Contacts of the helix formed by residues 113 - 123 (chain E) in PDB entry 1FQV
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 PRO 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E SER 3.8 5.1 - - - +
112E LEU* 1.3 103.6 - - + +
114E ASP* 1.3 66.0 + - - +
115E GLU* 4.2 11.0 - - + +
116E LEU* 3.0 32.9 + - + -
117E LEU* 3.2 9.9 + - - +
138E ARG* 3.8 1.1 + - - +
105F LEU* 5.1 5.4 - - + -
108F ASN* 5.5 2.7 - - - +
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Residues in contact with ASP 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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113E PRO* 1.3 71.3 - - - +
115E GLU* 1.3 75.5 + - - +
116E LEU 3.4 0.3 + - - -
117E LEU* 3.6 2.6 + - - +
118E LEU* 3.4 27.3 + - + +
138E ARG* 2.5 40.6 + - - +
141E ARG* 3.9 13.5 + - - -
142E LEU* 3.4 29.3 - - + +
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Residues in contact with GLU 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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113E PRO* 3.1 8.3 - - + +
114E ASP* 1.3 96.2 + - - +
116E LEU* 1.3 65.3 + - + +
118E LEU* 3.7 11.9 + - + +
119E GLY* 3.4 14.0 + - - -
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Residues in contact with LEU 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 LEU* 3.5 34.1 - - + -
113E PRO* 3.0 26.8 + - + +
115E GLU* 1.3 80.3 - - + +
117E LEU* 1.3 67.4 + - - +
118E LEU 3.1 2.0 - - - -
119E GLY* 2.9 11.5 + - - +
120E ILE* 3.0 17.7 + - + +
104F ILE* 5.0 7.9 - - + -
105F LEU* 4.7 6.5 - - + -
108F ASN* 3.3 47.3 - - + +
116F LEU* 4.8 15.0 - - + -
120F CYS* 5.4 2.2 - - - -
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Residues in contact with LEU 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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109E TRP* 4.9 5.8 - - + +
112E LEU* 4.0 21.3 - - + +
113E PRO 3.2 11.4 + - - +
114E ASP 4.1 1.6 - - - +
115E GLU 3.5 0.2 - - - -
116E LEU* 1.3 76.2 - - - +
118E LEU* 1.3 53.3 + - - +
120E ILE* 3.0 14.0 + - + +
121E PHE* 2.7 50.3 + - + -
138E ARG* 3.3 37.7 - - - +
139E TRP* 3.6 44.0 - - + +
142E LEU* 3.6 23.8 - - + -
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Residues in contact with LEU 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 ASP* 3.4 16.0 + - + +
115E GLU* 3.7 12.8 - - - +
116E LEU 3.1 0.4 - - - -
117E LEU* 1.3 76.7 - - - +
119E GLY* 1.3 53.7 + - - +
121E PHE* 3.6 4.2 - - + +
122E SER* 2.7 36.8 + - - -
142E LEU* 3.6 42.2 - - + +
145E ASP* 3.4 34.3 - - + +
147E SER* 3.8 11.7 - - - +
148E LEU* 3.9 12.8 - - + +
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Residues in contact with GLY 119 (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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115E GLU 3.4 7.7 + - - -
116E LEU* 2.9 9.3 + - - -
118E LEU* 1.3 78.4 - - - +
120E ILE* 1.3 62.0 + - - +
122E SER* 2.5 26.6 + - - -
123E CYS* 3.4 10.9 + - - -
120F CYS* 4.8 9.2 - - - -
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Residues in contact with ILE 120 (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 TRP* 4.7 9.4 - - + -
112E LEU* 3.5 31.4 - - + -
116E LEU* 3.0 10.0 + - + +
117E LEU* 3.4 16.4 - - + +
119E GLY* 1.3 74.8 - - - +
121E PHE* 1.3 69.9 + - + +
123E CYS* 3.0 19.2 + - - +
124E LEU* 3.7 7.7 + - + +
139E TRP* 6.1 0.7 - - + -
104F ILE* 4.9 5.4 - - + -
120F CYS* 4.1 34.3 - - + +
123F VAL* 4.1 29.8 - - + -
124F ALA* 4.3 4.1 - - - +
127F ILE* 4.4 16.6 - - + -
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Residues in contact with PHE 121 (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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117E LEU* 2.7 34.7 + - + +
118E LEU* 3.6 4.9 - - + +
120E ILE* 1.3 75.3 - - + +
122E SER* 1.3 56.3 + - - +
123E CYS 2.9 5.2 - - - -
124E LEU* 2.8 42.7 + - + +
129E LEU* 4.1 11.7 - - + +
132E VAL* 4.0 7.6 - - + -
139E TRP* 3.4 76.5 - + + -
142E LEU* 3.9 16.4 - - + -
143E ALA* 3.8 24.5 - - + -
148E LEU* 3.9 16.4 - - + -
427E ARG* 4.4 2.8 + - - -
127F ILE* 5.1 0.7 - - + -
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Residues in contact with SER 122 (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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118E LEU 2.7 17.4 + - - -
119E GLY* 2.5 24.1 + - - -
121E PHE* 1.3 72.4 - - - +
123E CYS* 1.3 60.2 + - - +
124E LEU 3.2 1.8 + - - +
148E LEU* 3.8 16.5 - - - +
427E ARG* 3.9 28.3 + - - +
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Residues in contact with CYS 123 (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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119E GLY 3.5 14.1 - - - -
120E ILE 3.0 10.7 + - - +
121E PHE 2.9 1.2 - - - -
122E SER* 1.3 82.0 + - - +
124E LEU* 1.3 61.6 + - - +
125E CYS 4.0 0.9 + - - -
117F ASP* 4.8 4.3 - - - -
120F CYS* 4.0 18.2 - - - -
121F LYS* 3.7 34.1 - - + +
124F ALA* 3.8 19.3 - - + +
128F LYS* 4.2 9.7 + - - -
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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