Contacts of the helix formed by residues 115 - 128 (chain C) in PDB entry 5IC6
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 SER 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C ASP 3.8 2.2 + - - -
114C CYS* 1.3 77.4 - - - +
116C CYS* 1.3 59.4 + - - +
117C ALA* 3.6 8.0 + - - +
118C LYS* 3.0 24.9 + - - +
119C MET* 2.9 27.0 + - - +
152C GLY* 4.3 0.9 - - - -
153C LYS* 3.8 16.4 - - - +
154C ASP* 3.4 21.8 - - - -
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Residues in contact with CYS 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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115C SER* 1.3 72.8 - - - +
117C ALA* 1.3 63.9 + - - +
119C MET* 3.2 12.8 + - - +
120C GLN* 3.0 28.5 + - + +
152C GLY* 3.9 8.0 - - - -
154C ASP* 3.2 23.5 + - - +
155C GLY* 3.4 33.0 - - - -
156C VAL 3.6 17.9 - - - +
157C THR* 4.1 14.4 - - - +
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Residues in contact with ALA 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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115C SER* 3.2 7.7 + - - +
116C CYS* 1.3 79.8 - - - +
118C LYS* 1.3 56.6 + - - +
120C GLN* 3.3 6.7 + - - +
121C ASP* 2.9 31.8 + - - +
154C ASP* 5.3 0.8 + - - +
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Residues in contact with LYS 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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111C TYR* 5.0 8.2 - - - -
114C CYS* 3.8 21.3 - - + -
115C SER* 3.0 29.8 + - - +
117C ALA* 1.3 75.4 - - - +
119C MET* 1.3 58.1 + - - +
121C ASP* 3.4 16.3 + - + +
122C LEU* 2.9 63.0 + - + +
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Residues in contact with MET 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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73C ILE* 3.9 25.1 - - + -
75C ASN* 3.7 19.7 - - - -
114C CYS* 3.6 15.9 - - + -
115C SER 2.9 12.7 + - - +
116C CYS* 3.6 8.1 - - - +
118C LYS* 1.3 75.8 - - - +
120C GLN* 1.3 62.4 + - - +
122C LEU* 3.5 4.7 + - - -
123C LEU* 3.2 30.0 + - - +
141C LEU* 5.1 1.8 - - - -
143C SER* 5.9 0.2 - - - -
150C ILE* 3.9 14.8 - - + -
151C TYR 3.8 4.0 - - - +
152C GLY* 3.5 28.7 - - - +
157C THR* 3.5 29.4 - - + -
162C LEU* 3.4 15.3 - - + +
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Residues in contact with GLN 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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116C CYS* 3.0 20.6 + - + +
117C ALA* 3.6 6.7 - - - +
119C MET* 1.3 77.3 - - - +
121C ASP* 1.3 57.7 + - - +
123C LEU* 3.5 1.0 + - - +
124C LYS* 3.0 31.4 + - - +
157C THR* 3.1 24.6 + - - +
161C ASP* 3.3 28.8 + - - +
162C LEU* 3.4 17.3 - - + +
165C HIS* 3.3 27.2 + - - -
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Residues in contact with ASP 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 ALA 2.9 17.5 + - - +
118C LYS* 3.9 17.1 + - + +
120C GLN* 1.3 76.4 - - - +
122C LEU* 1.3 57.9 + - - +
124C LYS* 4.2 6.3 - - - +
125C LYS* 2.9 66.2 + - - +
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Residues in contact with LEU 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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71C ILE* 4.1 8.8 - - + +
73C ILE* 4.1 13.5 - - + -
111C TYR* 3.6 64.2 - - + +
114C CYS* 4.1 13.0 - - - -
118C LYS* 2.9 43.9 + - - +
119C MET 3.7 5.2 - - - +
120C GLN 3.2 0.2 - - - -
121C ASP* 1.3 77.3 - - - +
123C LEU* 1.3 63.6 + - + +
125C LYS* 3.4 5.2 + - + +
126C ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 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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71C ILE* 4.9 7.6 - - + -
73C ILE* 3.8 25.8 - - + -
119C MET 3.2 20.2 + - - +
120C GLN 4.2 1.8 - - - +
122C LEU* 1.3 81.5 - - + +
124C LYS* 1.3 61.0 + - - +
126C ALA* 4.0 5.8 - - - -
127C SER* 2.8 26.3 + - - -
137C PHE* 5.3 0.2 - - + -
139C CYS* 4.1 24.0 - - + -
141C LEU* 5.6 0.9 - - + -
162C LEU* 3.3 47.6 - - + +
165C HIS* 4.5 2.5 - - + -
166C PHE* 3.3 28.0 - - + -
181C PHE* 4.1 9.0 - - + -
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Residues in contact with LYS 124 (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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120C GLN 3.0 19.3 + - - +
121C ASP* 3.7 8.7 - - - +
123C LEU* 1.3 75.7 - - - +
125C LYS* 1.3 85.5 + - + +
127C SER* 2.8 21.9 + - - +
128C GLU* 3.2 43.2 + - - +
165C HIS* 3.6 31.7 - - + +
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Residues in contact with LYS 125 (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 ASP* 2.9 47.0 + - - +
122C LEU* 3.7 6.1 - - + +
124C LYS* 1.3 99.0 - - + +
126C ALA* 1.3 63.0 + - - +
128C GLU* 3.1 26.5 + - - +
129C GLU* 3.3 20.1 + - + +
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Residues in contact with ALA 126 (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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69C LYS* 5.1 3.6 - - + -
71C ILE* 3.7 23.1 - - + -
122C LEU 2.9 17.7 + - - +
123C LEU* 3.5 5.2 - - - +
124C LYS 3.2 0.2 - - - -
125C LYS* 1.3 76.7 - - - +
127C SER* 1.3 55.8 + - - +
128C GLU 3.3 0.7 + - - -
129C GLU* 3.3 18.4 + - - +
131C HIS* 2.7 33.1 + - - -
137C PHE* 4.1 8.7 - - + -
166C PHE* 3.9 13.2 - - + -
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Residues in contact with SER 127 (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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123C LEU 2.8 13.6 + - - -
124C LYS* 2.8 19.1 + - - +
126C ALA* 1.3 76.0 - - - +
128C GLU* 1.3 63.6 + - - +
129C GLU 3.4 2.2 - - - +
165C HIS* 3.2 44.8 + - - +
166C PHE* 3.7 13.5 - - - -
170C ARG 4.1 7.1 + - - +
171C CYS* 3.3 25.7 - - - +
173C THR* 5.3 0.2 + - - -
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Residues in contact with GLU 128 (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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124C LYS* 3.2 52.4 + - + +
125C LYS* 3.1 24.5 + - - +
127C SER* 1.3 82.0 - - - +
129C GLU* 1.3 65.3 + - - +
170C ARG 6.0 0.9 - - - +
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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