Contacts of the helix formed by residues 120 - 133 (chain C) in PDB entry 2IK8
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 THR 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C LEU* 4.5 4.7 - - - +
119C MET* 1.3 78.6 - - - +
121C ALA* 1.3 59.0 + - - +
122C GLU* 3.7 9.3 + - - +
123C LEU* 3.1 28.5 + - + +
124C ALA* 2.9 30.2 + - - +
163C ALA 5.9 1.1 - - - -
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Residues in contact with ALA 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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120C THR* 1.3 74.1 - - - +
122C GLU* 1.3 57.5 + - - +
124C ALA* 3.7 7.1 - - - +
125C GLY* 3.0 22.3 + - - -
163C ALA 5.8 3.1 - - - -
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Residues in contact with GLU 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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106C GLN* 4.0 18.0 - - - +
110C LEU* 4.1 23.8 - - + +
120C THR* 3.2 7.6 + - - +
121C ALA* 1.3 76.3 - - - +
123C LEU* 1.3 67.1 + - - +
125C GLY* 2.9 3.7 + - - -
126C VAL* 2.8 28.3 + - + +
129C ARG* 4.4 4.1 + - - +
358C SO4 5.6 0.5 + - - -
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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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78C ILE* 3.9 27.8 - - + -
107C LEU* 3.6 33.4 - - + +
110C LEU* 3.3 37.6 - - + +
111C ALA* 4.8 5.2 - - + +
119C MET* 4.3 13.5 - - - -
120C THR* 3.1 27.4 + - + +
122C GLU* 1.3 76.5 - - - +
124C ALA* 1.3 65.7 + - - +
126C VAL* 3.0 7.5 + - + +
127C ILE* 2.9 34.7 + - + +
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Residues in contact with ALA 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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119C MET* 3.8 16.1 - - + -
120C THR 2.9 18.5 + - - +
121C ALA* 3.7 8.1 - - - +
123C LEU* 1.3 75.9 - - - +
125C GLY* 1.3 56.4 + - - +
127C ILE* 3.2 1.0 + - - -
128C LYS* 2.8 32.3 + - - +
159C LEU* 3.6 12.1 - - + +
163C ALA* 3.8 29.2 - - + -
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Residues in contact with GLY 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 ALA 3.0 13.1 + - - -
122C GLU* 2.9 10.1 + - - -
124C ALA* 1.3 74.6 - - - +
126C VAL* 1.3 61.7 + - - -
128C LYS* 3.1 7.5 + - - +
129C ARG* 3.0 47.1 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASP* 3.3 37.0 - - + +
106C GLN* 4.0 18.4 - - + -
107C LEU* 3.8 24.9 - - + -
110C LEU* 4.5 8.7 - - + -
122C GLU* 2.8 21.2 + - + +
123C LEU* 3.2 10.3 - - - +
125C GLY* 1.3 71.5 - - - +
127C ILE* 1.3 64.4 + - - +
129C ARG* 3.2 19.9 + - - +
130C LEU* 3.0 30.4 + - + +
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Residues in contact with ILE 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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77C THR* 4.5 7.4 - - + -
78C ILE* 4.4 14.4 - - + -
81C ILE* 4.2 20.4 - - + +
107C LEU* 4.0 20.9 - - + -
119C MET* 4.5 14.1 - - + -
123C LEU* 2.9 37.6 + - + +
124C ALA 3.8 1.3 - - - +
126C VAL* 1.3 74.3 - - - +
128C LYS* 1.3 56.6 + - - +
130C LEU* 4.0 6.1 - - - +
131C TRP* 3.0 27.9 + - - +
156C LEU* 3.2 32.3 - - + -
159C LEU* 3.3 16.4 - - + -
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Residues in contact with LYS 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 ALA 2.8 18.5 + - - +
125C GLY* 3.6 6.3 - - - +
127C ILE* 1.3 77.9 - - - +
129C ARG* 1.3 63.6 + - + +
131C TRP* 4.0 6.7 - - - +
132C LYS* 3.3 22.0 + - - +
159C LEU* 3.7 13.9 - - + +
160C ASP* 5.1 9.4 - - - +
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Residues in contact with ARG 129 (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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100C ARG* 3.5 28.8 + - - +
103C ASP* 2.9 32.3 + - - +
122C GLU* 4.4 5.3 + - - +
125C GLY* 3.0 29.8 + - - +
126C VAL* 3.3 31.2 - - - +
128C LYS* 1.3 76.6 - - + +
130C LEU* 1.3 64.1 + - - +
132C LYS* 3.5 6.7 + - - +
133C ASP* 3.4 15.6 + - - +
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Residues in contact with LEU 130 (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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81C ILE* 4.1 17.0 - - + -
85C ILE* 3.4 30.1 - - + -
95C PHE* 3.8 28.7 - - + -
100C ARG* 3.9 27.3 - - + +
103C ASP* 4.3 6.7 - - + -
104C ALA* 3.9 15.9 - - + +
107C LEU* 4.3 2.0 - - + -
126C VAL* 3.0 32.3 + - + +
127C ILE 4.0 3.6 - - - +
129C ARG* 1.3 76.5 - - - +
131C TRP* 1.3 61.8 + - - +
133C ASP 3.2 6.2 + - - -
136C VAL* 3.1 31.1 - - + +
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Residues in contact with TRP 131 (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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81C ILE* 4.6 3.8 - - + +
84C ILE* 4.2 9.2 - - + -
127C ILE 3.0 19.3 + - - +
128C LYS* 4.0 6.3 - - - +
129C ARG 3.3 0.4 - - - -
130C LEU* 1.3 77.1 - - - +
132C LYS* 1.3 61.0 + - - +
133C ASP 3.5 0.7 + - - +
136C VAL* 4.4 7.7 - - + +
137C GLN* 2.8 56.6 + - - +
140C PHE* 3.8 48.7 - + + -
153C ALA* 4.3 7.4 - - + -
156C LEU* 3.4 59.6 + - + -
157C ASN* 2.9 37.3 + - - +
159C LEU* 6.2 0.2 - - + -
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Residues in contact with LYS 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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128C LYS 3.3 14.7 + - - +
129C ARG* 3.8 7.6 - - - +
130C LEU 3.2 0.6 - - - -
131C TRP* 1.3 81.8 - - + +
133C ASP* 1.3 64.0 + - - +
134C SER* 3.4 2.3 + - - -
137C GLN* 4.6 4.7 - - - +
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Residues in contact with ASP 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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95C PHE* 3.3 15.4 - - - +
96C GLY* 2.7 23.7 + - - -
97C ASP* 3.1 25.5 + - - +
100C ARG* 3.5 31.1 + - - +
129C ARG 3.4 3.2 + - - -
130C LEU 3.2 14.3 + - - +
132C LYS* 1.3 78.2 - - - +
134C SER* 1.3 61.1 + - - +
135C GLY 3.3 8.0 + - - -
136C VAL* 3.1 12.2 + - + +
137C GLN* 2.9 26.2 + - - +
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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