Contacts of the helix formed by residues 80 - 90 (chain B) in PDB entry 1LNU
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 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.4 6.0 + - - -
64B VAL* 3.3 24.8 - - - +
75B ALA* 3.7 7.2 - - - -
77B THR 2.5 20.2 + - - -
78B GLU 2.7 0.6 + - - -
79B LEU* 1.3 72.2 - - - +
81B ARG* 1.3 63.8 + - - -
82B PRO* 3.2 3.4 - - - -
83B ASP* 2.7 19.9 + - - +
84B ALA 3.0 9.1 + - - -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 3.3 25.5 + - + +
77B THR 5.8 0.4 - - - -
78B GLU* 3.0 51.1 + - - +
80B GLY* 1.3 72.4 - - - +
82B PRO* 1.3 73.4 - - + +
84B ALA* 4.4 2.2 - - - -
85B GLU* 3.1 33.1 + - + +
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 3.6 20.2 - - + +
12B VAL* 3.3 25.5 - - + +
14B GLY* 6.1 0.2 - - - -
78B GLU 3.6 7.4 - - - +
79B LEU* 3.9 4.7 - - - -
80B GLY 3.2 4.9 - - - -
81B ARG* 1.3 99.3 - - + +
83B ASP* 1.3 66.6 + - - +
85B GLU* 3.8 2.9 - - + +
86B TYR* 3.3 21.1 + - - +
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 2.4 40.9 + - - -
11B ALA* 3.9 6.7 - - - +
12B VAL* 3.3 8.4 - - - +
63B TYR* 2.9 35.6 + - - -
64B VAL* 3.9 4.5 - - + -
80B GLY 2.7 10.7 + - - +
82B PRO* 1.3 69.5 - - - +
84B ALA* 1.3 64.2 + - - +
87B TRP* 3.0 64.1 + - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 4.5 4.8 - - + +
73B HIS* 3.9 23.2 - - + +
74B ARG* 4.2 2.0 - - - -
75B ALA* 3.7 31.6 - - + +
80B GLY 3.0 11.2 + - - +
81B ARG* 3.9 6.3 - - - +
83B ASP* 1.3 75.3 - - - +
85B GLU* 1.3 60.7 + - + +
88B ASN* 2.4 37.6 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ARG* 3.1 24.5 + - + +
82B PRO* 3.8 3.1 - - + +
84B ALA* 1.3 78.9 - - + +
86B TYR* 1.3 67.8 + - - +
88B ASN* 3.1 10.6 + - - +
89B SER* 3.1 22.4 + - - -
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS 5.2 0.9 - - - -
12B VAL* 3.2 37.9 - - + -
82B PRO 3.3 6.6 + - - +
83B ASP 4.1 1.1 - - - +
85B GLU* 1.3 78.9 - - - +
87B TRP* 1.3 77.2 + + + +
89B SER* 2.6 28.4 + - - -
90B GLN* 3.3 27.5 + - + +
93B ILE* 4.1 17.3 - - + -
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASN* 4.5 2.2 - - - -
9B ASN* 3.2 25.2 - - + +
10B LYS 2.5 35.6 + - - +
11B ALA* 4.0 3.1 - - - +
12B VAL 4.8 0.8 - - - +
56B TYR* 3.5 39.5 - + - -
63B TYR* 4.7 1.1 - - - -
64B VAL* 3.7 21.3 - - + -
73B HIS* 3.4 30.1 - + + +
83B ASP* 3.0 44.1 + - + +
86B TYR* 1.3 86.9 - + + +
88B ASN* 1.3 58.9 + - - +
89B SER 3.5 0.3 + - - -
90B GLN 3.8 2.1 - - - +
93B ILE* 3.3 44.6 - - + +
94B LEU* 3.1 23.2 + - - +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 3.3 17.4 + - - +
73B HIS* 2.6 45.7 + - - +
84B ALA* 2.4 28.5 + - - +
85B GLU* 3.1 13.5 + - - +
87B TRP* 1.3 77.3 - - - +
89B SER* 1.3 60.1 + - - +
94B LEU* 2.6 46.6 - - + +
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLU 3.1 9.9 + - - -
86B TYR* 2.6 29.5 + - - -
88B ASN* 1.3 80.8 - - - +
90B GLN* 1.3 67.6 + - - +
91B PRO* 3.3 14.6 - - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TYR* 3.3 30.9 + - + +
87B TRP 3.9 0.8 + - - -
89B SER* 1.3 86.3 + - - +
91B PRO* 1.3 74.0 - - - +
92B GLU* 3.5 24.4 - - - +
93B ILE* 2.8 39.8 + - + +
94B LEU* 2.8 17.2 + - - +
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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