Contacts of the helix formed by residues 70 - 81 (chain A) in PDB entry 2J3R
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A HIS* 1.3 81.2 + - + +
71A PHE* 1.3 63.5 + - - +
72A ARG* 2.8 36.0 + - + +
73A GLU* 2.9 33.9 + - - +
74A THR* 3.2 22.5 + - - -
144A MET* 6.1 1.3 - - - -
167A PHE* 5.9 1.3 - - - -
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Residues in contact with PHE 71 (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 ASP* 1.3 75.5 - - - +
72A ARG* 1.3 61.8 + - - +
74A THR* 3.4 19.8 + - + -
75A ALA* 3.2 17.0 + - - +
96A TRP* 3.3 21.7 - + - -
100A GLY 3.6 18.6 - - - +
101A ASP 3.4 25.1 - - - -
103A PHE* 3.4 33.2 - + - -
139A LEU* 5.0 2.5 - - + -
144A MET* 4.7 7.0 - - - -
146A VAL* 3.9 19.1 - - + -
165A MET* 4.1 12.1 - - + -
166A ARG* 4.3 3.6 - - - -
167A PHE* 3.6 45.9 - + + -
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Residues in contact with ARG 72 (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 ASP* 2.8 12.9 + - + +
71A PHE* 1.3 77.3 - - - +
73A GLU* 1.3 63.1 + - + +
75A ALA* 3.5 6.1 + - - +
76A ASP* 3.4 22.4 + - - +
96A TRP* 3.3 65.7 - - + +
97A SER 4.8 1.6 + - - -
98A PRO 5.9 0.8 + - - -
100A GLY* 4.2 20.3 - - - +
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Residues in contact with GLU 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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68A CYS* 4.6 5.4 - - - -
69A HIS* 3.1 47.1 + - - +
70A ASP* 2.9 35.5 + - - +
72A ARG* 1.3 74.3 - - + +
74A THR* 1.3 61.5 + - - +
75A ALA 3.1 0.4 - - - -
76A ASP* 2.8 29.1 + - - +
77A VAL* 2.9 19.8 + - + +
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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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68A CYS* 3.4 31.1 - - - +
69A HIS 4.7 0.2 + - - -
70A ASP 3.2 11.9 + - - -
71A PHE* 3.6 23.8 - - + -
72A ARG 3.4 0.4 - - - -
73A GLU* 1.3 79.3 - - - +
75A ALA* 1.3 57.8 + - - +
77A VAL* 3.4 1.4 + - - +
78A ILE* 2.9 56.0 + - + +
103A PHE* 5.8 0.2 - - + -
139A LEU* 4.0 18.2 - - + -
144A MET* 3.5 19.6 - - + +
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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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71A PHE 3.2 3.2 + - - -
72A ARG 3.6 2.7 - - - +
73A GLU 3.1 0.8 - - - -
74A THR* 1.3 78.8 - - - +
76A ASP* 1.3 57.9 + - - +
78A ILE* 3.5 2.1 + - - +
79A ALA* 3.0 24.9 + - - +
93A ILE* 3.0 21.7 - - + +
96A TRP* 3.5 31.0 - - + -
103A PHE* 3.5 35.2 - - + -
105A LEU* 4.8 0.9 - - - +
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Residues in contact with ASP 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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72A ARG 3.4 13.9 + - - +
73A GLU* 2.8 15.5 + - + +
75A ALA* 1.3 76.1 - - - +
77A VAL* 1.3 59.7 + - + +
80A LYS* 2.7 65.4 + - + +
81A VAL* 5.5 0.2 - - - -
93A ILE* 3.5 17.3 - - - +
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Residues in contact with VAL 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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59A PHE* 3.5 33.7 - - + -
68A CYS* 3.8 24.7 - - + +
73A GLU* 2.9 19.2 + - + +
74A THR 3.8 5.8 - - - +
76A ASP* 1.3 75.6 - - + +
78A ILE* 1.3 58.8 + - - +
81A VAL* 3.2 17.4 + - + +
82A ALA* 2.8 26.9 + - - +
1068A PLM 4.2 12.3 - - + -
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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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74A THR* 2.9 44.0 + - + +
75A ALA* 3.7 7.4 - - - +
77A VAL* 1.3 78.6 - - - +
79A ALA* 1.3 57.6 + - - +
82A ALA* 4.0 5.4 - - - -
83A PHE* 2.7 53.6 + - + +
103A PHE* 4.7 4.3 - - + -
105A LEU* 4.4 12.8 - - + -
135A LEU* 4.1 22.0 - - + -
139A LEU* 4.0 22.7 - - + -
165A MET* 4.6 8.3 - - + -
1068A PLM 3.8 22.4 - - + -
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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 17.2 + - - +
78A ILE* 1.3 77.2 - - - +
80A LYS* 1.3 62.6 + - + +
83A PHE* 3.9 4.1 - - - +
89A ILE 4.1 0.7 - - - +
90A THR* 3.0 21.2 - - - +
91A PRO* 3.3 38.6 - - + +
93A ILE* 3.8 12.8 - - + -
105A LEU* 3.6 21.8 - - + -
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Residues in contact with LYS 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 ASP* 2.7 48.5 + - + +
79A ALA* 1.3 78.4 - - + +
81A VAL* 1.3 63.3 + - + +
84A LYS* 3.4 24.4 - - - +
90A THR* 3.9 15.6 + - + -
91A PRO 5.6 0.7 - - - +
93A ILE* 5.3 3.8 - - + -
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Residues in contact with VAL 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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59A PHE* 3.4 24.7 - - + -
63A SER* 4.7 13.9 - - - +
77A VAL* 3.2 24.3 + - + +
80A LYS* 1.3 83.7 - - + +
82A ALA* 1.3 58.6 + - - +
83A PHE 3.4 0.7 - - - -
84A LYS* 2.9 6.1 + - - +
85A MET* 2.7 42.2 + - + +
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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