Contacts of the helix formed by residues 79 - 90 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A THR* 1.3 72.9 - - - +
80A TYR* 1.3 64.0 + - - +
82A LYS* 3.1 20.8 + - + +
83A ILE* 2.9 33.5 + - - +
56B LEU* 3.6 47.1 - - + -
58B TYR* 4.8 3.1 - - - +
123B ILE 5.7 0.4 - - - +
124B LEU* 3.8 19.1 - - + -
125B ARG 3.5 31.9 + - - +
126B LYS 3.8 1.9 + - - +
127B HIS* 3.9 8.5 - - + -
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Residues in contact with TYR 80 (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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78A THR* 3.6 4.9 - - - +
79A MET* 1.3 80.9 - - - +
81A ASP* 1.3 67.2 + - - +
83A ILE* 3.4 3.8 + - - +
84A LEU* 3.0 43.1 + - + +
99A GLY 4.6 1.3 + - - -
66B PHE* 3.9 12.0 - + - -
67B ARG 3.5 21.3 - - - -
68B TYR* 3.3 7.5 - - - +
69B CYS* 3.0 31.5 + - - -
104B ARG* 3.7 20.4 - - - -
105B PRO* 3.5 34.2 - - + +
108B PHE* 3.8 11.7 - + + -
126B LYS 3.2 16.7 + - - +
127B HIS 3.8 24.5 - - - +
128B SER* 4.2 3.4 - - - -
129B ALA 4.2 2.2 - - - -
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Residues in contact with ASP 81 (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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76A ALA* 3.8 21.2 - - + +
77A GLU* 4.2 5.7 + - - +
78A THR* 2.8 29.3 + - - +
80A TYR* 1.3 76.6 - - - +
82A LYS* 1.3 66.6 + - - +
84A LEU* 3.3 10.3 + - - +
85A LYS* 3.1 22.9 + - - +
100A GLN* 5.1 0.5 - - - -
101A ALA* 4.0 14.2 + - - +
104B ARG* 2.7 44.2 + - - -
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Residues in contact with LYS 82 (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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76A ALA* 3.6 30.7 + - + -
77A GLU 4.7 1.8 - - - -
78A THR 3.0 25.4 + - - +
79A MET* 3.1 28.3 + - + +
81A ASP* 1.3 78.1 - - - +
83A ILE* 1.3 63.5 + - - +
85A LYS* 3.2 6.4 + - - +
86A ASN* 3.1 31.3 + - - +
56B LEU* 4.5 7.0 - - + -
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Residues in contact with ILE 83 (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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79A MET* 2.9 17.7 + - - +
80A TYR 3.9 3.1 - - - +
82A LYS* 1.3 75.1 - - - +
84A LEU* 1.3 64.9 + - - +
86A ASN* 3.9 7.1 - - - +
87A LEU* 3.0 37.9 + - + +
54B LEU* 3.5 42.2 - - + -
56B LEU* 3.7 32.8 - - + -
66B PHE* 4.2 11.4 - - + -
124B LEU* 5.6 0.2 - - + -
127B HIS* 3.8 32.8 - - + +
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Residues in contact with LEU 84 (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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80A TYR* 3.0 41.0 + - + +
81A ASP* 3.5 14.1 - - - +
82A LYS 3.2 0.2 - - - -
83A ILE* 1.3 75.4 - - - +
85A LYS* 1.3 67.4 + - - +
87A LEU* 3.4 7.0 + - + +
88A SER* 3.1 21.2 + - - -
98A VAL 3.8 18.4 - - - +
99A GLY* 3.6 26.5 - - - +
100A GLN* 4.6 2.5 - - - +
66B PHE* 4.0 12.1 - - + -
68B TYR* 3.9 31.0 - - + -
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Residues in contact with LYS 85 (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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74A GLU 4.9 11.4 + - - +
81A ASP 3.1 12.7 + - - +
82A LYS* 3.4 10.8 - - - +
84A LEU* 1.3 76.2 - - - +
86A ASN* 1.3 61.0 + - - +
88A SER* 2.7 39.1 + - - -
89A ARG* 3.2 6.8 + - + +
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Residues in contact with ASN 86 (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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82A LYS* 3.1 18.4 + - - +
83A ILE 3.9 2.9 - - - +
85A LYS* 1.3 86.6 - - - +
87A LEU* 1.3 58.7 + - + +
89A ARG* 3.3 9.6 + - - +
90A SER* 2.9 32.6 + - - +
53B ASP 5.4 0.7 - - - +
54B LEU 2.9 31.6 + - - +
55B GLY* 3.5 20.5 + - - -
56B LEU* 3.7 11.3 - - - +
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Residues in contact with LEU 87 (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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83A ILE* 3.0 35.2 + - + +
84A LEU* 3.7 8.7 - - + +
85A LYS 3.1 0.4 + - - -
86A ASN* 1.3 75.7 - - - +
88A SER* 1.3 57.5 + - - +
90A SER* 3.6 3.6 - - - -
91A ARG* 2.8 60.5 + - + +
47B ILE* 5.1 5.6 - - + -
49B LEU* 3.9 25.8 - - + -
53B ASP* 3.8 22.9 - - + +
54B LEU* 5.0 0.4 - - - -
66B PHE* 3.8 28.7 - - + -
68B TYR* 6.1 0.7 - - + -
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Residues in contact with SER 88 (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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84A LEU 3.1 13.9 + - - -
85A LYS* 2.7 19.2 + - - -
87A LEU* 1.3 69.1 - - - +
89A ARG* 1.3 55.7 + - - -
90A SER 2.7 13.8 + - - -
91A ARG 2.9 24.7 + - - -
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Residues in contact with ARG 89 (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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85A LYS* 3.2 7.8 + - + +
86A ASN* 3.6 10.5 - - - +
88A SER* 1.3 77.7 - - - +
90A SER* 1.3 58.0 + - - +
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Residues in contact with SER 90 (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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86A ASN* 2.9 18.9 + - - +
87A LEU* 3.5 10.0 - - - -
88A SER 2.7 2.0 + - - -
89A ARG* 1.3 81.1 - - - +
91A ARG* 1.3 73.3 + - - +
53B ASP 4.3 11.5 + - - -
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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