Contacts of the helix formed by residues 83 - 93 (chain N) in PDB entry 6Y5D
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 THR 83 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86M GLN* 3.3 28.3 - - + +
89M ALA* 3.7 4.0 - - - -
79N ARG* 3.5 26.6 + - - +
81N THR* 4.0 5.4 - - + +
82N VAL* 1.3 77.4 - - - +
84N ALA* 1.3 66.9 + - - +
85N MET* 3.6 14.4 + - - +
86N ASP* 2.8 39.4 + - - +
87N VAL* 3.3 11.6 + - - +
105V A 6.0 5.2 - - - -
106V G 6.1 0.9 - - - +
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Residues in contact with ALA 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M GLN* 3.2 8.2 + - - +
88M SER* 3.5 34.3 - - - +
89M ALA* 3.7 13.0 - - - +
92M ALA* 4.7 1.9 - - + +
83N THR* 1.3 73.2 - - - +
85N MET* 1.3 58.8 + - + +
87N VAL* 3.1 6.3 + - - +
88N VAL* 2.9 31.2 + - - +
101N PHE* 4.6 20.2 - - + +
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Residues in contact with MET 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N THR* 3.1 10.6 + - - +
84N ALA* 1.3 79.3 - - + +
86N ASP* 1.3 55.7 + - - +
88N VAL* 3.2 9.7 + - + +
89N TYR* 3.0 76.2 + - + +
101N PHE 3.6 23.1 - - - +
102N GLY* 4.1 3.8 - - - -
103N GLY* 3.9 28.0 - - - +
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Residues in contact with ASP 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N ALA* 3.6 23.2 - - - +
73N TYR* 3.8 16.2 - - + +
74N THR* 3.4 12.0 + - - +
79N ARG* 3.0 28.0 + - - -
82N VAL* 4.0 5.2 - - + -
83N THR* 2.8 36.7 + - - +
85N MET* 1.3 74.6 - - - +
87N VAL* 1.3 60.3 + - - +
89N TYR* 3.5 15.8 + - - +
90N ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M PHE* 5.6 0.2 - - + -
89M ALA* 3.7 24.7 - - + +
92M ALA* 3.8 15.7 - - + -
93M LEU* 3.5 38.4 - - + +
66N VAL* 4.5 0.2 - - + -
70N ALA* 4.1 8.3 - - + -
82N VAL* 4.2 11.0 - - + -
83N THR 3.3 11.0 + - - +
84N ALA 3.1 8.2 + - - +
86N ASP* 1.3 76.3 - - - +
88N VAL* 1.3 59.2 + - - +
90N ALA* 3.2 2.9 + - - +
91N LEU* 2.8 45.1 + - + +
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Residues in contact with VAL 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M ALA* 5.3 1.1 - - + -
84N ALA 2.9 19.8 + - - +
85N MET* 3.2 19.3 + - + +
87N VAL* 1.3 76.4 - - + +
89N TYR* 1.3 59.7 + - + +
91N LEU* 3.3 8.4 + - - +
92N LYS* 2.7 38.6 + - + +
96N ARG 4.8 0.5 - - - +
97N THR* 6.0 0.4 - - - -
98N LEU* 4.4 33.3 + - + +
101N PHE* 3.7 32.1 - - + +
102N GLY 5.5 0.2 - - - +
103N GLY* 5.3 7.9 - - - -
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Residues in contact with TYR 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N TYR* 3.4 40.1 + + + +
85N MET* 3.0 62.5 + - + +
86N ASP* 3.8 14.1 - - - +
88N VAL* 1.3 79.9 - - + +
90N ALA* 1.3 62.4 + - - +
92N LYS* 3.3 11.8 - - + +
93N ARG* 3.2 28.6 + - - +
84P TYR* 3.5 62.0 + + + +
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Residues in contact with ALA 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N VAL* 3.0 34.8 - - + +
69N ASP* 3.5 19.7 - - + -
70N ALA* 3.6 4.9 - - + +
73N TYR* 3.8 2.7 - - - -
86N ASP 3.0 19.0 + - - +
87N VAL 3.2 5.6 + - - +
89N TYR* 1.3 75.5 - - - +
91N LEU* 1.3 62.4 + - - +
93N ARG* 3.3 16.4 - - - +
94N GLN* 3.4 16.8 + - - +
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Residues in contact with LEU 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M ALA 4.2 0.4 - - - +
93M LEU* 5.2 1.8 - - + -
96M ALA* 3.5 35.4 - - + -
62N PHE* 4.1 10.8 - - + -
66N VAL* 3.6 32.8 - - + -
87N VAL* 2.8 32.3 + - + +
88N VAL* 3.7 2.9 - - - +
90N ALA* 1.3 74.1 - - - +
92N LYS* 1.3 69.6 + - - +
94N GLN* 2.9 15.4 + - - +
96N ARG* 3.2 35.8 - - + +
98N LEU* 3.7 29.6 - - + -
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Residues in contact with LYS 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N VAL* 2.7 26.2 + - + +
89N TYR* 3.3 15.3 - - + +
91N LEU* 1.3 72.1 - - - +
93N ARG* 1.3 61.0 + - + +
95N GLY* 2.9 20.1 + - - -
96N ARG 3.2 18.1 + - - -
97N THR* 4.2 22.9 + - + +
80P ARG* 5.1 3.1 - - - +
84P TYR* 3.4 29.0 + - + +
69T ASP* 5.2 4.3 - - - -
72T GLU* 2.8 33.4 + - - -
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Residues in contact with ARG 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N ASP* 3.2 32.7 + - - +
73N TYR* 3.5 27.3 + - - +
89N TYR 3.2 7.4 + - - +
90N ALA 3.3 14.1 - - - +
92N LYS* 1.3 81.8 - - + +
94N GLN* 1.3 60.8 + - + +
95N GLY 3.2 2.7 + - - -
201O PTD 6.1 0.5 - - - +
77P GLU* 3.4 22.3 + - - +
101P LEU* 2.6 50.3 + - - +
102P LEU* 3.6 12.9 - - - +
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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