Contacts of the helix formed by residues 120 - 134 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP 3.4 2.4 + - - -
119A ILE* 1.3 74.6 - - - +
121A THR* 1.3 83.3 + - - +
122A LYS* 3.4 13.5 + - + +
123A GLU* 2.3 65.7 + - + +
124A ILE* 2.9 12.4 + - - +
164A HIS* 4.6 7.6 + - - -
158B GLY* 5.4 5.4 - - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 1.3 75.5 + - - +
122A LYS* 1.3 54.5 + - - -
124A ILE* 2.5 35.9 + - + +
125A ALA* 2.7 13.8 + - + -
164A HIS* 3.2 47.6 + - - +
167A ALA* 4.2 8.6 - - + +
168A THR* 5.3 9.0 - - - +
155B ILE 3.9 8.4 + - - +
156B ALA* 2.9 37.9 - - - +
158B GLY* 5.3 2.2 - - - -
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 2.9 12.8 + - + +
121A THR* 1.3 78.7 - - - +
123A GLU* 1.3 64.7 + - - +
125A ALA* 3.0 9.5 + - + +
126A ALA* 2.7 33.9 + - + +
156B ALA 3.8 14.1 - - - +
157B GLU* 3.6 39.3 + - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.4 18.6 - - + +
112A PRO* 4.9 12.9 - - + +
118A ASP 3.1 8.5 - - - +
119A ILE* 3.1 16.5 - - + +
120A THR* 2.3 57.0 + - + +
122A LYS* 1.3 74.2 - - - +
124A ILE* 1.3 59.4 + - - +
126A ALA* 3.2 7.7 - - - +
127A MSE 3.2 20.8 + - - +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.9 7.9 - - + -
119A ILE* 4.4 17.0 - - + -
120A THR 2.9 15.0 + - - +
121A THR* 2.5 19.9 + - + +
123A GLU* 1.3 67.7 - - - +
125A ALA* 1.3 69.6 + - - +
127A MSE 3.0 20.9 + - + +
128A LEU* 2.8 24.0 + - + +
144A ARG* 6.5 0.7 - - - -
147A LEU* 3.5 33.9 - - + -
151A PHE* 4.6 7.4 - - + -
164A HIS* 4.9 2.7 - - + -
165A VAL* 4.3 26.7 - - + +
168A THR* 5.4 11.4 - - + -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 2.7 11.9 + - + +
122A LYS* 3.3 16.4 - - + +
124A ILE* 1.3 77.8 - - - +
126A ALA* 1.3 52.2 + - - +
128A LEU* 2.4 31.3 + - - +
129A ASN* 2.5 30.1 + - - +
168A THR* 5.3 11.9 - - - +
156B ALA* 5.0 6.5 - - + +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 2.7 24.3 + - + +
123A GLU* 3.2 14.4 - - - +
125A ALA* 1.3 74.1 - - - +
127A MSE 1.3 64.1 + - - +
129A ASN* 3.1 8.5 + - - +
130A GLY* 3.1 16.6 + - - -
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Residues in contact with MSE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA 5.3 1.8 - - - +
107A ILE* 5.0 14.1 - - - -
110A GLY* 4.0 35.0 - - - +
111A LEU* 4.5 14.6 - - + -
123A GLU 3.2 8.4 + - - +
124A ILE* 3.0 26.2 - - + +
125A ALA 3.2 0.8 - - - -
126A ALA* 1.3 76.1 - - - +
128A LEU* 1.3 121.5 + - + +
130A GLY* 2.8 17.0 + - - +
131A TYR* 3.4 22.6 + - + -
143A ILE* 4.3 18.8 - - + -
147A LEU* 5.6 4.9 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 2.8 18.9 + - + +
125A ALA* 2.4 23.6 + - - +
127A MSE 1.3 85.0 - - + +
129A ASN* 1.3 56.5 + - - +
131A TYR* 2.9 28.9 + - - +
132A ILE* 3.4 14.5 + - + -
140A ALA* 3.5 42.6 - - + +
143A ILE* 3.9 6.1 - - + -
144A ARG* 3.8 24.7 - - + +
168A THR* 5.5 8.5 - - + +
169A ARG 4.9 11.9 - - - +
170A ALA* 6.1 0.2 - - - -
171A ALA 5.5 4.5 - - - +
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA* 2.5 44.1 + - - +
126A ALA* 3.5 9.4 - - - +
128A LEU* 1.3 71.4 - - - +
130A GLY* 1.3 65.8 + - - +
131A TYR 2.9 2.5 - - - -
132A ILE* 2.9 23.4 + - - +
133A ASP* 2.9 40.3 + - - +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA 3.1 8.6 + - - -
127A MSE 2.8 16.1 + - - -
129A ASN* 1.3 73.6 - - - +
131A TYR* 1.3 65.2 + - - +
133A ASP* 3.7 5.7 + - - +
134A GLU* 3.3 31.1 + - - +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 4.8 9.3 + - + -
109A ARG* 3.0 45.2 + - - +
110A GLY* 5.7 2.2 - - - -
127A MSE 3.6 25.6 - - + -
128A LEU* 2.9 11.7 + - - +
130A GLY* 1.3 82.7 - - - +
132A ILE* 1.3 58.6 + - - +
134A GLU* 3.8 12.7 + - - +
135A GLY 3.6 1.9 + - - -
136A LYS* 3.0 41.8 + - + +
139A SER* 3.9 9.2 - - - -
140A ALA* 4.4 13.7 - - + -
143A ILE* 3.4 28.9 - - + -
8I C 4.1 12.8 - - - -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 3.4 14.2 + - + +
129A ASN* 2.9 32.8 + - - +
131A TYR* 1.3 75.5 - - - +
133A ASP* 1.3 70.4 + - - +
135A GLY* 2.6 28.1 + - - -
136A LYS 4.6 1.1 - - - +
137A ALA* 4.6 11.1 + - + +
140A ALA* 4.7 6.5 - - + -
169A ARG 6.0 1.6 - - - +
171A ALA* 4.5 23.1 - - + +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 2.9 27.1 + - - +
130A GLY* 3.9 6.7 - - - +
132A ILE* 1.3 94.5 - - - +
134A GLU* 1.3 59.1 + - + +
135A GLY* 3.4 1.2 + - - -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLY 3.3 19.3 + - - +
131A TYR* 4.2 15.0 - - - +
132A ILE 3.1 1.0 - - - -
133A ASP* 1.3 76.5 - - + +
135A GLY* 1.3 57.9 + - - +
136A LYS* 3.4 26.7 + - + +
8I C 5.3 3.3 + - - -
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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