Contacts of the helix formed by residues 138 - 152 (chain A) in PDB entry 1ZRF
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 ASP 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE 4.2 0.4 + - - -
137A LEU* 1.3 80.6 - - - +
139A VAL* 1.3 63.3 + - - +
140A THR* 3.1 10.9 + - - -
141A GLY* 2.7 34.7 + - - -
142A ARG* 3.0 16.9 + - - +
10X G 3.4 14.8 - - - +
11X A 4.7 13.1 + - - +
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Residues in contact with VAL 139 (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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138A ASP* 1.3 72.4 - - - +
140A THR* 1.3 61.2 + - - +
142A ARG* 3.7 27.7 - - - +
143A ILE* 2.9 46.4 + - + +
176A VAL* 4.6 4.0 - - + -
177A GLY 5.2 0.2 - - - +
178A CYS* 3.7 30.5 - - + -
182A THR* 3.9 3.8 - - + -
186A ILE* 3.7 10.5 - - + -
9X A 5.3 0.7 - - - +
10X G 2.7 42.7 + - - +
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Residues in contact with THR 140 (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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138A ASP* 3.1 12.9 + - - -
139A VAL* 1.3 77.8 - - - +
141A GLY* 1.3 59.2 + - - +
143A ILE* 3.9 1.4 - - - +
144A ALA* 3.0 30.0 + - + +
186A ILE* 3.6 34.6 - - + +
189A MET* 5.8 0.7 - - - +
190A LEU* 4.8 14.7 - - + +
193A GLN* 6.4 0.7 - - - +
10X G 4.6 4.8 + - - -
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Residues in contact with GLY 141 (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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137A LEU* 4.2 19.7 - - - +
138A ASP* 2.7 22.1 + - - -
140A THR* 1.3 75.0 - - - +
142A ARG* 1.3 60.6 + - - +
144A ALA* 3.4 6.2 + - - +
145A GLN* 3.1 23.9 + - - +
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Residues in contact with ARG 142 (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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133A ASN 3.5 19.1 - - - -
134A LEU* 3.5 23.2 + - - +
137A LEU* 2.6 47.9 + - + -
138A ASP* 3.0 20.6 + - - +
139A VAL* 3.2 27.1 + - - +
141A GLY* 1.3 75.7 - - - +
143A ILE* 1.3 58.8 + - - +
145A GLN* 3.4 4.2 + - - +
146A THR* 2.9 31.5 + - - -
176A VAL* 2.8 36.1 + - + +
177A GLY 3.6 14.6 + - - -
305A DIO 3.4 29.9 - - - +
10X G 5.2 0.2 + - - -
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Residues in contact with ILE 143 (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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139A VAL* 2.9 37.4 + - + +
140A THR 4.0 3.4 - - - +
142A ARG* 1.3 72.8 - - - +
144A ALA* 1.3 61.4 - - - +
146A THR* 3.7 2.6 - - - -
147A LEU* 2.9 48.5 + - + +
172A ILE* 4.1 11.0 - - + -
176A VAL* 3.9 21.3 - - + -
183A VAL* 3.9 35.2 - - + +
186A ILE* 4.0 17.0 - - + -
187A LEU* 4.3 13.0 - - + -
190A LEU* 4.5 7.4 - - + -
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Residues in contact with ALA 144 (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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140A THR* 3.0 21.7 + - + +
141A GLY* 3.7 7.0 - - - +
142A ARG 3.3 0.2 - - - -
143A ILE* 1.3 80.3 - - - +
145A GLN* 1.3 60.2 + - - +
147A LEU* 3.5 3.9 + - - +
148A LEU* 3.2 28.9 + - + +
190A LEU* 5.1 4.7 - - + +
303A DIO 3.9 33.1 - - - +
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Residues in contact with GLN 145 (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 GLU* 4.7 12.4 + - - +
133A ASN* 2.7 41.0 + - - +
137A LEU* 4.0 9.7 - - + +
141A GLY 3.1 14.5 + - - +
142A ARG* 3.7 3.8 - - - +
144A ALA* 1.3 76.5 - - - +
146A THR* 1.3 66.2 + - - +
148A LEU* 3.4 10.5 + - - +
