Contacts of the helix formed by residues 103 - 118 (chain E) in PDB entry 1FPY
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 ASP 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E PHE* 6.1 0.2 - - - +
22E THR 4.5 4.5 + - - +
57E TRP* 4.6 3.6 - - - -
89E CYS 5.5 0.3 - - - +
90E ASP* 3.8 6.8 - - - +
91E ILE* 2.9 53.2 + - + +
100E TYR* 3.1 18.9 + - + +
102E ARG* 1.3 74.5 - - - +
104E PRO* 1.3 62.4 - - - +
105E ARG* 2.9 18.6 + - - +
106E SER* 2.8 47.2 + - - -
107E ILE* 3.0 13.0 + - - +
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Residues in contact with PRO 104 (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 THR* 3.5 16.6 - - + +
23E ASP 3.7 20.4 - - - +
24E THR* 4.0 8.3 - - - +
57E TRP* 4.2 5.4 - - + -
102E ARG 3.0 12.5 - - - +
103E ASP* 1.3 89.4 - - - +
105E ARG* 1.3 56.5 + - - +
107E ILE* 3.4 6.0 + - + +
108E ALA 3.0 22.7 + - - -
366E ASN* 3.8 15.3 - - - +
368E TYR* 3.4 23.0 - - + +
369E LEU* 3.6 27.4 - - + +
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Residues in contact with ARG 105 (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 THR* 5.5 3.8 + - - +
70E ASP* 3.1 33.1 + - - +
73E THR* 3.5 12.5 - - - +
88E ARG* 3.8 13.6 - - - +
89E CYS 4.0 14.8 + - - +
90E ASP* 3.1 31.6 + - - +
103E ASP* 2.9 15.8 + - - +
104E PRO* 1.3 76.6 - - - +
106E SER* 1.3 66.8 + - - +
108E ALA* 3.3 2.6 + - - +
109E LYS* 3.1 36.6 + - + +
229E THR* 4.6 11.1 - - + +
233E ASP* 2.9 37.7 + - - -
368E TYR* 3.9 31.7 - - + -
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Residues in contact with SER 106 (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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90E ASP* 4.6 7.7 + - - +
91E ILE 3.9 1.9 + - - -
92E LEU* 4.8 1.2 - - - +
98E GLN 5.1 0.3 + - - -
99E GLY* 3.8 22.1 - - - -
100E TYR 3.8 14.6 - - - -
103E ASP* 2.8 28.0 + - - -
105E ARG* 1.3 76.1 - - - +
107E ILE* 1.3 52.4 + - - +
109E LYS* 3.0 13.5 + - - +
110E ARG* 2.7 45.4 + - - +
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Residues in contact with ILE 107 (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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100E TYR 5.0 0.7 - - - +
101E ASP 3.6 24.7 - - - +
102E ARG* 4.4 5.6 - - - +
103E ASP 3.0 15.7 + - - +
104E PRO* 3.5 10.3 - - + +
106E SER* 1.3 77.3 - - - +
108E ALA* 1.3 62.1 + - - +
110E ARG* 3.4 13.0 + - - +
111E ALA* 3.1 19.4 + - - +
369E LEU* 4.1 19.5 - - + -
372E ALA* 4.7 2.5 - - + -
433E VAL* 3.6 19.9 - - + +
434E PHE* 3.5 46.4 - - + -
438E ALA* 4.7 5.6 - - + -
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Residues in contact with ALA 108 (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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104E PRO 3.0 14.1 + - - +
105E ARG 3.6 7.6 - - - +
106E SER 3.2 0.4 - - - -
107E ILE* 1.3 78.4 - - - +
109E LYS* 1.3 63.2 + - - +
111E ALA* 3.4 1.8 + - - -
112E GLU* 3.1 16.6 + - - +
228E MET* 3.5 26.7 - - + +
229E THR* 3.5 18.5 + - - +
368E TYR* 3.9 28.0 - - + +
372E ALA* 4.7 3.4 - - - -
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Residues in contact with LYS 109 (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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70E ASP* 4.3 6.7 + - - -
90E ASP* 3.1 38.4 + - - +
105E ARG* 3.1 36.0 + - + +
106E SER* 3.0 11.1 + - - +
108E ALA* 1.3 73.8 - - - +
110E ARG* 1.3 67.2 + - - +
112E GLU* 2.9 9.0 + - - +
113E ASP* 2.9 31.9 + - - +
229E THR* 4.0 20.2 - - + +
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Residues in contact with ARG 110 (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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99E GLY* 3.1 24.5 + - - -
100E TYR 3.9 3.5 + - - -
101E ASP* 3.0 33.7 + - - +
106E SER* 2.7 26.0 + - - +
107E ILE* 3.5 12.6 - - - +
109E LYS* 1.3 72.6 - - - +
111E ALA* 1.3 62.3 + - - +
