Contacts of the helix formed by residues 60 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D THR* 3.6 21.1 + - - -
59D SER* 1.3 82.9 + - - +
61D GLN* 1.3 61.1 + - - +
62D ALA* 3.8 12.2 - - + +
63D ALA* 3.3 36.2 + - - +
64D LEU 4.3 0.7 + - - -
80D ILE* 3.9 2.7 - - - +
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Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.1 21.5 + - - +
59D SER 4.1 0.4 + - - -
60D ASN* 1.3 70.1 - - - +
62D ALA* 1.3 60.9 + - - +
63D ALA 3.2 2.2 - - - -
64D LEU* 3.0 24.2 + - + +
65D ILE* 3.1 30.7 + - + +
69D LEU* 5.3 1.6 - - + -
72D THR* 2.7 30.7 + - - +
78D PHE* 3.6 37.7 - - + +
80D ILE* 4.3 7.1 - - + +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ASN* 3.5 13.3 - - + +
61D GLN* 1.3 78.8 - - - +
63D ALA* 1.3 57.2 + - - +
65D ILE* 3.8 13.3 - - - +
66D SER* 3.0 28.8 + - - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D TYR* 3.8 15.0 - - + +
58D THR* 3.5 22.7 - - + -
60D ASN* 3.3 29.1 - - - +
61D GLN 3.2 0.6 - - - -
62D ALA* 1.3 78.4 - - - +
64D LEU* 1.3 60.8 + - - +
66D SER* 3.5 6.0 + - - -
67D LEU* 3.3 30.0 + - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA* 4.5 4.0 - - + +
46D PHE* 3.4 36.4 - - + +
47D GLN* 3.7 19.7 - - + +
50D TYR* 4.7 1.1 - - + -
58D THR* 3.2 32.1 - - + +
60D ASN 4.4 1.1 - - - +
61D GLN* 3.0 10.5 + - - +
63D ALA* 1.3 74.2 - - - +
65D ILE* 1.3 63.6 + - - +
67D LEU* 3.5 12.5 + - - +
68D GLY 3.5 1.0 + - - -
69D LEU* 3.3 43.6 + - + +
78D PHE* 4.6 11.9 - - + -
80D ILE* 3.8 22.0 - - + -
90D MET* 4.6 0.7 - - - -
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D GLN* 3.1 46.2 + - + +
62D ALA* 3.9 10.8 - - - +
64D LEU* 1.3 72.6 - - - +
66D SER* 1.3 65.7 + - - +
68D GLY* 3.3 11.1 + - - -
69D LEU* 3.5 22.7 - - + +
70D LYS 3.9 19.7 - - - +
71D SER* 4.7 13.2 - - - +
72D THR 5.4 0.2 - - - +
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA 3.0 17.5 + - - -
63D ALA* 3.7 8.3 - - - -
64D LEU 3.4 0.2 - - - -
65D ILE* 1.3 78.5 - - - +
67D LEU* 1.3 63.4 + - - +
68D GLY 3.5 0.3 + - - -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE* 3.9 21.8 - - + +
49D MET* 3.6 28.0 - - + +
50D TYR* 3.4 52.0 - - + +
53D ASP* 4.6 14.4 - - - +
54D ASN* 5.7 0.4 - - - +
63D ALA 3.3 15.8 + - - +
64D LEU* 3.8 9.9 - - - +
65D ILE 3.3 0.8 - - - -
66D SER* 1.3 83.2 - - - +
68D GLY* 1.3 54.6 + - - +
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D PHE* 3.4 18.3 - - - -
64D LEU 3.5 0.2 + - - -
65D ILE 3.3 7.9 + - - -
66D SER 3.3 0.6 - - - -
67D LEU* 1.3 80.0 - - - +
69D LEU* 1.3 69.0 + - - +
70D LYS* 3.6 3.5 + - - +
106E ASP* 4.8 11.1 - - - +
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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