Contacts of the helix formed by residues 120 - 134 (chain B) in PDB entry 1Z19
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLY* 5.9 0.5 - - - -
118B ASP 3.3 4.3 + - - -
119B ILE* 1.3 73.8 - - - +
121B THR* 1.3 69.1 + - - +
122B LYS* 3.3 18.7 + - + +
123B GLU* 2.7 66.3 + - + +
124B ILE* 3.0 15.4 + - - +
164B HIS* 5.2 2.9 - - - -
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE* 3.7 36.3 - - + +
156A ALA* 5.1 2.7 - - - -
161A THR* 4.8 8.4 + - - +
119B ILE 4.0 1.4 + - - -
120B THR* 1.3 74.8 + - - +
122B LYS* 1.3 51.0 + - - +
124B ILE* 3.3 5.9 + - - +
125B ALA* 2.7 37.9 + - - +
164B HIS* 3.1 39.8 + - - +
167B ALA* 4.2 10.3 - - + +
168B THR* 3.7 18.6 - - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE 4.4 1.4 + - - -
156A ALA 3.6 21.7 - - - +
157A GLU* 4.3 17.5 - - - +
158A GLY* 4.2 15.2 - - - +
120B THR* 2.9 16.4 + - + +
121B THR* 1.3 79.9 - - - +
123B GLU* 1.3 57.8 + - + +
125B ALA* 3.2 3.3 + - - +
126B ALA* 2.8 29.2 + - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.1 16.8 - - + +
112B PRO* 4.4 20.8 - - + +
118B ASP 3.9 7.3 - - - +
119B ILE* 4.0 7.0 - - + -
120B THR* 2.7 47.1 + - + +
122B LYS* 1.3 72.5 - - + +
124B ILE* 1.3 70.0 + - - +
126B ALA* 3.1 15.6 + - - +
127B MSE 3.2 12.8 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 4.4 9.6 - - + -
119B ILE* 4.0 20.9 - - + -
120B THR 3.0 12.8 + - - +
121B THR* 3.6 6.3 - - - +
123B GLU* 1.3 76.2 - - - +
125B ALA* 1.3 65.3 + - - +
127B MSE 3.2 12.7 + - + +
128B LEU* 3.3 31.6 + - + +
144B ARG* 6.0 0.2 - - + -
147B LEU* 3.6 27.1 - - + -
151B PHE* 4.4 7.2 - - + -
164B HIS* 4.1 19.5 - - + +
165B VAL* 3.4 31.2 - - + -
168B THR* 4.5 8.3 - - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ALA* 3.4 35.7 - - + +
121B THR 2.7 22.1 + - - +
122B LYS 3.3 5.2 - - - +
124B ILE* 1.3 75.4 - - - +
126B ALA* 1.3 58.6 + - - +
128B LEU* 3.5 9.4 + - - +
129B ASN* 2.7 38.8 + - - +
168B THR* 4.8 8.9 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LYS* 2.8 16.9 + - + +
123B GLU* 3.4 13.0 - - - +
125B ALA* 1.3 74.0 - - - +
127B MSE 1.3 57.4 + - - +
129B ASN* 3.4 10.2 + - - +
130B GLY* 3.0 22.9 + - - -
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Residues in contact with MSE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 4.7 7.6 - - - +
107B ILE* 4.8 5.2 - - + -
110B GLY* 4.2 27.1 - - - +
111B LEU* 4.5 17.7 - - + -
123B GLU 3.2 7.0 + - - +
124B ILE* 3.2 18.4 + - + +
126B ALA* 1.3 75.5 - - - +
128B LEU* 1.3 91.2 + - + +
130B GLY* 2.5 25.3 + - - -
131B TYR* 3.0 30.0 + - + -
143B ILE* 3.7 20.2 - - + -
147B LEU* 4.7 9.4 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE* 3.3 27.0 + - + +
125B ALA* 3.8 7.0 - - - +
127B MSE 1.3 102.6 - - + +
129B ASN* 1.3 59.1 + - - +
131B TYR* 3.0 7.3 + - - +
132B ILE* 2.8 38.5 + - + +
140B ALA* 3.7 31.5 - - + +
143B ILE* 4.0 4.9 - - + -
144B ARG* 3.9 29.2 - - + +
168B THR* 3.9 24.5 - - + -
169B ARG 5.4 1.1 - - - +
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ALA* 5.4 5.7 + - - +
125B ALA* 2.7 36.0 + - - +
126B ALA* 3.6 9.1 - - - +
128B LEU* 1.3 73.4 - - - +
130B GLY* 1.3 61.3 + - - +
132B ILE* 4.0 18.8 - - - +
133B ASP* 2.8 43.9 + - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.0 10.5 + - - -
127B MSE 2.5 18.2 + - - -
129B ASN* 1.3 74.6 - - - +
131B TYR* 1.3 60.5 + - - -
133B ASP* 3.4 10.1 + - - +
134B GLU* 3.3 25.7 + - - +
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Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA* 3.4 26.1 + - + +
109B ARG* 4.5 8.3 + - - -
110B GLY* 6.3 0.4 - - - -
127B MSE 3.0 34.2 + - + -
128B LEU* 3.6 7.9 - - + +
130B GLY* 1.3 78.2 - - - +
132B ILE* 1.3 63.2 + - - +
134B GLU* 3.0 18.5 + - - +
136B LYS* 2.9 48.6 + - + +
139B SER* 3.8 19.7 - - - -
140B ALA* 4.1 8.7 - - + -
143B ILE* 3.6 26.5 - - + -
10C C 4.0 22.7 + - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 2.8 26.1 + - + +
129B ASN* 3.2 22.6 + - - +
131B TYR* 1.3 76.6 - - - +
133B ASP* 1.3 62.0 + - - +
135B GLY* 3.0 19.1 + - - -
136B LYS 4.4 3.1 - - - +
137B ALA* 4.6 13.8 + - + +
140B ALA* 3.8 13.9 - - + -
169B ARG 6.0 0.2 - - - +
171B ALA* 3.4 28.0 - - + -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN* 2.8 29.7 + - - +
130B GLY* 3.8 6.8 - - - +
131B TYR 3.2 0.2 - - - -
132B ILE* 1.3 78.6 - - - +
134B GLU* 1.3 59.4 + - + +
135B GLY 3.1 5.1 + - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 3.3 19.8 - - - +
131B TYR* 3.0 15.5 + - - +
133B ASP* 1.3 78.0 - - + +
135B GLY* 1.3 61.7 + - - +
136B LYS* 3.3 39.4 + - - +
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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