Contacts of the helix formed by residues 64 - 74 (chain E) in PDB entry 1F80
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 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E LEU 3.3 14.0 + - - +
25E GLU* 3.3 27.6 - - - +
26E ALA 3.5 9.9 - - - +
27E SER* 3.9 7.9 - - - -
28E PHE* 3.2 12.7 - - - -
63E ALA* 1.3 80.9 - - + +
65E VAL* 1.3 60.0 + - - +
66E GLY 4.1 0.2 - - - -
67E ASP* 2.8 45.7 + - - +
68E ALA 2.8 11.1 + - - -
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LEU* 4.0 20.9 - - + -
7E VAL* 4.2 6.5 - - + -
11E ILE* 3.5 27.4 - - + -
22E VAL* 3.9 24.9 - - + -
23E LYS 3.6 19.5 - - - +
24E LEU* 4.0 1.1 + - - -
26E ALA* 3.2 15.8 + - + +
28E PHE* 3.5 14.3 - - + -
32E LEU* 4.1 8.5 - - + -
64E THR* 1.3 74.4 - - - +
66E GLY* 1.3 57.9 + - - +
68E ALA* 3.1 3.2 + - - +
69E VAL* 2.9 27.1 + - + +
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Residues in contact with GLY 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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24E LEU* 2.9 46.0 + - - -
64E THR* 4.1 0.4 - - - -
65E VAL* 1.3 77.0 - - - +
67E ASP* 1.3 58.4 + - - +
69E VAL* 3.6 1.1 - - - +
70E ASN* 2.8 39.8 + - - +
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Residues in contact with ASP 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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61E LYS 4.3 5.5 - - - +
62E ILE* 3.0 31.7 - - + +
63E ALA* 3.2 13.4 + - - +
64E THR* 2.8 45.1 + - - +
66E GLY* 1.3 76.2 - - - +
68E ALA* 1.3 55.3 + - - +
70E ASN* 4.0 8.5 + - - +
71E TYR* 3.0 23.2 + - - +
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Residues in contact with ALA 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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7E VAL* 4.6 12.6 - - + -
28E PHE* 3.8 20.0 - - + -
36E PN2 5.2 1.3 - - - -
46E LEU* 4.7 16.4 - - + -
62E ILE* 3.8 10.0 - - - +
64E THR 2.8 10.8 + - - +
65E VAL* 3.2 9.9 - - - +
66E GLY 3.1 0.2 - - - -
67E ASP* 1.3 74.6 - - - +
69E VAL* 1.3 67.6 + - - +
71E TYR* 3.2 4.2 + - - +
72E ILE* 2.9 31.8 + - + +
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Residues in contact with VAL 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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1E ALA 5.8 2.0 - - - +
3E THR* 3.4 20.9 - - - +
4E LEU* 4.1 37.0 - - + +
7E VAL* 4.4 9.9 - - + -
24E LEU* 4.1 10.3 - - + -
65E VAL* 2.9 20.6 + - + +
66E GLY* 3.6 7.6 - - - +
68E ALA* 1.3 74.6 - - - +
70E ASN* 1.3 66.8 + - - +
72E ILE* 3.0 11.6 + - - +
73E GLN* 2.8 37.2 + - - +
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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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66E GLY* 2.8 26.6 + - - +
67E ASP* 4.0 8.1 + - - +
69E VAL* 1.3 74.4 - - - +
71E TYR* 1.3 62.9 + - - +
73E GLN* 3.5 19.3 + - - +
74E ASN* 2.4 39.8 + - - +
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Residues in contact with TYR 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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52E MET* 4.0 27.6 - - + +
53E GLU 3.6 16.2 + - - -
54E ILE* 4.2 14.6 - - + -
58E ASP* 3.3 42.9 + - + +
61E LYS* 5.0 19.7 - - + +
62E ILE* 4.0 28.3 - - + -
67E ASP 3.0 19.4 + - - +
68E ALA 3.5 4.3 - - - +
70E ASN* 1.3 78.3 - - - +
72E ILE* 1.3 68.8 + - + +
74E ASN* 3.4 17.1 + - - +
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Residues in contact with ILE 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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3E THR* 4.5 11.0 - - + -
7E VAL* 3.4 33.0 - - + -
46E LEU* 4.7 13.5 - - + -
50E PHE* 3.6 46.2 - - + -
52E MET* 3.8 35.6 - - + +
54E ILE* 6.4 0.7 - - + -
68E ALA* 2.9 20.5 + - + +
69E VAL* 3.4 7.0 - - - +
71E TYR* 1.3 79.0 - - + +
73E GLN* 1.3 62.0 + - - +
74E ASN 3.1 10.9 + - - +
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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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1E ALA 4.8 10.3 - - - +
3E THR* 4.3 16.7 + - + +
69E VAL* 2.8 36.9 + - - +
70E ASN* 3.8 22.7 - - - +
71E TYR 3.4 0.2 - - - -
72E ILE* 1.3 74.5 - - - +
74E ASN* 1.3 65.6 + - + +
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Residues in contact with ASN 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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52E MET* 5.6 1.7 - - - +
70E ASN* 2.4 38.1 + - - +
71E TYR* 3.4 13.1 + - - +
72E ILE 3.1 7.7 + - - +
73E GLN* 1.3 86.6 + - + +
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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