Contacts of the helix formed by residues 64 - 73 (chain E) in PDB entry 2FPO
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 64 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ILE* 4.2 0.2 - - - -
61E ALA* 2.8 24.2 + - - -
62E GLY 3.1 2.0 + - - -
63E SER* 1.3 73.0 - - - +
65E ALA* 1.3 59.8 + - - +
66E LEU 3.1 3.4 - - - -
67E GLY* 3.9 7.0 - - - -
68E LEU* 2.7 39.3 + - - +
80E LEU* 5.3 1.1 - - - -
91E LEU* 3.9 17.7 - - - -
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Residues in contact with ALA 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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12E ILE* 3.6 20.2 - - + +
36E THR 6.3 0.4 - - - +
40E ARG* 3.3 35.6 + - + +
61E ALA 4.2 2.0 + - - -
63E SER* 3.4 5.0 + - - +
64E GLY* 1.3 76.0 - - - +
66E LEU* 1.3 60.7 + - + +
69E GLU* 3.2 26.0 + - - +
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Residues in contact with LEU 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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39E VAL* 5.3 5.8 - - + -
40E ARG* 3.7 26.5 - - + -
43E LEU* 4.2 8.1 - - + -
44E PHE* 3.3 22.0 - - + -
58E ASP* 3.5 15.0 + - - +
60E PHE 6.2 0.2 - - - +
61E ALA 5.3 0.4 + - - -
64E GLY 3.1 0.6 - - - -
65E ALA* 1.3 78.6 - - + +
67E GLY* 1.3 60.9 + - - +
69E GLU 3.5 0.3 + - - -
70E ALA* 2.9 26.9 + - - +
125E PHE* 3.8 38.4 - - + -
127E ASP* 5.1 10.1 - - + +
155E TYR* 4.0 21.8 - - + -
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Residues in contact with GLY 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ASP* 3.8 7.1 + - - -
64E GLY* 3.3 5.4 + - - -
66E LEU* 1.3 80.0 - - - +
68E LEU* 1.3 61.1 + - - +
70E ALA* 3.3 6.8 + - - +
71E LEU* 3.1 32.7 + - - +
78E ALA* 4.7 2.4 - - - +
80E LEU* 3.8 28.5 - - - -
125E PHE* 4.7 4.7 - - - -
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Residues in contact with LEU 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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12E ILE* 4.2 9.0 - - + -
14E ILE* 4.1 16.3 - - + +
19E TRP* 3.8 5.9 - - + -
24E LEU* 4.0 24.0 - - + -
63E SER 3.8 16.8 - - - +
64E GLY 2.7 26.9 + - - +
65E ALA 4.8 0.7 - - - +
67E GLY* 1.3 71.7 - - - -
69E GLU* 1.3 55.5 + - - +
71E LEU* 3.5 7.5 + - + -
72E SER* 2.9 29.6 + - - -
80E LEU* 5.0 1.8 - - + +
91E LEU* 4.1 13.9 - - + -
94E ASN* 4.6 8.1 - - + +
95E LEU* 3.5 37.0 - - + +
98E LEU* 4.0 14.6 - - + -
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Residues in contact with GLU 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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14E ILE* 3.7 7.3 - - - +
15E ILE* 3.0 28.3 + - + +
16E GLY 2.7 31.2 + - - +
40E ARG* 3.0 21.2 + - - -
44E PHE* 3.7 24.0 - - + -
65E ALA 3.2 20.1 + - - +
66E LEU 3.7 3.8 - - - +
67E GLY 3.3 0.6 - - - -
68E LEU* 1.3 78.6 - - - +
70E ALA* 1.3 61.8 + - - +
72E SER* 3.3 4.0 + - - -
73E ARG* 2.8 51.9 + - - +
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Residues in contact with ALA 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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44E PHE* 3.7 14.0 - - + -
51E ILE* 3.8 21.0 - - + +
56E CYS* 4.0 19.3 - - + -
66E LEU 2.9 17.8 + - - +
67E GLY* 3.3 6.3 + - - +
69E GLU* 1.3 75.0 - - - +
71E LEU* 1.3 61.7 + - + +
73E ARG* 3.1 12.0 + - - +
74E TYR 3.2 0.5 + - - -
75E ALA* 3.0 22.6 + - + +
125E PHE* 4.2 7.2 - - + -
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Residues in contact with LEU 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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85D ARG* 5.0 0.7 + - - -
18E GLN* 3.2 12.6 + - - -
19E TRP* 3.6 17.7 - - + -
67E GLY 3.1 20.1 + - - +
68E LEU* 3.8 5.6 - - + +
70E ALA* 1.3 72.5 - - - +
72E SER* 1.3 66.6 + - - +
74E TYR* 2.9 13.3 + - - -
75E ALA* 4.0 8.6 + - + +
77E GLY* 4.1 4.3 - - - +
78E ALA* 3.9 21.3 - - + +
80E LEU* 5.0 1.8 - - + -
95E LEU* 3.8 18.6 - - + -
100E ALA* 4.7 4.0 - - + -
102E ASN* 3.5 44.1 + - - +
103E ALA* 3.8 22.0 - - + -
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Residues in contact with SER 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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14E ILE* 3.4 11.8 - - - +
16E GLY 2.7 26.0 + - - -
17E GLY* 3.3 1.2 - - - -
18E GLN* 2.8 32.9 + - - +
19E TRP* 2.9 41.0 + - - -
68E LEU 2.9 18.6 + - - -
69E GLU 3.5 5.4 - - - -
71E LEU* 1.3 75.2 - - - +
73E ARG* 1.3 56.8 - - - +
74E TYR* 3.2 6.6 + - - -
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Residues in contact with ARG 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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15E ILE* 3.8 17.0 - - - +
16E GLY* 3.4 18.9 - - - +
17E GLY* 4.0 15.5 - - - +
41E GLU* 5.2 7.5 + - - +
44E PHE* 3.5 46.4 + - - +
45E ASN* 4.8 5.3 + - - +
48E ALA* 5.8 2.6 - - - +
51E ILE* 3.7 31.3 - - + +
52E VAL* 3.8 5.2 - - - +
69E GLU* 2.8 42.9 + - - +
70E ALA 3.1 8.7 + - - +
72E SER* 1.3 76.2 - - - +
74E TYR* 1.3 75.5 + - - +
75E ALA 3.5 0.5 + - - -
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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