Contacts of the helix formed by residues 76 - 81 (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 GLY 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.7 11.6 - - - -
14A PRO 3.4 24.5 - - - +
15A GLU* 2.9 20.8 + - - +
74A GLY 3.0 0.6 + - - -
75A THR* 1.3 76.3 - - - +
77A VAL* 1.3 60.8 + - - +
78A GLY 3.3 1.0 + - - -
79A ALA* 3.5 10.1 + - - +
80A LEU* 3.4 17.8 + - - +
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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
----------------------------------------------------------
13A PHE* 3.8 13.4 - - + -
72A PRO 3.9 0.9 - - - +
73A GLY* 3.6 31.9 - - - -
74A GLY 3.0 9.7 + - - +
75A THR 2.9 1.8 + - - -
76A GLY* 1.3 76.1 - - - +
78A GLY* 1.3 66.9 + - - +
80A LEU* 3.1 7.5 + - - +
81A MET* 2.9 38.6 + - - +
105A SER* 3.6 32.3 - - - +
108A LEU* 4.5 1.1 - - + -
109A VAL* 3.8 17.9 - - + -
217A ARG* 4.7 8.3 - - - +
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Residues in contact with GLY 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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75A THR 3.4 8.4 + - - -
76A GLY 3.3 0.8 - - - -
77A VAL* 1.3 82.9 - - - +
79A ALA* 1.3 62.3 + - - +
81A MET* 3.5 18.5 + - - +
82A GLU* 4.0 5.2 + - - +
217A ARG* 4.7 10.0 - - - +
220A ILE* 3.6 34.4 - - - +
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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 THR 4.9 0.4 + - - -
76A GLY* 3.5 10.3 + - - +
77A VAL 3.3 0.6 - - - -
78A GLY* 1.3 75.9 - - - +
80A LEU* 1.3 64.1 - - - +
82A GLU* 3.1 16.1 + - - +
83A ASP* 3.4 12.1 + - - +
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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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11A LEU* 4.7 9.6 - - + -
13A PHE* 3.4 41.1 - - + -
40A TRP* 3.8 32.3 - - + -
71A ILE* 4.6 4.7 - - + -
76A GLY 3.4 8.8 + - - +
77A VAL* 3.1 10.6 + - - +
79A ALA* 1.3 80.2 - - - +
81A MET* 1.3 59.2 + - - +
82A GLU 3.1 1.4 + - - -
83A ASP* 3.2 19.3 + - - +
86A ALA* 3.9 18.9 - - + +
87A LEU* 3.7 13.8 - - - +
90A ILE* 5.0 1.1 - - + -
109A VAL* 4.0 28.3 - - + -
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Residues in contact with MET 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 VAL* 2.9 31.4 + - + +
78A GLY* 3.6 8.3 - - - +
79A ALA 3.2 0.6 - - - -
80A LEU* 1.3 75.3 - - - +
82A GLU* 1.3 62.4 + - - +
83A ASP 3.6 0.4 - - - -
87A LEU* 3.4 18.4 - - - +
108A LEU* 3.7 47.3 - - + +
109A VAL* 4.2 4.3 - - - -
112A ALA* 3.6 19.3 - - + +
134A LEU* 4.2 7.9 - - + -
217A ARG* 4.4 13.2 - - - -
220A ILE* 3.8 15.3 - - + -
221A THR* 3.5 35.0 - - - +
224A ALA* 4.2 8.4 - - + +
227A ARG* 4.7 1.4 + - - -
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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