Contacts of the helix formed by residues 73 - 84 (chain A) in PDB entry 5HOO
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 GLU 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 5.1 14.1 - - + +
72A TYR* 1.3 82.1 - - - +
74A ASP* 1.3 67.4 + - - +
75A ALA* 3.2 5.5 - - + +
76A GLU* 2.8 28.8 + - + +
77A LEU 3.3 5.2 + - - -
106A ARG* 3.5 6.3 - - - +
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Residues in contact with ASP 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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70A LYS* 3.7 13.3 + - - -
73A GLU* 1.3 72.8 - - - +
75A ALA* 1.3 56.9 + - - +
77A LEU* 3.4 6.6 + - - +
78A GLN* 3.0 25.8 + - - +
106A ARG* 3.1 23.2 + - - +
109A GLU* 3.0 21.4 - - - +
110A MET* 3.2 33.2 - - + +
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Residues in contact with ALA 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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73A GLU* 3.2 4.0 - - + +
74A ASP* 1.3 76.0 - - - +
76A GLU* 1.3 60.2 + - - +
77A LEU 3.3 0.2 - - - -
78A GLN* 3.7 11.6 - - + +
79A ALA* 3.0 27.5 + - - +
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Residues in contact with GLU 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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71A ARG 4.7 1.8 - - - +
72A TYR* 3.6 29.7 - - + +
73A GLU* 2.8 22.0 + - + +
75A ALA* 1.3 79.3 - - - +
77A LEU* 1.3 56.9 + - - +
79A ALA* 3.8 10.5 - - - +
80A LEU* 3.6 19.1 - - - +
96A LEU* 4.1 16.1 - - + +
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Residues in contact with LEU 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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72A TYR* 4.1 18.6 - - + +
73A GLU 3.3 3.2 + - - +
74A ASP 3.6 6.5 - - - +
76A GLU* 1.3 76.4 - - - +
78A GLN* 1.3 66.6 + - - +
79A ALA 3.2 2.0 - - - -
80A LEU* 3.0 14.5 + - + +
81A LEU* 3.2 13.4 + - + +
92A LEU* 4.1 27.1 - - + -
96A LEU* 4.1 21.0 - - + +
103A VAL* 4.8 4.9 - - + -
106A ARG* 3.8 30.1 - - + -
107A LEU* 3.7 31.9 - - + -
110A MET* 3.9 15.0 - - + -
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Residues in contact with GLN 78 (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 ASP 3.0 18.3 + - - +
75A ALA* 3.7 11.9 - - + +
77A LEU* 1.3 75.9 - - - +
79A ALA* 1.3 63.0 + - - +
81A LEU* 3.1 12.8 + - - +
82A ASP* 2.9 59.6 + - - +
110A MET* 3.8 7.8 - - + +
112A LYS* 3.0 38.9 + - - +
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Residues in contact with ALA 79 (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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75A ALA 3.0 18.1 + - - +
76A GLU* 3.8 11.7 - - - +
78A GLN* 1.3 75.3 - - - +
80A LEU* 1.3 66.3 + - + +
82A ASP* 3.5 10.1 + - - +
83A GLU* 3.3 26.2 + - - +
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Residues in contact with LEU 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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76A GLU* 3.6 17.5 - - + +
77A LEU* 3.0 11.2 + - - +
79A ALA* 1.3 81.0 - - + +
81A LEU* 1.3 59.3 + - - +
83A GLU* 3.3 25.3 - - - +
84A ASP 3.2 18.5 + - - -
87A GLN* 3.5 15.2 - - - +
92A LEU* 4.2 22.9 - - + +
95A GLN* 3.6 47.8 - - + +
96A LEU* 4.6 12.6 - - + -
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Residues in contact with LEU 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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77A LEU* 3.2 18.7 + - + +
78A GLN* 3.1 16.6 + - - +
80A LEU* 1.3 75.3 - - - +
82A ASP* 1.3 62.9 + - - +
84A ASP 3.7 3.8 - - - +
85A ASP* 3.0 55.4 + - - +
87A GLN* 5.4 1.1 - - + -
92A LEU* 4.2 26.2 - - + -
107A LEU* 4.1 20.2 - - + -
110A MET* 4.8 1.1 - - + -
112A LYS* 3.9 27.1 - - + -
171B TYR* 3.9 24.0 - - + +
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Residues in contact with ASP 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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78A GLN* 2.9 46.7 + - - +
79A ALA* 3.8 8.8 - - - +
81A LEU* 1.3 75.6 - - - +
83A GLU* 1.3 64.3 + - - +
84A ASP* 3.6 0.3 + - - -
85A ASP* 5.1 2.0 + - - +
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Residues in contact with GLU 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 ALA* 3.3 12.7 + - - +
80A LEU* 3.3 37.8 - - - +
82A ASP* 1.3 80.0 - - - +
84A ASP* 1.3 62.6 + - + +
95A GLN* 5.0 4.3 + - - -
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Residues in contact with ASP 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 LEU 3.2 7.5 + - - +
81A LEU* 3.3 7.3 - - - +
82A ASP 3.3 0.8 - - - -
83A GLU* 1.3 83.6 - - + +
85A ASP* 1.3 68.2 + - - +
86A ALA* 3.3 24.3 + - - +
87A GLN* 3.1 36.8 - - - +
91A GLN* 5.3 0.9 + - - -
179B THR* 5.3 2.8 + - - +
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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