Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 2J51
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP 4.0 5.4 - - - +
67A THR* 3.5 13.1 - - - -
68A LYS* 2.9 46.0 + - - +
69A SER* 3.3 18.3 + - - +
70A GLU 3.1 1.4 - - - -
71A GLU* 1.3 73.9 - - + +
73A LEU* 1.3 64.2 + - - +
74A GLU 3.1 2.5 - - - -
75A ASP* 2.9 29.3 + - - +
76A TYR* 3.1 29.7 + - + +
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Residues in contact with LEU 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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21A TYR* 4.2 26.5 - - + +
24A VAL* 5.4 5.8 - - + -
67A THR* 4.0 18.4 - - + +
69A SER 4.3 1.6 - - - +
70A GLU* 3.0 28.2 + - + +
72A GLU* 1.3 77.2 - - - +
74A GLU* 1.3 60.7 + - - +
76A TYR* 3.1 19.1 + - - +
77A MET* 3.3 19.7 + - + +
99A TYR* 3.6 55.4 - - + -
104A LEU* 5.0 14.2 - - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.1 25.1 + - + +
70A GLU 5.6 0.2 - - - +
71A GLU* 3.3 23.5 + - - +
72A GLU 3.1 1.0 - - - -
73A LEU* 1.3 77.4 - - + +
75A ASP* 1.3 66.5 + - - +
76A TYR 3.3 0.7 + - - -
77A MET* 3.5 18.9 + - - +
78A VAL* 4.6 5.9 + - - +
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Residues in contact with ASP 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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71A GLU 4.4 5.7 - - - +
72A GLU* 2.9 29.4 + - - +
74A GLU* 1.3 80.1 - - - +
76A TYR* 1.3 75.6 + - + +
77A MET 3.5 0.4 + - - -
78A VAL* 5.0 3.7 + - - +
79A GLU* 5.6 1.0 + - - +
175A GLY 5.1 6.6 - - - +
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Residues in contact with TYR 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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45A PHE* 5.8 3.4 - - + -
65A ILE* 3.7 41.9 - - + +
66A ASP 4.7 1.7 + - - -
67A THR* 4.3 8.7 - - + -
72A GLU* 3.1 49.2 + - + -
73A LEU* 3.1 6.4 + - - +
75A ASP* 1.3 91.5 + - + +
77A MET* 1.3 63.8 + - - +
78A VAL 3.5 2.0 - - - -
79A GLU* 3.5 19.0 + - - +
80A ILE* 3.3 24.5 + - + +
104A LEU* 3.4 34.1 - - + -
106A ILE* 5.2 2.7 - - + -
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Residues in contact with MET 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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21A TYR* 3.7 60.3 - - + -
22A GLU* 5.7 0.7 - - + -
23A HIS* 4.8 9.2 - - + +
24A VAL* 4.0 15.7 - - + -
73A LEU* 3.3 20.6 + - - +
74A GLU* 3.5 12.3 + - - +
75A ASP 3.5 0.2 - - - -
76A TYR* 1.3 79.1 - - - +
78A VAL* 1.3 62.1 + - + +
80A ILE* 3.8 22.4 - - + -
81A ASP* 2.9 31.8 + - + +
104A LEU* 6.1 1.8 - - - -
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Residues in contact with VAL 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 GLU 4.6 5.8 + - - +
75A ASP 5.0 3.1 + - - +
76A TYR 3.5 0.4 - - - -
77A MET* 1.3 76.5 - - + +
79A GLU* 1.3 58.5 + - - +
81A ASP* 3.3 6.5 + - - +
82A ILE* 2.9 42.9 + - + +
174A PHE 5.5 0.7 - - - +
177A SER* 3.7 23.8 - - - +
178A ALA* 4.9 0.2 - - - -
179A LYS* 4.3 17.5 - - + +
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Residues in contact with GLU 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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63A LYS* 3.6 30.9 + - - +
75A ASP 5.6 1.3 + - - +
76A TYR* 3.5 21.8 + - - +
77A MET 3.2 0.2 - - - -
78A VAL* 1.3 77.0 - - - +
80A ILE* 1.3 65.4 + - - +
82A ILE* 3.3 3.4 + - - +
