Contacts of the helix formed by residues 123 - 132 (chain C) in PDB entry 1C3Q
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 ASN 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C ARG* 4.0 2.2 - - - +
122C GLY* 1.3 76.2 - - - -
124C ALA* 1.3 65.6 + - - +
125C ALA* 3.0 12.0 + - - +
126C GLU* 2.7 63.5 + - - +
127C ILE* 3.1 18.0 + - - +
167C ILE* 3.9 1.1 - - - -
168C THR* 3.7 17.5 - - - +
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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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123C ASN* 1.3 74.6 - - - +
125C ALA* 1.3 63.0 + - - +
127C ILE* 3.3 2.8 + - - +
128C ALA* 3.0 24.9 + - - +
141C VAL* 3.3 24.7 - - + +
150C ILE* 3.9 20.2 - - + -
153C LEU* 4.0 6.3 - - + +
167C ILE* 3.4 28.5 - - + +
168C THR 4.5 0.8 + - - -
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Residues in contact with ALA 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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98C ALA 4.7 0.7 - - - +
123C ASN* 3.0 11.0 + - - +
124C ALA* 1.3 78.0 - - - +
126C GLU* 1.3 65.1 + - + +
128C ALA* 3.3 5.8 + - - +
129C HIS* 3.0 41.7 + - + +
138C ILE* 5.2 4.7 - - + -
141C VAL* 3.5 15.8 - - + +
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Residues in contact with GLU 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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94C ASP* 4.7 2.6 - - - +
95C PRO* 3.7 24.0 - - + +
96C VAL* 3.4 10.5 - - - +
97C GLY* 2.7 30.6 + - - +
98C ALA* 3.7 17.1 - - + +
121C ARG* 5.0 1.4 + - - -
122C GLY* 3.5 8.8 - - - -
123C ASN* 2.7 54.5 + - - +
125C ALA* 1.3 73.8 - - + +
127C ILE* 1.3 56.1 + - - +
129C HIS 3.6 0.2 + - - -
130C THR* 2.7 37.6 + - - -
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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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95C PRO* 4.4 5.8 - - + -
120C ILE* 3.7 33.4 - - + +
122C GLY* 4.2 18.6 - - - +
123C ASN 3.1 14.5 + - - +
124C ALA 3.7 5.6 - - - +
125C ALA 3.3 0.2 - - - -
126C GLU* 1.3 72.7 - - - +
128C ALA* 1.3 67.8 + - - +
130C THR* 3.2 4.6 + - - +
131C VAL* 3.0 28.6 + - + +
153C LEU* 4.7 4.9 - - + -
157C ALA* 4.2 16.6 - - + -
165C ILE* 4.0 25.4 - - + -
166C ALA 4.9 0.2 - - - +
167C ILE* 3.9 28.7 - - + -
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Residues in contact with ALA 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 3.0 17.9 + - - +
125C ALA* 3.3 5.1 + - - +
127C ILE* 1.3 78.3 - - - +
129C HIS* 1.3 60.2 + - - +
131C VAL* 3.4 1.5 - - - +
132C GLY 3.1 3.3 + - - -
133C VAL* 2.8 49.0 + - + +
138C ILE* 3.5 22.7 - - + -
141C VAL* 4.4 9.9 - - + -
153C LEU* 4.3 11.0 - - + +
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Residues in contact with HIS 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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98C ALA 3.9 6.4 + - - +
99C GLY* 3.4 42.8 + - - +
105C THR* 3.9 10.2 - - + +
109C ARG* 2.9 29.6 + - - -
125C ALA* 3.0 33.3 + - + +
126C GLU 4.0 0.7 - - - +
128C ALA* 1.3 75.0 - - - +
130C THR* 1.3 62.4 + - - +
132C GLY* 3.3 2.1 + - - -
133C VAL 5.0 1.8 - - - +
138C ILE* 3.6 38.9 - - + +
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Residues in contact with THR 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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93C LEU* 5.3 1.1 - - + -
95C PRO* 3.7 13.8 - - + +
98C ALA* 3.3 18.3 - - - +
105C THR* 5.1 2.7 - - - -
108C ALA* 4.0 17.7 - - + +
109C ARG* 3.2 27.2 + - + +
112C ILE* 3.3 33.2 - - + +
120C ILE* 5.3 4.9 - - + -
126C GLU 2.7 23.3 + - - -
127C ILE* 3.2 7.8 + - + -
129C HIS* 1.3 77.4 - - - +
131C VAL* 1.3 61.1 + - + +
161C LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 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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109C ARG* 5.0 0.7 - - - -
120C ILE* 6.0 0.2 - - + -
127C ILE* 3.0 24.8 + - + +
128C ALA* 3.4 9.2 - - - +
130C THR* 1.3 78.9 - - + +
132C GLY* 1.3 60.5 + - - +
133C VAL* 3.7 18.4 - - + +
153C LEU* 4.9 3.1 - - + -
157C ALA* 3.7 27.6 - - + -
160C LYS* 3.2 43.2 + - + +
161C LEU* 3.7 29.2 - - + -
165C ILE* 5.3 0.9 - - + -
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Residues in contact with GLY 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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109C ARG* 3.5 22.7 - - - -
128C ALA 3.1 3.9 + - - -
129C HIS 3.3 1.7 + - - -
130C THR 3.3 4.2 + - - -
131C VAL* 1.3 80.2 - - - +
133C VAL* 1.3 71.0 + - - +
134C THR* 3.1 6.4 + - - -
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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