Contacts of the helix formed by residues 113 - 123 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C SER 3.8 3.8 - - - +
112C LEU* 1.3 88.2 - - + +
114C ASP* 1.3 65.7 + - - +
115C GLU* 3.0 12.6 - - + +
116C LEU* 2.9 49.5 + - + -
117C LEU* 3.2 9.9 + - - +
138C ARG* 3.8 1.3 + - - +
105D LEU* 4.6 6.5 - - + -
108D ASN* 5.3 3.4 - - - +
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 1.3 72.1 - - - +
115C GLU* 1.3 75.6 + - - +
116C LEU 3.4 0.3 + - - -
117C LEU* 3.5 2.8 + - - +
118C LEU* 3.3 28.0 + - + +
138C ARG* 2.4 40.7 + - - +
141C ARG* 3.7 14.0 + - - -
142C LEU* 3.4 28.5 - - + +
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PRO* 3.0 9.8 - - + +
114C ASP* 1.3 95.5 + - - +
116C LEU* 1.3 65.1 + - + +
118C LEU* 3.8 12.7 - - + +
119C GLY* 3.4 14.2 + - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 3.5 23.8 - - + -
113C PRO* 2.9 37.4 + - + +
115C GLU* 1.3 81.8 - - + +
117C LEU* 1.3 64.8 + - - +
118C LEU 3.1 1.8 - - - -
119C GLY* 3.0 4.7 + - - +
120C ILE* 3.0 26.8 + - - +
104D ILE* 4.8 9.2 - - + -
105D LEU* 4.1 9.2 - - + -
108D ASN* 3.3 49.6 - - + +
116D LEU* 4.8 15.3 - - + -
120D CYS* 5.1 2.6 - - - -
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 5.0 4.9 - - + +
112C LEU* 4.1 21.3 - - + -
113C PRO 3.2 10.0 + - - +
114C ASP 3.5 1.8 + - - +
116C LEU* 1.3 76.0 - - - +
118C LEU* 1.3 53.2 + - - +
120C ILE* 3.1 12.2 + - + +
121C PHE* 2.6 51.6 + - + -
138C ARG* 3.3 38.8 - - - +
139C TRP* 3.6 45.5 - - + +
142C LEU* 3.5 24.5 - - + -
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASP* 3.3 17.5 - - + +
115C GLU* 3.8 13.7 - - + +
116C LEU 3.1 0.2 - - - -
117C LEU* 1.3 78.6 - - - +
119C GLY* 1.3 55.4 + - - +
121C PHE* 3.7 3.7 - - + +
122C SER* 2.8 32.3 + - - -
142C LEU* 3.6 42.8 - - + +
145C ASP* 3.4 33.2 - - + +
147C SER* 4.0 11.0 - - - +
148C LEU* 3.8 12.8 - - + +
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLU 3.4 8.1 + - - -
116C LEU* 3.0 9.5 + - - -
118C LEU* 1.3 78.9 - - - +
120C ILE* 1.3 61.3 + - - +
122C SER* 2.6 24.9 + - - -
123C CYS* 3.5 10.6 + - - -
120D CYS* 4.3 11.5 - - - +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 4.7 4.7 - - + -
112C LEU* 3.6 31.4 - - + -
116C LEU 3.0 9.5 + - - +
117C LEU* 3.5 14.6 - - + +
119C GLY* 1.3 74.8 - - - +
121C PHE* 1.3 69.2 + - + +
123C CYS* 3.0 19.8 + - - +
124C LEU* 3.8 6.1 + - - +
139C TRP* 6.1 1.8 - - + -
104D ILE* 4.5 13.2 - - + -
120D CYS* 4.2 28.7 - - + +
123D VAL* 3.7 34.3 - - + -
124D ALA* 4.3 2.8 - - - +
127D ILE* 4.5 15.9 - - + -
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Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 2.6 36.7 + - + +
118C LEU* 3.7 5.4 - - + +
120C ILE* 1.3 77.0 - - + +
122C SER* 1.3 56.6 + - - +
123C CYS 3.0 4.9 - - - -
124C LEU* 2.8 42.8 + - + +
129C LEU* 4.0 11.3 - - + +
132C VAL* 4.0 8.1 - - + -
139C TRP* 3.4 76.7 - + + -
142C LEU* 3.9 16.2 - - + -
143C ALA* 3.7 24.5 - - + -
148C LEU* 3.8 16.8 - - + -
427C ARG* 4.3 2.6 + - - -
127D ILE* 5.0 0.2 - - + -
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU 2.8 17.0 + - - -
119C GLY* 2.6 25.1 + - - -
121C PHE* 1.3 73.0 - - - +
123C CYS* 1.3 60.4 + - - +
124C LEU 3.2 2.7 + - - +
148C LEU* 3.7 16.1 - - - +
427C ARG* 3.8 30.6 + - - +
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Residues in contact with CYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY 3.6 13.7 - - - -
120C ILE 3.0 10.3 + - - +
121C PHE 3.0 0.8 - - - -
122C SER* 1.3 78.9 - - - +
124C LEU* 1.3 61.1 + - - +
125C CYS 3.9 1.2 + - - -
117D ASP* 4.7 2.7 - - - -
120D CYS* 3.9 17.7 - - - +
121D LYS* 3.6 35.2 - - + +
124D ALA* 3.4 22.6 - - + +
128D LYS* 4.1 9.0 + - - -
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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