Contacts of the helix formed by residues 56 - 70 (chain E) in PDB entry 4LQL
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 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E PRO* 5.2 10.3 - - + -
55E THR* 1.3 93.2 + - - +
57E ALA* 1.3 62.2 + - - +
58E ASP* 4.6 6.6 - - - +
59E SER* 3.6 20.7 + - - -
60E ILE* 3.6 22.0 + - - +
88E ASN* 4.0 7.6 - - - -
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Residues in contact with ALA 57 (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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199B GLN* 5.8 3.8 - - - +
56E THR* 1.3 73.2 - - - +
58E ASP* 1.3 63.3 + - - +
59E SER 2.7 5.3 + - - -
60E ILE* 2.7 26.7 + - - +
61E THR* 2.9 17.4 + - - +
87E LYS 5.5 0.2 - - - +
88E ASN* 3.1 40.6 - - - +
91E ARG* 6.3 2.5 - - + -
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Residues in contact with ASP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B HIS* 6.4 2.7 - - - -
177B LYS* 5.9 3.3 - - - -
56E THR* 4.6 5.8 - - - +
57E ALA* 1.3 77.2 + - - +
59E SER* 1.3 57.3 + - - +
61E THR* 4.0 11.1 - - - -
62E LYS* 3.3 22.5 + - - +
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LEU* 4.5 16.5 - - - +
53E VAL 4.5 14.0 + - - -
54E ALA* 5.2 2.9 - - - -
55E THR* 5.0 2.2 - - - -
56E THR* 3.6 26.1 + - - -
57E ALA 2.7 6.3 + - - -
58E ASP* 1.3 76.3 - - - +
60E ILE* 1.3 59.2 + - - +
62E LYS* 3.2 6.6 + - - +
63E PHE* 2.8 35.0 + - - -
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Residues in contact with ILE 60 (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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54E ALA* 4.4 17.3 - - + -
55E THR 5.3 2.2 - - - +
56E THR 3.6 13.5 - - - +
57E ALA 2.7 11.2 + - - +
59E SER* 1.3 70.2 - - - +
61E THR* 1.3 60.0 + - - +
62E LYS 2.9 5.2 + - - -
63E PHE* 4.2 7.9 - - + +
64E MET* 3.0 34.2 + - + +
88E ASN* 3.1 25.6 - - + +
89E TRP* 3.3 70.9 - - + +
92E GLY* 4.0 9.1 - - - -
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Residues in contact with THR 61 (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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175B HIS* 6.1 2.7 - - - +
57E ALA* 2.9 18.4 + - - +
58E ASP* 4.2 9.0 - - - -
60E ILE* 1.3 76.2 - - - +
62E LYS* 1.3 57.7 + - - +
65E LYS* 3.1 31.5 - - + +
91E ARG* 4.0 30.2 - - + +
92E GLY* 4.5 8.9 + - - +
95E LEU* 4.9 8.5 - - + -
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Residues in contact with LYS 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ASP 3.3 19.6 + - - +
59E SER* 3.3 8.5 - - - +
60E ILE 2.9 0.4 - - - -
61E THR* 1.3 80.3 - - - +
63E PHE* 1.3 56.5 + - + +
65E LYS* 4.7 0.7 - - - -
66E GLU* 2.8 45.6 + - + +
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Residues in contact with PHE 63 (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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10E TRP* 4.6 7.7 - - + -
12E VAL* 4.1 27.1 - - + -
51E LYS* 5.9 3.1 - - + -
52E LEU* 4.5 22.7 - - + -
54E ALA* 5.6 5.8 - - + -
59E SER* 2.8 27.5 + - - +
60E ILE* 4.0 9.2 - - + +
62E LYS* 1.3 74.1 - - + +
64E MET* 1.3 71.6 + - + +
66E GLU* 3.1 8.7 + - - +
67E ALA* 3.3 10.6 + - - +