113E ASP* 3.1 13.3 + - - +
114E TYR* 3.0 23.7 + - - +
431E GLY 5.5 1.7 - - - +
432E GLY 3.5 18.9 + - - -
433E VAL* 3.0 37.9 + - + +
435E THR* 3.5 20.0 - - - +
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Residues in contact with ALA 111 (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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107E ILE 3.1 9.8 + - - +
108E ALA 3.5 9.0 - - - +
110E ARG* 1.3 80.3 - - - +
112E GLU* 1.3 60.0 + - - +
114E TYR* 3.6 3.4 + - - +
115E LEU* 3.2 15.8 + - - +
228E MET* 4.2 14.6 - - + -
372E ALA* 4.2 8.1 - - + -
375E LEU* 3.7 19.0 - - + +
376E MET* 4.0 13.5 - - - -
433E VAL* 3.7 23.7 - - + +
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Residues in contact with GLU 112 (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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108E ALA 3.1 16.2 + - - +
109E LYS* 2.9 12.0 + - - +
111E ALA* 1.3 72.9 - - - +
113E ASP* 1.3 66.5 + - - +
115E LEU* 3.3 19.1 + - - +
116E ARG* 3.5 29.3 + - - +
123E THR* 4.9 4.2 - - - +
124E VAL* 4.0 22.3 + - + +
227E THR* 3.8 13.7 + - - -
228E MET* 3.9 24.9 + - + +
229E THR* 3.1 39.9 + - - +
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Residues in contact with ASP 113 (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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109E LYS* 2.9 24.4 + - - +
110E ARG* 3.3 12.9 + - - +
112E GLU* 1.3 72.9 - - - +
114E TYR* 1.3 51.3 + - - +
115E LEU 3.0 4.0 - - - -
116E ARG* 3.0 30.6 + - - +
117E ALA* 2.8 34.2 + - - +
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Residues in contact with TYR 114 (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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110E ARG 3.0 15.6 + - - +
111E ALA 3.7 4.3 - - - +
113E ASP* 1.3 76.1 - - - +
115E LEU* 1.3 61.3 + - - +
117E ALA* 3.7 10.3 - - + -
118E THR* 3.1 40.8 + - + +
376E MET* 4.3 11.4 - - + -
379E LEU* 3.6 31.2 - - + -
383E LYS* 3.1 27.3 - - - +
430E ALA* 3.6 18.0 - - + +
431E GLY* 3.1 42.8 - - - +
433E VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 115 (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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111E ALA 3.2 12.2 + - - +
112E GLU* 3.3 13.9 - - - +
113E ASP 3.0 0.6 - - - -
114E TYR* 1.3 77.0 - - - +
116E ARG* 1.3 60.6 + - - +
118E THR* 3.0 19.5 + - - +
119E GLY 3.5 2.9 + - - -
120E ILE* 3.8 4.0 + - + -
121E ALA* 3.2 54.5 - - + +
122E ASP 4.1 2.2 - - - -
123E THR* 3.7 15.0 - - - +
124E VAL* 3.8 26.2 - - + -
274E LEU* 3.8 7.4 - - + -
375E LEU* 4.4 1.6 - - + -
379E LEU* 3.3 41.3 - - + -
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Residues in contact with ARG 116 (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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112E GLU* 3.5 28.2 + - - +
113E ASP* 3.0 33.4 + - - +
115E LEU* 1.3 78.4 - - - +
117E ALA* 1.3 57.8 + - - +
119E GLY* 3.0 18.9 + - - -
121E ALA 3.4 5.8 - - - +
122E ASP* 3.3 50.4 + - + +
123E THR* 4.7 6.7 - - - +
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Residues in contact with ALA 117 (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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113E ASP 2.8 16.7 + - - +
114E TYR* 3.7 13.0 - - + +
116E ARG* 1.3 74.1 - - - +
118E THR* 1.3 58.0 + - + +
119E GLY* 2.9 9.7 + - - -
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Residues in contact with THR 118 (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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114E TYR* 3.1 46.9 + - + +
115E LEU* 3.0 13.7 + - - +
117E ALA* 1.3 74.9 - - + +
119E GLY* 1.3 52.6 + - - +
120E ILE* 2.7 47.7 + - + +
379E LEU* 4.9 0.3 - - - +
383E LYS* 4.8 9.4 - - + -
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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