 4.8 0.2 - - - +
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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