Contacts of the helix formed by residues 83 - 97 (chain A) in PDB entry 3NOR
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.2 12.5 - - - -
60A PHE* 5.7 0.6 - - - -
79A ALA 3.4 10.0 + - - +
80A LEU* 3.2 24.3 + - - +
81A MET 3.6 0.8 - - - -
82A GLU* 1.3 76.1 - - - +
84A PRO* 1.3 68.3 - - - +
85A GLN* 3.3 12.3 + - - +
86A ALA* 3.1 28.5 + - + +
87A LEU* 2.9 24.6 + - - +
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Residues in contact with PRO 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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82A GLU 3.3 12.3 - - - +
83A ASP* 1.3 85.3 - - - +
85A GLN* 1.3 63.1 + - + +
87A LEU* 4.0 6.7 - - + +
88A ALA* 3.0 30.9 + - - +
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Residues in contact with GLN 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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41A LYS* 6.4 0.4 - - + -
60A PHE* 4.4 16.0 - - + -
83A ASP* 3.2 8.8 + - - +
84A PRO* 1.3 80.1 - - + +
86A ALA* 1.3 68.9 + - - +
88A ALA* 3.3 8.2 + - - +
89A PHE* 3.0 23.7 + - - +
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Residues in contact with ALA 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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11A LEU* 5.5 2.2 - - + -
40A TRP* 5.1 0.4 - - + -
60A PHE* 4.0 24.0 - - + -
80A LEU* 3.9 22.4 - - + +
83A ASP* 3.1 32.9 + - + +
85A GLN* 1.3 76.4 - - - +
87A LEU* 1.3 58.9 + - - +
89A PHE* 3.3 2.8 + - - +
90A ILE* 2.9 39.2 + - + +
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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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80A LEU 3.7 16.4 - - - +
81A MET 3.4 22.4 - - - +
82A GLU* 4.7 1.6 - - - -
83A ASP 2.9 23.9 + - - +
84A PRO* 4.0 6.3 - - + +
86A ALA* 1.3 77.5 - - - +
88A ALA* 1.3 58.3 + - - +
90A ILE* 3.3 5.2 + - + +
91A ARG* 2.9 35.5 + - - +
109A VAL* 3.8 34.3 - - + +
112A ALA* 4.0 18.8 - - + +
113A ALA* 3.9 15.3 - - + +
224A ALA* 6.1 0.2 - - + -
227A ARG* 6.5 1.3 - - - -
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Residues in contact with ALA 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 PRO 3.0 18.2 + - - +
85A GLN* 3.7 9.2 - - - +
87A LEU* 1.3 77.2 - - - +
89A PHE* 1.3 56.9 + - - +
91A ARG* 3.5 7.7 + - - +
92A GLN* 2.9 44.4 + - - +
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Residues in contact with PHE 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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11A LEU* 3.8 18.8 - - + -
39A ILE* 3.6 30.3 - - + -
60A PHE* 3.5 58.3 - + + -
63A CYS* 3.8 14.1 - - + -
66A LEU* 4.6 0.7 - - + -
69A ILE* 4.3 7.9 - - + -
85A GLN 3.0 16.5 + - - +
86A ALA 3.6 3.6 - - - +
88A ALA* 1.3 74.7 - - - +
90A ILE* 1.3 69.3 + - + +
92A GLN* 3.2 20.8 + - - +
93A GLN* 3.0 57.5 + - + +
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Residues in contact with ILE 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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11A LEU* 4.1 21.3 - - + -
69A ILE* 4.5 9.3 - - + +
71A ILE* 3.9 24.2 - - + -
80A LEU* 5.0 1.3 - - + -
86A ALA* 2.9 29.0 + - + +
87A LEU* 3.8 7.4 - - + +
89A PHE* 1.3 77.7 - - + +
91A ARG* 1.3 56.3 + - - +
93A GLN* 3.8 1.0 - - - +
94A ALA* 2.9 33.3 + - + +
109A VAL* 3.6 30.5 - - + -
110A LEU* 4.0 16.4 - - + -
113A ALA* 4.4 5.2 - - + -
115A LEU* 3.7 20.9 - - + -
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Residues in contact with ARG 91 (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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87A LEU* 2.9 21.6 + - - +
88A ALA* 3.8 7.2 - - - +
90A ILE* 1.3 72.6 - - - +
92A GLN* 1.3 64.7 + - - +
94A ALA* 3.9 5.4 - - - +
95A ALA* 3.1 22.9 + - - +
113A ALA* 2.9 50.0 + - + +
114A GLY* 3.8 16.2 + - - -
115A LEU* 3.9 17.2 - - + +
228A LEU* 5.9 0.8 - - - +
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Residues in contact with GLN 92 (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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88A ALA* 2.9 35.8 + - - +
89A PHE* 3.2 23.5 + - - +
91A ARG* 1.3 77.0 - - + +
93A GLN* 1.3 68.1 + - + +
95A ALA* 3.4 15.4 + - - +
96A ARG* 4.3 3.6 + - - +
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Residues in contact with GLN 93 (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 CYS* 4.1 8.3 + - - -
64A PRO 3.5 18.6 + - - -
65A PRO* 3.9 4.3 - - - +
66A LEU* 2.9 40.7 + - + +
69A ILE* 3.8 20.2 - - + -
89A PHE* 3.0 53.6 + - + +
90A ILE 3.9 0.2 - - - +
92A GLN* 1.3 78.9 + - + +
94A ALA* 1.3 64.7 + - - +
95A ALA 3.4 0.3 + - - -
96A ARG* 3.5 2.8 + - - +
97A ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 94 (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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69A ILE* 5.0 3.5 - - + +
90A ILE* 2.9 20.2 + - + +
91A ARG 3.9 1.3 - - - +
93A GLN* 1.3 77.1 - - - +
95A ALA* 1.3 65.8 + - - +
96A ARG 3.2 0.9 + - - -
97A ALA* 3.7 7.6 + - - +
100A VAL* 3.9 32.7 - - + +
115A LEU* 3.6 35.7 - - + -
148A ASN* 5.4 0.9 + - - -
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Residues in contact with ALA 95 (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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91A ARG 3.1 11.6 + - - +
92A GLN* 3.5 14.1 - - - +
93A GLN 3.2 0.6 - - - -
94A ALA* 1.3 77.7 - - - +
96A ARG* 1.3 72.0 + - + +
97A ALA 5.2 0.2 - - - +
115A LEU* 5.8 0.2 - - - +
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Residues in contact with ARG 96 (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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65A PRO* 6.5 0.9 - - + -
66A LEU 4.7 1.7 - - - +
92A GLN 4.3 2.6 + - - +
93A GLN 3.5 3.9 + - - +
95A ALA* 1.3 89.7 + - + +
97A ALA* 1.3 70.6 + - - +
98A ARG* 3.3 2.3 + - - -
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Residues in contact with ALA 97 (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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66A LEU* 3.4 22.4 + - + +
67A ASP 4.1 3.4 - - - +
69A ILE* 4.4 8.3 - - + +
93A GLN 3.1 20.0 + - - +
94A ALA 3.7 4.7 + - - +
95A ALA 5.2 0.3 - - - +
96A ARG* 1.3 78.3 - - - +
98A ARG* 1.3 63.8 + - - +
99A TYR 3.7 19.3 - - - +
100A VAL* 4.2 11.6 - - + +
148A ASN* 3.3 13.7 + - - -
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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