Contacts of the helix formed by residues 68 - 77 (chain A) in PDB entry 1AU0
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 MET 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.8 10.5 - - - +
29A SER* 3.8 15.3 - - - +
30A SER* 3.2 23.9 + - - +
67A TYR* 1.3 73.2 - - - +
69A THR* 1.3 68.1 - - + +
71A ALA* 2.9 15.2 + - - +
72A PHE* 2.9 32.0 + - + -
132A SER* 3.8 12.8 - - - +
133A VAL 3.7 24.0 - - - +
134A ALA* 4.1 9.4 - - + -
163A ALA* 3.7 20.4 - - + -
209A LEU* 3.5 30.3 - - + +
211A SER* 4.1 4.9 - - - +
300A SDK 4.8 5.2 - - - -
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Residues in contact with THR 69 (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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67A TYR* 3.8 8.7 - - - +
68A MET* 1.3 77.7 - - - +
70A ASN* 1.3 70.4 + - - +
72A PHE* 3.2 10.8 + - - +
73A GLN* 2.9 30.0 + - - +
110A TYR* 3.5 39.7 - - + -
112A GLU* 3.7 27.2 + - - +
211A SER* 3.9 14.1 - - - +
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Residues in contact with ASN 70 (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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57A VAL* 3.6 10.7 - - + +
59A GLU* 3.0 32.6 - - + +
60A ASN* 3.4 24.0 + - - +
67A TYR* 3.2 26.0 + - - +
68A MET 3.1 1.0 - - - -
69A THR* 1.3 87.3 + - - +
71A ALA* 1.3 58.3 + - - +
73A GLN* 3.6 8.2 - - - +
74A TYR* 3.1 24.6 + - - +
77A LYS* 5.8 0.2 + - - -
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Residues in contact with ALA 71 (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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26A TRP* 3.6 21.8 - - + -
30A SER* 3.6 23.1 - - - +
34A LEU* 6.2 0.7 - - - -
53A LEU* 3.9 17.2 - - + +
57A VAL* 3.9 12.1 - - - +
67A TYR 3.4 1.2 + - - -
68A MET 2.9 9.7 + - - +
70A ASN* 1.3 76.2 - - - +
72A PHE* 1.3 65.0 + - - +
74A TYR* 3.3 3.6 + - - +
75A VAL* 3.2 26.3 + - - +
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Residues in contact with PHE 72 (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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30A SER* 3.9 26.5 - - - -
34A LEU* 4.7 8.7 - - + -
68A MET* 2.9 26.0 + - + -
69A THR* 3.2 14.3 + - - +
71A ALA* 1.3 73.9 - - - +
73A GLN* 1.3 66.5 + - - +
74A TYR 3.0 1.6 - - - -
75A VAL* 2.9 17.4 + - - -
76A GLN* 3.1 9.1 + - - +
107A CYS* 3.6 12.2 - - - -
109A GLY 4.5 4.0 - - - +
110A TYR* 3.7 29.6 - + + -
132A SER* 3.9 19.3 - - - -
211A SER* 3.1 28.7 - - - -
212A PHE* 4.4 0.7 - - - -
213A PRO* 3.7 40.6 - - + -
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Residues in contact with GLN 73 (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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69A THR 2.9 13.4 + - - +
70A ASN* 3.6 9.4 - - - +
72A PHE* 1.3 79.0 - - - +
74A TYR* 1.3 56.6 + - - +
76A GLN* 3.4 31.3 + - - +
77A LYS* 2.9 65.9 + - - +
110A TYR* 3.2 35.3 + - - -
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Residues in contact with TYR 74 (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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52A ASN* 3.7 25.5 + - - -
53A LEU* 3.8 23.1 - - + -
56A CYS* 3.4 43.6 - - + +
57A VAL* 3.8 16.2 - - + -
59A GLU* 4.9 4.9 - - - +
70A ASN 3.1 14.8 + - - +
71A ALA 3.4 6.5 - - - +
72A PHE 3.0 1.0 - - - -
73A GLN* 1.3 78.1 - - - +
75A VAL* 1.3 61.7 + - + +
77A LYS* 3.8 13.2 - - + +
78A ASN* 2.8 72.9 + - + +
80A GLY 4.6 4.9 - - - -
81A ILE* 5.6 0.2 - - + -
96A CYS* 4.5 0.9 - - - -
98A TYR* 4.1 6.8 - - - +
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Residues in contact with VAL 75 (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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34A LEU* 4.1 15.5 - - + -
53A LEU* 4.2 1.3 - - + -
71A ALA 3.2 13.7 + - - +
72A PHE* 2.9 11.8 + - - +
74A TYR* 1.3 84.3 - - + +
76A GLN* 1.3 57.8 + - - +
79A ARG* 3.0 24.3 + - - -
80A GLY 3.2 24.0 + - - +
81A ILE* 3.9 34.3 - - + -
105A ALA 4.1 10.5 - - - +
106A LYS* 4.2 10.8 - - - -
107A CYS* 4.2 16.3 + - + +
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Residues in contact with GLN 76 (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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72A PHE 3.1 9.7 + - - +
73A GLN* 3.4 29.3 + - - +
74A TYR 3.1 0.4 - - - -
75A VAL* 1.3 79.7 - - - +
77A LYS* 1.3 61.0 + - - +
79A ARG* 3.2 27.8 + - - +
107A CYS* 3.4 28.3 - - - +
108A ARG* 4.0 5.9 - - - +
109A GLY* 2.9 31.0 - - - +
110A TYR* 4.9 0.2 - - - -
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Residues in contact with LYS 77 (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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59A GLU* 5.0 19.9 + - - +
70A ASN 5.7 0.2 - - - -
73A GLN* 2.9 55.6 + - - +
74A TYR* 3.5 15.9 - - + +
76A GLN* 1.3 78.5 - - - +
78A ASN* 1.3 62.6 + - + +
79A ARG* 4.8 6.9 + - - +
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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