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Residues in contact with MET 64 (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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60E ILE* 3.0 23.3 + - + +
63E PHE* 1.3 79.6 - - + +
65E LYS* 1.3 62.7 + - - +
67E ALA* 3.3 18.7 - - - +
68E ASN* 3.4 12.0 + - - +
76E VAL* 5.5 4.0 - - + -
89E TRP* 5.9 4.9 - - + -
92E GLY* 3.7 29.8 - - - +
93E THR* 4.7 0.9 - - - +
95E LEU* 5.4 2.0 - - + -
96E LEU* 3.8 32.3 - - + +
100E LEU* 5.2 5.8 - - + -
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Residues in contact with LYS 65 (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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68B ASN* 5.1 13.9 - - + +
69B TYR* 3.8 15.4 - - + -
71B ASP* 5.8 3.6 - - - +
61E THR* 3.1 27.9 + - + +
62E LYS 3.6 1.5 + - - +
63E PHE 3.2 1.0 - - - -
64E MET* 1.3 77.4 - - - +
66E GLU* 1.3 65.3 + - - +
68E ASN* 3.2 34.2 - - + +
69E TYR 3.4 4.3 + - - -
95E LEU* 4.4 24.0 - - + +
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Residues in contact with GLU 66 (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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69B TYR* 3.8 29.8 + - + +
10E TRP* 4.0 16.4 - - + -
62E LYS* 2.8 29.1 + - + +
63E PHE* 3.1 4.2 + - - +
65E LYS* 1.3 69.5 - - + +
67E ALA* 1.3 69.6 + - - +
69E TYR* 3.7 2.8 - - - +
70E ASN* 3.3 20.3 + - - +
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Residues in contact with ALA 67 (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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10E TRP* 3.8 15.0 - - + -
63E PHE 3.3 8.5 + - - +
64E MET* 3.3 12.8 - - - +
66E GLU* 1.3 73.2 - - - +
68E ASN* 1.3 57.2 + - - +
69E TYR 2.5 17.3 + - - -
70E ASN 2.7 23.5 + - - +
73E VAL* 4.0 24.7 - - + -
76E VAL* 5.1 10.8 - - + -
96E LEU* 6.1 0.9 - - + -
98E LYS* 4.2 16.2 - - + -
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Residues in contact with ASN 68 (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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65B LYS* 4.3 12.1 - - - +
68B ASN* 5.1 13.6 - - + +
69B TYR* 6.0 0.9 - - + -
97B GLN* 5.0 7.3 - - - +
64E MET 3.4 12.7 + - - +
65E LYS* 3.2 24.1 + - + +
67E ALA* 1.3 75.8 - - - +
69E TYR* 1.3 64.5 + - - +
71E ASP* 4.3 3.5 - - - +
95E LEU* 2.8 23.9 + - - +
96E LEU* 4.3 0.7 - - - +
97E GLN* 3.2 41.6 + - + +
98E LYS* 4.3 16.9 - - - +
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Residues in contact with TYR 69 (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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65B LYS* 3.3 24.2 - - + +
66B GLU* 3.1 45.2 - - + +
69B TYR* 3.3 60.7 - + + +
65E LYS 3.4 0.8 + - - -
66E GLU 3.7 2.2 - - - +
67E ALA 2.5 4.9 + - - -
68E ASN* 1.3 77.3 - - - +
70E ASN* 1.3 63.0 - - + +
71E ASP* 2.7 35.2 + - - +
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Residues in contact with ASN 70 (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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10E TRP* 4.6 17.7 - - + -
66E GLU 3.3 12.8 + - - +
67E ALA 2.7 13.5 + - - +
69E TYR* 1.3 79.8 - - + +
71E ASP* 1.3 64.3 + - - +
72E ASP* 2.9 27.2 + - - -
73E VAL* 3.1 17.9 + - - +
98E LYS* 3.5 1.6 + - - -
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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