Contacts of the helix formed by residues 120 - 134 (chain C) in PDB entry 1Z1G
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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118C ASP 3.5 1.5 + - - -
119C ILE* 1.3 69.3 - - - +
121C THR* 1.3 78.8 + - - +
122C LYS* 3.3 14.2 + - + +
123C GLU* 2.3 72.1 + - + +
124C ILE* 3.0 12.3 + - - +
164C HIS* 4.3 6.9 + - - -
158D GLY* 5.7 3.3 - - - -
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Residues in contact with THR 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 72.6 + - - +
122C LYS* 1.3 68.0 + - - +
124C ILE* 2.8 24.5 + - - +
125C ALA* 2.8 14.5 + - + +
164C HIS* 2.9 43.9 + - - +
167C ALA* 4.5 15.8 - - + +
168C THR* 5.4 5.3 - - - +
155D ILE* 3.6 27.4 + - + +
156D ALA* 3.7 16.6 - - + +
158D GLY* 5.5 2.5 - - - -
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Residues in contact with LYS 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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120C THR* 2.8 16.7 + - + +
121C THR* 1.3 78.8 - - - +
123C GLU* 1.3 53.0 + - - +
125C ALA* 3.0 3.7 + - + +
126C ALA* 2.7 42.2 + - + +
156D ALA 4.0 15.0 - - - +
157D GLU* 4.3 42.0 - - + +
158D GLY* 5.2 1.3 - - - +
159D HIS* 6.1 0.6 - - + -
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Residues in contact with GLU 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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111C LEU* 4.3 20.2 - - + +
112C PRO* 4.6 15.8 - - + +
118C ASP 3.2 8.5 - - - +
119C ILE* 3.2 13.9 - - + -
120C THR* 2.3 56.4 + - + +
122C LYS* 1.3 73.0 - - + +
124C ILE* 1.3 61.0 + - - +
126C ALA* 3.1 20.4 - - - +
127C MSE 3.2 10.7 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 4.6 7.9 - - + -
119C ILE* 3.8 27.8 - - + -
120C THR 3.0 10.9 + - - +
121C THR* 2.8 17.1 + - - +
123C GLU* 1.3 75.6 - - - +
125C ALA* 1.3 71.1 + - - +
127C MSE 3.2 17.6 + - + +
128C LEU* 2.8 27.6 + - + +
147C LEU* 4.2 21.3 - - + -
151C PHE* 4.6 3.4 - - + -
164C HIS* 4.2 11.9 - - + -
165C VAL* 4.2 27.4 - - + +
168C THR* 4.9 13.9 - - + +
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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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121C THR* 2.8 13.4 + - + +
122C LYS* 3.6 11.7 - - + +
124C ILE* 1.3 79.3 - - - +
126C ALA* 1.3 56.6 + - - +
128C LEU* 2.7 10.0 + - + -
129C ASN* 2.5 48.0 + - - +
168C THR* 4.6 13.0 - - - +
156D ALA* 4.5 15.0 - - + +
157D GLU* 6.3 0.9 - - + -
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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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122C LYS* 2.7 22.4 + - + +
123C GLU* 3.1 17.0 - - - +
125C ALA* 1.3 73.6 - - - +
127C MSE 1.3 63.6 + - - +
129C ASN* 3.4 7.0 + - - +
130C GLY* 3.1 16.1 + - - -
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Residues in contact with MSE 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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106C ALA 5.3 1.8 - - - +
107C ILE* 5.0 12.3 - - - -
110C GLY* 4.0 38.1 - - - +
111C LEU* 4.9 10.1 - - + -
123C GLU 3.2 9.1 + - - +
124C ILE* 3.2 21.8 - - + +
126C ALA* 1.3 75.7 - - - +
128C LEU* 1.3 117.4 + - + +
130C GLY* 2.8 17.2 + - - +
131C TYR* 3.3 26.8 + - + -
143C ILE* 4.5 18.8 - - + -
147C LEU* 5.4 7.9 - - + -
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Residues in contact with LEU 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 ILE* 2.8 18.8 + - + +
125C ALA* 2.7 17.7 + - - +
127C MSE 1.3 88.1 - - + +
129C ASN* 1.3 60.5 + - - +
131C TYR* 2.9 29.0 + - - +
132C ILE* 3.3 11.0 + - + +
140C ALA* 3.9 25.8 - - + +
143C ILE* 4.7 4.0 - - + -
144C ARG* 3.7 39.9 - - + +
147C LEU* 6.4 0.9 - - + -
168C THR* 4.3 14.1 - - + +
169C ARG 4.0 19.7 - - - +
171C ALA 5.3 3.1 - - - +
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Residues in contact with ASN 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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125C ALA* 2.5 28.5 + - - +
126C ALA* 3.7 6.1 - - - +
128C LEU* 1.3 75.9 - - - +
130C GLY* 1.3 64.9 + - - +
132C ILE* 3.0 26.3 + - - +
133C ASP* 2.9 39.7 + - - +
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Residues in contact with GLY 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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126C ALA 3.1 9.9 + - - -
127C MSE 2.8 17.3 + - - -
129C ASN* 1.3 72.3 - - - +
131C TYR* 1.3 68.3 + - - +
133C ASP* 3.7 6.2 + - - +
134C GLU* 3.5 25.5 + - - +
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Residues in contact with TYR 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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106C ALA* 4.7 21.9 + - + +
109C ARG* 5.1 13.0 + - - -
110C GLY* 5.6 3.3 + - - -
127C MSE 3.7 26.7 - - + +
128C LEU* 2.9 12.2 + - - +
130C GLY* 1.3 83.0 - - - +
132C ILE* 1.3 59.0 + - - +
134C GLU* 3.9 10.7 + - - +
135C GLY 3.7 1.4 + - - -
136C LYS* 2.9 50.1 + - + +
139C SER* 4.6 6.7 - - - -
140C ALA* 4.4 12.8 - - + -
143C ILE* 3.3 30.3 - - + -
8K C 5.1 13.2 - - - -
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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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128C LEU* 3.3 10.4 + - + +
129C ASN* 3.0 30.8 + - - +
131C TYR* 1.3 75.6 - - - +
133C ASP* 1.3 66.2 + - - +
134C GLU 3.1 0.2 - - - -
135C GLY* 2.7 28.1 + - - -
137C ALA* 4.6 11.2 - - + +
140C ALA* 4.6 10.1 - - + +
169C ARG 5.9 1.1 - - - +
171C ALA* 3.7 32.3 - - + +
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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
----------------------------------------------------------
129C ASN* 2.9 28.9 + - - +
130C GLY* 4.1 6.0 - - - +
132C ILE* 1.3 84.8 - - - +
134C GLU* 1.3 59.2 + - + +
135C GLY 3.3 0.7 + - - -
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Residues in contact with GLU 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 GLY 3.5 17.5 + - - +
131C TYR* 3.9 12.9 + - - +
132C ILE 3.1 0.6 - - - -
133C ASP* 1.3 76.8 - - - +
135C GLY* 1.3 59.7 + - - +
136C LYS* 3.3 23.2 + - + +
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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