149A ASN* 3.0 25.2 + - + +
305A DIO 4.3 10.8 + - - -
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Residues in contact with THR 146 (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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142A ARG 2.9 22.2 + - - -
143A ILE* 3.2 5.1 + - - -
145A GLN* 1.3 78.1 + - - +
147A LEU* 1.3 63.6 + - + +
149A ASN* 3.3 6.9 + - + +
150A LEU* 3.1 42.1 + - + +
172A ILE* 5.3 8.5 - - + -
175A ILE* 4.0 27.1 - - + +
176A VAL* 3.5 17.6 - - + +
305A DIO 3.5 16.1 + - - -
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Residues in contact with LEU 147 (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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143A ILE* 2.9 28.3 + - + +
144A ALA 3.8 4.0 - - - +
145A GLN 3.3 0.2 - - - -
146A THR* 1.3 78.1 - - + +
148A LEU* 1.3 61.9 + - - +
150A LEU* 3.6 6.3 + - + +
151A ALA* 3.1 24.4 + - - +
165A ILE* 4.1 21.6 - - + +
172A ILE* 4.2 26.7 - - + -
187A LEU* 3.9 21.8 - - + -
190A LEU* 4.1 9.0 - - + -
196A ILE* 4.5 13.0 - - + -
203A ILE* 4.2 12.8 - - + -
205A VAL* 3.8 14.1 - - + +
303A DIO 4.1 15.7 - - - +
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Residues in contact with LEU 148 (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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144A ALA* 3.2 15.6 + - + +
145A GLN* 3.8 10.3 - - - +
146A THR 3.3 0.2 - - - -
147A LEU* 1.3 78.0 - - - +
149A ASN* 1.3 64.4 + - - +
151A ALA* 3.4 5.4 + - - +
152A LYS* 3.4 38.7 + - - +
205A VAL* 3.8 21.3 - - + -
206A TYR 5.2 1.1 - - - +
207A GLY 5.3 2.0 - - - +
208A THR* 4.1 21.1 - - - +
303A DIO 3.6 24.0 - - - -
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Residues in contact with ASN 149 (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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145A GLN* 3.0 21.5 + - + +
146A THR* 3.3 8.3 + - - +
148A LEU* 1.3 77.7 - - - +
150A LEU* 1.3 69.6 + - - +
152A LYS* 3.2 14.6 + - - +
153A GLN* 3.4 29.5 + - - +
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Residues in contact with LEU 150 (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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63A TYR* 4.6 22.2 - - + -
89A LYS* 6.2 0.4 - - - +
146A THR* 3.1 36.7 + - + +
147A LEU* 4.0 6.5 - - + +
149A ASN* 1.3 83.6 - - - +
151A ALA* 1.3 62.5 + - - +
152A LYS 3.0 1.6 + - - -
153A GLN* 3.1 28.0 + - + +
155A ASP* 4.8 2.2 - - - +
156A ALA* 3.5 8.5 - - - +
165A ILE* 3.8 28.5 - - + +
167A ILE* 3.9 29.6 - - + -
172A ILE* 5.4 0.4 - - + -
175A ILE* 4.8 3.1 - - + -
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Residues in contact with ALA 151 (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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147A LEU 3.1 16.8 + - - +
148A LEU* 3.6 8.3 - - - +
149A ASN 3.3 0.4 - - - -
150A LEU* 1.3 77.7 - - - +
152A LYS* 1.3 58.5 + - - +
153A GLN 3.5 0.4 - - - -
156A ALA* 3.4 3.9 - - - +
163A MET* 3.3 48.8 - - + +
165A ILE* 3.7 14.1 - - + +
205A VAL* 4.1 19.3 - - + -
208A THR* 4.6 6.7 - - - +
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Residues in contact with LYS 152 (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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148A LEU* 3.4 28.7 - - - +
149A ASN* 3.2 7.9 + - - +
150A LEU 3.0 1.0 - - - -
151A ALA* 1.3 80.5 - - - +
153A GLN* 1.3 68.0 + - - +
154A PRO* 4.7 0.9 - - - +
163A MET* 5.1 4.7 - - + -
208A THR* 2.7 46.5 + - - +
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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