Contacts of the helix formed by residues 70 - 80 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E GLY* 4.2 0.9 - - - -
26E VAL* 3.8 17.7 - - + -
27E ASN* 3.5 26.7 - - + +
68E GLY 4.7 0.9 - - - +
69E ALA* 1.3 79.4 - - - +
71E HIS* 1.3 65.9 + - - +
72E LYS* 3.6 5.7 + - - +
73E GLN* 3.0 39.2 + - - +
74E ALA* 3.0 17.8 + - - +
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Residues in contact with HIS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 3.1 31.6 + - + +
23E THR* 4.1 2.2 - - - -
24E GLY 3.0 41.1 + - - +
25E GLY* 4.4 0.2 - - - -
27E ASN* 3.0 19.2 + - - +
28E THR* 4.5 6.5 - - + -
35E ILE* 5.5 0.9 - - + -
70E THR* 1.3 72.8 - - - +
72E LYS* 1.3 84.0 + - + +
74E ALA* 3.3 5.8 + - - +
75E VAL* 3.1 43.7 + - + +
99E IOD 4.2 9.3 - - + +
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Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ASN* 5.1 4.2 - - - +
70E THR* 3.3 6.0 + - - +
71E HIS* 1.3 101.0 + - + +
73E GLN* 1.3 59.0 + - + +
75E VAL* 3.4 24.7 + - - +
76E GLU* 2.9 41.3 + - + +
79E ARG* 5.5 1.6 - - - +
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Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLY 4.0 3.3 - - - +
69E ALA* 3.4 14.1 - - + -
70E THR* 3.0 43.8 + - - +
72E LYS* 1.3 75.8 - - + +
74E ALA* 1.3 61.0 + - - +
76E GLU* 3.3 6.1 + - - +
77E THR* 2.8 35.8 + - - +
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Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 5.0 3.6 - - + -
35E ILE* 3.6 44.2 - - + -
66E LEU* 4.6 9.0 - - + +
69E ALA* 4.0 9.7 - - + +
70E THR 3.0 9.9 + - - +
71E HIS 3.6 7.2 - - - +
73E GLN* 1.3 76.3 - - - +
75E VAL* 1.3 62.6 + - - +
77E THR* 3.2 8.3 + - - -
78E LEU* 3.0 29.4 + - + +
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 4.0 14.8 - - + -
71E HIS* 3.1 37.9 + - + +
72E LYS* 3.7 22.4 - - + +
74E ALA* 1.3 74.5 - - - +
76E GLU* 1.3 62.5 + - - +
78E LEU* 3.3 12.5 + - - +
79E ARG* 3.0 56.1 + - - +
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Residues in contact with GLU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LYS* 2.9 28.2 + - + +
73E GLN* 3.8 6.3 - - - +
75E VAL* 1.3 76.0 - - - +
77E THR* 1.3 59.4 + - - +
79E ARG* 3.1 31.9 + - - +
80E ASN* 2.8 57.5 + - - +
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Residues in contact with THR 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 3.9 20.8 - - + +
64E VAL* 5.7 6.5 - - + +
66E LEU* 3.9 25.7 - - + +
73E GLN* 2.8 28.6 + - - +
74E ALA 3.5 4.5 - - - -
76E GLU* 1.3 74.1 - - - +
78E LEU* 1.3 62.5 + - - +
80E ASN* 3.6 8.6 + - - +
81E THR* 3.3 18.4 - - - +
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 4.1 20.7 - - + +
20E ILE* 4.8 15.7 - - + +
22E VAL* 3.8 34.5 - - + -
35E ILE* 5.5 3.1 - - + -
58E VAL* 4.8 8.1 - - + -
61E VAL* 3.6 26.9 - - + -
66E LEU* 5.6 1.6 - - + -
74E ALA* 3.0 18.6 + - + +
75E VAL* 3.5 9.2 - - - +
77E THR* 1.3 77.5 - - - +
79E ARG* 1.3 56.6 + - - +
81E THR* 2.8 26.1 + - - +
87E LEU* 4.1 16.4 - - + -
98E IOD 4.1 8.8 - - - +
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Residues in contact with ARG 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LYS* 3.8 9.2 + - - +
16E ASN* 6.0 3.1 - - - +
72E LYS* 5.5 1.6 - - - +
75E VAL* 3.0 44.9 + - - +
76E GLU* 3.1 29.4 + - - +
78E LEU* 1.3 77.1 - - - +
80E ASN* 1.3 61.4 + - - +
81E THR* 3.0 12.3 + - - +
98E IOD 4.4 6.1 - - - -
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Residues in contact with ASN 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER 3.9 8.8 - - - +
49A ASP 4.6 4.9 - - - +
76E GLU* 2.8 42.4 + - - +
77E THR* 3.6 5.6 + - - +
78E LEU 3.3 1.0 - - - -
79E ARG* 1.3 77.4 - - - +
81E THR* 1.3 63.7 + - - +
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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