Contacts of the helix formed by residues 72 - 83 (chain A) in PDB entry 2H0D
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 ASP 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA* 2.7 22.2 + - + +
30A THR* 2.7 32.2 + - - +
37A SER* 4.2 0.7 + - - -
70A ARG 3.4 1.0 + - - -
71A SER* 1.3 71.4 - - - +
73A LYS* 1.3 64.2 + - - +
74A THR 3.7 1.6 + - - -
75A LEU* 3.1 30.0 + - + +
76A GLN* 3.0 23.1 + - - +
68B LEU* 3.6 13.4 - - + +
70B ARG* 2.5 44.5 + - - -
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Residues in contact with LYS 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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71A SER* 3.5 9.8 + - - +
72A ASP* 1.3 72.7 - - - +
74A THR* 1.3 59.5 - - - +
76A GLN* 3.4 5.8 + - - +
77A ASP* 2.9 62.2 + - - +
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Residues in contact with THR 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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72A ASP* 3.3 1.2 + - - -
73A LYS* 1.3 80.0 - - - +
75A LEU* 1.3 63.6 + - - +
77A ASP* 3.1 10.0 + - - +
78A ILE* 3.1 22.5 + - - +
48B GLU* 3.7 27.7 - - + +
68B LEU 4.6 5.8 + - - -
69B HIS* 5.2 6.2 - - - -
70B ARG* 3.7 20.8 + - + +
106B PHE* 3.6 25.4 - - + -
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Residues in contact with LEU 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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15A HIS 4.5 7.9 - - - +
25A PHE* 3.8 23.6 - - + -
28A ALA* 3.9 13.0 - - + -
37A SER* 3.4 36.6 - - - +
72A ASP* 3.1 26.6 + - + +
74A THR* 1.3 75.3 - - - +
76A GLN* 1.3 63.8 + - - +
78A ILE* 3.3 7.1 + - + +
79A VAL* 3.1 37.2 + - + +
70B ARG* 5.7 0.7 - - - +
105B ASN* 4.9 8.3 - - - +
106B PHE* 4.5 22.0 - - + -
109B LEU* 4.9 10.8 - - + -
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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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25A PHE* 3.0 30.5 + - - +
27A ASP* 3.0 20.5 - - - +
28A ALA* 2.9 38.8 - - - +
72A ASP 3.0 15.8 + - - +
73A LYS* 3.8 5.6 - - - +
75A LEU* 1.3 77.3 - - - +
77A ASP* 1.3 63.5 + - - +
79A VAL* 3.5 6.2 + - - +
80A TYR* 3.1 59.9 + - + +
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Residues in contact with ASP 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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73A LYS* 2.9 50.5 + - - +
74A THR* 3.1 11.4 + - - +
76A GLN* 1.3 77.4 - - - +
78A ILE* 1.3 56.9 + - - +
80A TYR* 3.5 7.9 + - - +
81A LYS* 3.0 37.1 + - + +
48B GLU* 4.0 25.5 - - + +
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Residues in contact with ILE 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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16A LEU* 4.2 10.3 - - + -
74A THR 3.1 10.1 + - - +
75A LEU* 3.3 8.7 + - + +
77A ASP* 1.3 75.1 - - - +
79A VAL* 1.3 53.6 + - - +
81A LYS* 3.0 4.9 + - - +
82A LEU* 2.7 60.9 + - + +
46B HIS* 5.9 4.3 - - + -
48B GLU* 3.8 22.2 + - + +
49B LEU* 3.8 19.7 - - + -
106B PHE* 3.1 44.0 - - + -
109B LEU* 4.4 13.5 - - + -
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Residues in contact with VAL 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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16A LEU* 3.8 36.6 - - + +
24A TYR* 4.4 2.0 - - + -
25A PHE* 3.8 39.0 - - + +
75A LEU* 3.1 19.0 + - + +
76A GLN* 3.7 9.9 - - - +
78A ILE* 1.3 72.7 - - - +
80A TYR* 1.3 57.9 + - - +
82A LEU* 4.9 0.2 - - - -
83A VAL* 2.9 45.0 + - + +
86A LEU* 3.5 24.2 - - + -
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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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26A ILE* 3.7 32.9 - - + +
27A ASP* 4.8 1.6 + - - -
76A GLN* 3.1 50.7 + - + +
77A ASP* 3.8 8.3 - - - +
79A VAL* 1.3 76.8 - - - +
81A LYS* 1.3 59.8 - - + +
83A VAL 3.7 12.8 - - - +
84A PRO* 5.5 0.3 - - - +
86A LEU* 4.0 11.9 - - + -
87A PHE* 3.8 62.1 - + + +
90A GLU* 4.2 10.2 - - + +
91A MET* 4.4 7.4 - - + +
94A ARG* 4.6 2.4 + - - -
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Residues in contact with LYS 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 ASP* 3.0 20.6 + - + +
78A ILE* 3.0 5.1 + - - +
80A TYR* 1.3 78.6 - - + +
82A LEU* 1.3 63.1 + - - +
83A VAL 5.1 0.3 - - - -
84A PRO* 5.8 0.7 - - - +
38B ILE* 5.4 2.4 - - - +
45B LEU* 3.1 29.3 + - - +
46B HIS* 4.4 16.6 + - + +
47B SER* 4.3 5.9 + - - -
48B GLU* 2.9 39.5 + - - +
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Residues in contact with LEU 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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12A LEU* 4.1 20.2 - - + -
16A LEU* 4.3 17.9 - - + -
78A ILE* 2.7 43.0 + - + +
79A VAL 4.2 1.1 - - - +
81A LYS* 1.3 74.7 - - - +
83A VAL* 1.3 59.4 + - - +
84A PRO* 2.9 15.5 - - - +
38B ILE* 3.7 29.3 - - + +
40B VAL* 4.6 13.0 - - + -
46B HIS* 3.4 32.3 - - + +
109B LEU* 4.2 6.1 - - + -
113B ILE* 4.0 24.5 - - + -
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Residues in contact with VAL 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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9A ILE* 4.0 5.6 - - + -
16A LEU* 3.9 18.8 - - + -
24A TYR* 3.7 43.3 - - + +
79A VAL* 2.9 24.1 + - + +
80A TYR 3.7 11.0 - - - +
81A LYS 5.1 0.2 - - - -
82A LEU* 1.3 74.6 - - - +
84A PRO* 1.3 66.1 - - - +
85A GLY 3.5 0.3 + - - -
86A LEU* 3.3 33.6 + - + +
87A PHE 4.7 0.2 + - - -
32B ILE* 3.6 26.7 - - + -
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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