Contacts of the helix formed by residues 70 - 80 (chain A) in PDB entry 3LNX
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY* 4.0 1.3 - - - -
26A VAL* 3.9 16.6 - - + -
27A ASN* 3.5 22.9 - - + +
68A GLY 3.6 0.9 + - - +
69A ALA* 1.3 79.0 - - - +
71A HIS* 1.3 65.6 + - - +
72A LYS* 3.5 8.2 + - - +
73A GLN* 3.0 46.4 + - - +
74A ALA* 3.0 18.9 + - - +
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Residues in contact with HIS 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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22A VAL* 3.2 39.2 + - + +
23A THR* 4.0 5.1 - - - -
24A GLY 2.8 29.0 + - - +
25A GLY* 3.8 2.7 - - - -
27A ASN* 3.0 21.3 + - - +
28A THR* 4.6 5.0 - - + +
35A ILE* 4.7 0.8 - - - +
70A THR* 1.3 72.9 - - - +
72A LYS* 1.3 65.2 + - + +
74A ALA* 3.2 6.4 + - - +
75A VAL* 3.0 40.8 + - + +
100A IOD 4.3 12.8 - - + -
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Residues in contact with LYS 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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27A ASN* 5.9 2.7 - - - +
70A THR* 3.3 7.7 + - - +
71A HIS* 1.3 80.5 - - + +
73A GLN* 1.3 65.2 + - + +
75A VAL* 3.3 2.8 + - - +
76A GLU* 3.0 29.0 + - + +
100A IOD 3.8 23.8 - - + -
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Residues in contact with GLN 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 GLY 3.9 4.5 - - - +
69A ALA* 3.5 13.6 - - + -
70A THR* 3.0 45.1 + - - +
72A LYS* 1.3 79.1 - - + +
74A ALA* 1.3 57.7 + - - +
76A GLU* 3.3 6.9 + - - +
77A THR* 2.9 34.2 + - - +
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Residues in contact with ALA 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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22A VAL* 5.3 2.5 - - + -
35A ILE* 3.5 46.9 - - + -
66A LEU* 4.4 8.1 - - + +
69A ALA* 4.1 8.2 - - + +
70A THR 3.0 8.2 + - - +
71A HIS 3.6 6.3 - - - +
73A GLN* 1.3 76.0 - - - +
75A VAL* 1.3 64.2 + - + +
77A THR* 3.3 8.1 + - - -
78A LEU* 3.0 29.7 + - + +
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Residues in contact with VAL 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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22A VAL* 3.9 24.2 - - + -
71A HIS* 3.0 34.4 + - + +
72A LYS 3.7 4.0 - - - +
74A ALA* 1.3 75.9 - - - +
76A GLU* 1.3 57.7 + - + +
78A LEU* 3.3 9.5 + - + +
79A ARG* 3.0 52.6 + - + +
100A IOD 4.2 18.4 - - + -
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Residues in contact with GLU 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 LYS* 3.0 22.3 + - + +
73A GLN* 3.6 7.4 - - - +
75A VAL* 1.3 74.7 - - + +
77A THR* 1.3 60.0 + - - +
79A ARG* 3.2 28.7 + - - +
80A ASN* 2.8 40.7 + - + +
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Residues in contact with THR 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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61A VAL* 3.8 27.9 - - + +
64A VAL* 5.4 6.7 - - + +
66A LEU* 3.8 20.9 - - + +
73A GLN* 2.9 19.2 + - - +
74A ALA 3.3 5.6 + - - -
76A GLU* 1.3 76.6 - - - +
78A LEU* 1.3 63.6 + - - +
80A ASN* 3.6 8.9 + - - +
81A THR* 3.5 16.3 - - - +
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Residues in contact with LEU 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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18A LEU* 4.1 16.0 - - + +
20A ILE* 4.5 15.7 - - + +
22A VAL* 4.1 28.3 - - + -
35A ILE* 5.2 5.2 - - + -
58A VAL* 4.9 7.2 - - + -
61A VAL* 3.6 29.4 - - + -
66A LEU* 5.4 3.1 - - + -
74A ALA* 3.0 22.3 + - + +
75A VAL* 3.6 11.0 - - + +
77A THR* 1.3 77.6 - - - +
79A ARG* 1.3 53.7 + - + +
81A THR* 2.7 29.3 + - - +
87A LEU* 3.9 17.3 - - + -
97A IOD 4.1 17.6 - - + +
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Residues in contact with ARG 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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13A LYS* 3.4 13.9 + - - -
75A VAL* 3.0 38.7 + - + +
76A GLU* 3.2 30.7 + - - +
78A LEU* 1.3 75.7 - - + +
80A ASN* 1.3 54.3 + - - +
81A THR 2.7 16.7 + - - +
97A IOD 4.2 19.7 - - + -
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Residues in contact with ASN 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 GLU* 2.8 27.2 + - + +
77A THR* 3.6 6.4 + - - +
78A LEU 3.4 0.6 - - - -
79A ARG* 1.3 67.8 - - - +
81A THR* 1.3 64.3 + - - +
48F SER 4.3 10.0 - - - +
49F ASP 4.8 3.5 - - - +
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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