83A LEU* 3.0 39.3 + - + +
106A ILE* 4.4 11.3 - - + +
108A ILE* 5.1 1.0 - - - +
173A ASP* 4.5 4.3 - - - +
174A PHE* 3.4 35.0 + - + +
175A GLY* 3.5 27.1 + - - +
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Residues in contact with ILE 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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23A HIS* 3.7 28.7 - - + +
24A VAL* 4.5 9.6 - - + -
76A TYR 3.3 18.9 + - - +
77A MET* 3.4 22.9 + - + +
79A GLU* 1.3 76.4 - - - +
81A ASP* 1.3 57.2 + - - +
83A LEU* 3.3 6.3 + - - +
84A ALA* 2.8 27.9 + - - +
94A LEU* 4.0 11.1 - - + +
97A ALA* 4.2 11.9 - - + -
104A LEU* 5.0 5.4 - - + -
106A ILE* 3.4 49.1 - - + -
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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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22A GLU* 5.5 0.5 - - - +
23A HIS* 3.3 28.0 + - + -
77A MET* 2.9 19.4 + - + +
78A VAL* 3.6 7.2 - - - +
79A GLU 3.3 0.2 - - - -
80A ILE* 1.3 77.1 - - - +
82A ILE* 1.3 57.2 + - - +
84A ALA 3.3 0.5 + - - -
85A SER* 2.8 39.2 + - - -
179A LYS* 2.6 36.0 + - + +
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Residues in contact with ILE 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 VAL* 2.9 33.7 + - + +
79A GLU 3.3 4.5 + - - +
81A ASP* 1.3 73.7 - - - +
83A LEU* 1.3 59.0 + - - +
85A SER* 3.8 6.1 - - - -
86A CYS* 2.9 53.2 + - - +
151A ILE* 3.8 18.8 - - + -
174A PHE* 3.7 34.1 - - + +
177A SER* 3.3 34.5 - - - -
179A LYS* 4.0 22.2 - - + -
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Residues in contact with LEU 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 GLU* 3.0 36.9 + - + +
80A ILE* 3.7 4.7 - - - +
82A ILE* 1.3 78.3 - - - +
84A ALA* 1.3 61.8 + - - +
86A CYS* 4.0 12.5 + - - +
92A VAL* 3.7 41.8 - - + +
93A LYS* 4.4 4.7 - - - +
94A LEU* 3.7 30.5 + - + +
106A ILE* 4.1 25.4 - - + -
108A ILE* 4.3 15.3 - - + -
173A ASP 5.9 0.4 - - - +
174A PHE* 3.8 22.2 - - + -
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Residues in contact with ALA 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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23A HIS* 3.5 42.5 - - + +
80A ILE 2.8 21.0 + - - +
81A ASP 3.9 0.7 - - - +
83A LEU* 1.3 73.7 - - - +
85A SER* 1.3 60.5 + - - +
86A CYS 4.3 2.9 - - - +
94A LEU* 3.7 18.1 - - + +
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Residues in contact with SER 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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23A HIS* 5.8 1.8 - - - -
81A ASP* 2.8 26.4 + - - -
82A ILE* 3.5 5.4 + - - -
83A LEU 3.3 0.2 - - - -
84A ALA* 1.3 78.5 - - - +
86A CYS* 1.3 66.1 + - - +
87A ASP* 3.7 4.2 + - - +
145A TYR* 4.1 4.2 + - - -
151A ILE* 5.0 1.0 - - - +
179A LYS* 3.7 27.5 + - - -
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Residues in contact with CYS 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 ILE* 2.9 33.2 + - - +
83A LEU 4.0 11.2 + - - +
84A ALA 3.6 3.5 - - - +
85A SER* 1.3 79.7 + - - +
87A ASP* 1.3 59.7 + - - +
88A HIS 3.9 1.1 + - - -
91A ILE* 4.1 23.6 - - + -
92A VAL 5.5 0.2 - - - +
93A LYS* 4.8 10.4 - - - +
145A TYR* 3.6 24.7 - - + -
146A LEU* 3.9 23.3 - - - -
151A ILE* 3.9 11.7 - - - -
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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