Contacts of the helix formed by residues 131 - 141 (chain C) in PDB entry 3IO6
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 GLU 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C PRO* 3.3 19.5 - - + +
127C LYS* 3.3 23.2 + - - +
128C THR* 3.1 29.1 + - - +
129C TRP 3.0 1.4 + - - -
130C GLU* 1.3 76.8 - - + +
132C ILE* 1.3 59.4 + - - +
133C PRO* 3.4 2.0 - - - -
134C ALA* 3.4 11.3 + - + +
135C LEU* 3.0 31.4 + - + +
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Residues in contact with ILE 132 (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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126C PRO* 4.5 7.0 - - + -
128C THR 4.3 7.0 - - - +
129C TRP* 2.9 45.6 + - + +
131C GLU* 1.3 74.7 - - - +
133C PRO* 1.4 70.9 - - + +
135C LEU* 3.3 6.6 + - + +
136C ASP* 2.9 22.3 + - + +
146C ALA* 4.0 12.0 - - + +
147C LEU* 3.8 25.1 - - + -
198C LEU* 4.5 16.4 - - + -
203C HIS* 5.6 4.9 - - + -
204C MET* 6.1 2.5 - - + -
224C MET* 4.2 20.9 - - + -
248C PRO* 4.8 10.3 - - + -
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Residues in contact with PRO 133 (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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129C TRP 3.7 4.7 - - - +
130C GLU 3.3 17.0 - - - +
131C GLU 3.5 1.1 - - - -
132C ILE* 1.4 94.1 - - + +
134C ALA* 1.3 62.8 + - - +
136C ASP* 3.0 14.4 + - - +
137C LYS* 3.3 18.0 + - - +
194C PHE* 4.6 5.8 - - + -
198C LEU* 3.5 24.0 - - + -
201C ASN* 6.0 0.4 - - - +
203C HIS* 3.7 31.9 + - + +
451C ZN 4.1 7.9 - - - -
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Residues in contact with ALA 134 (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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130C GLU 5.7 0.4 - - - +
131C GLU* 3.4 14.8 + - + +
133C PRO* 1.3 80.7 - - - +
135C LEU* 1.3 61.7 + - - +
137C LYS* 3.6 12.8 + - - +
138C GLU* 3.4 18.4 + - - +
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Residues in contact with LEU 135 (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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122C LEU* 3.8 32.3 - - + -
126C PRO* 4.1 16.8 - - + -
131C GLU* 3.0 22.8 + - + +
132C ILE* 3.5 7.6 - - - +
134C ALA* 1.3 75.6 - - - +
136C ASP* 1.3 63.9 + - - +
138C GLU* 3.1 34.9 + - - +
139C LEU* 3.1 22.7 + - + +
146C ALA* 4.3 9.0 - - + -
224C MET* 3.8 28.5 - - + -
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Residues in contact with ASP 136 (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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132C ILE* 2.9 10.5 + - + +
133C PRO 3.0 9.1 + - - +
135C LEU* 1.3 77.0 - - - +
137C LYS* 1.3 53.4 + - - +
139C LEU* 2.9 3.4 + - - -
140C LYS* 2.7 65.1 + - - +
145C SER* 3.4 8.5 - - - -
146C ALA* 2.7 43.4 + - + +
203C HIS* 3.3 38.1 - - + +
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Residues in contact with LYS 137 (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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133C PRO 3.3 12.7 + - - +
134C ALA* 3.9 11.2 - - - +
135C LEU 3.3 0.4 - - - -
136C ASP* 1.3 76.2 - - - +
138C GLU* 1.3 60.5 + - - +
140C LYS* 4.4 6.8 - - + +
141C ALA* 3.6 20.3 + - - +
203C HIS* 4.0 11.9 - - + +
451C ZN 3.1 31.1 - - - -
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Residues in contact with GLU 138 (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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122C LEU* 5.7 1.6 - - - +
134C ALA 3.4 9.5 + - - +
135C LEU* 3.1 28.1 + - - +
137C LYS* 1.3 80.4 - - - +
139C LEU* 1.3 69.0 + - + +
141C ALA* 3.7 13.3 - - - +
142C LYS* 4.1 10.8 + - + +
453C CA 2.2 31.1 - - - -
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Residues in contact with LEU 139 (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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121C LEU* 4.0 23.1 - - + +
122C LEU* 5.4 4.7 - - + -
135C LEU* 3.5 23.1 - - + +
136C ASP 2.9 6.1 + - - +
138C GLU* 1.3 88.0 - - + +
140C LYS* 1.3 59.8 + - - +
141C ALA 3.1 1.8 - - - -
142C LYS* 2.8 30.1 + - + +
143C GLY 3.1 8.3 + - - -
144C LYS* 3.1 31.2 + - + +
145C SER 3.6 8.5 - - - +
146C ALA* 3.6 30.1 - - + -
223C ALA* 3.8 15.7 - - + -
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Residues in contact with LYS 140 (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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136C ASP* 2.7 54.9 + - - +
137C LYS* 4.4 5.6 - - + +
139C LEU* 1.3 71.8 - - - +
141C ALA* 1.3 58.3 + - - +
143C GLY* 2.9 20.9 + - - +
144C LYS 3.2 12.1 + - - +
145C SER* 3.8 19.1 - - - -
202C LYS 3.6 17.4 + - - -
203C HIS* 4.5 5.1 + - - +
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Residues in contact with ALA 141 (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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137C LYS 3.6 18.0 + - - +
138C GLU* 3.7 9.0 - - - +
139C LEU 3.1 0.2 - - - -
140C LYS* 1.3 76.8 - - - +
142C LYS* 1.3 60.3 + - + +
143C GLY 3.5 0.2 - - - -
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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