Contacts of the helix formed by residues 79 - 89 (chain C) in PDB entry 1AGQ
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 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C THR* 1.3 73.2 - - - +
80C TYR* 1.3 57.5 + - - +
82C LYS* 3.1 14.9 + - - +
83C ILE* 2.8 58.6 + - + +
56D LEU* 3.3 42.2 - - + -
124D LEU* 4.2 19.1 - - + -
125D ARG 3.4 35.0 + - - +
126D LYS 3.8 2.4 + - - +
127D HIS* 3.9 6.3 - - + -
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Residues in contact with TYR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C THR* 3.1 8.0 - - - +
79C MET* 1.3 78.8 - - - +
81C ASP* 1.3 66.6 + - - +
83C ILE* 3.3 4.5 + - - +
84C LEU* 2.9 53.1 + - + +
99C GLY 4.7 1.0 + - - -
66D PHE* 3.8 22.9 - + - -
67D ARG 3.6 19.7 - - - -
68D TYR* 3.5 5.3 - - + +
69D CYS* 3.0 31.4 + - - +
104D ARG* 3.7 9.6 - - - -
105D PRO* 3.1 38.9 - - + +
108D PHE* 3.8 8.7 - + + -
126D LYS 3.2 15.9 + - - +
127D HIS 3.9 13.0 - - - +
128D SER* 4.2 0.4 - - - -
129D ALA 4.1 10.8 - - - -
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ALA 5.5 0.8 - - - +
76C ALA* 3.8 19.9 - - - +
77C GLU* 4.9 3.1 + - - +
78C THR* 3.1 24.7 + - - +
80C TYR* 1.3 79.0 - - - +
82C LYS* 1.3 65.3 + - - +
84C LEU* 3.8 5.2 - - - +
85C LYS* 3.1 24.4 + - - +
100C GLN* 3.8 15.3 + - + +
101C ALA* 3.7 17.0 + - - +
104D ARG* 2.7 46.9 + - - -
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Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA* 3.3 31.0 + - + +
78C THR 3.0 16.7 + - - +
79C MET* 3.1 22.6 + - - +
81C ASP* 1.3 76.9 - - - +
83C ILE* 1.3 63.9 + - - +
85C LYS* 3.4 5.2 + - - +
86C ASN* 3.1 31.3 + - - +
56D LEU* 4.1 21.3 - - + -
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C MET* 2.8 42.2 + - + +
80C TYR 3.5 3.6 - - - +
82C LYS* 1.3 76.8 - - - +
84C LEU* 1.3 67.1 + - - +
86C ASN* 3.1 6.7 + - - +
87C LEU* 2.9 38.7 + - + +
54D LEU* 3.9 45.1 - - + +
56D LEU* 4.4 2.5 - - + -
66D PHE* 3.7 25.8 - - + -
124D LEU* 4.9 0.2 - - + -
127D HIS* 3.8 25.6 - - + +
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TYR* 2.9 44.4 + - + +
81C ASP* 3.8 7.2 - - - +
82C LYS 3.4 0.2 - - - -
83C ILE* 1.3 76.0 - - - +
85C LYS* 1.3 63.3 + - - +
87C LEU* 3.2 5.0 + - - +
88C SER* 3.0 24.3 + - - -
93C LEU* 3.8 22.1 - - + +
98C VAL* 3.7 22.0 - - - +
99C GLY 3.4 36.3 - - - +
100C GLN* 4.2 17.2 - - + +
66D PHE* 4.0 15.5 - - + -
68D TYR* 4.4 3.6 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C GLU* 4.0 33.4 + - - +
76C ALA* 5.3 10.1 - - + -
81C ASP 3.1 17.8 + - - +
82C LYS* 3.5 4.9 - - - +
84C LEU* 1.3 76.3 - - - +
86C ASN* 1.3 65.3 + - - +
88C SER* 3.3 5.1 + - - -
89C ARG* 3.0 76.8 + - + +
100C GLN* 3.7 26.5 + - - +
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Residues in contact with ASN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LYS* 3.1 22.5 + - - +
83C ILE 3.1 5.4 + - - +
85C LYS* 1.3 82.0 - - - +
87C LEU* 1.3 59.1 + - - +
89C ARG* 3.4 7.3 + - - +
90C SER* 2.8 32.2 + - - -
53D ASP 5.2 0.4 - - - +
54D LEU 2.6 33.3 + - - +
55D GLY* 3.2 23.1 + - - +
56D LEU* 3.8 12.7 - - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ILE* 2.9 39.7 + - + +
84C LEU 3.7 4.3 - - - +
86C ASN* 1.3 73.2 - - + +
88C SER* 1.3 60.3 + - - +
90C SER* 3.4 3.1 - - - +
92C ARG* 2.6 56.1 + - + -
93C LEU* 3.0 30.1 + - + -
47D ILE* 5.4 0.4 - - + -
49D LEU* 3.8 28.3 - - + -
53D ASP 3.5 25.1 - - - +
54D LEU* 4.9 2.0 - - - -
66D PHE* 3.9 16.6 - - + -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU 3.0 16.7 + - - -
85C LYS* 3.6 7.6 - - - -
87C LEU* 1.3 75.2 - - - +
89C ARG* 1.3 64.3 + - - +
91C ARG* 3.1 16.5 + - - -
93C LEU* 4.4 14.0 + - - +
100C GLN* 4.9 6.5 - - - -
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LYS* 3.0 62.3 + - + +
86C ASN* 3.9 7.4 - - - +
88C SER* 1.3 73.8 - - - +
90C SER* 1.3 57.3 + - - +
91C ARG* 3.0 9.7 + - - +
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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