Contacts of the helix formed by residues 139 - 152 (chain A) in PDB entry 4I0A
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PHE 4.1 1.2 + - - -
138A LEU* 1.4 76.3 - - - +
140A VAL* 1.3 68.3 + - - +
141A THR* 3.0 20.9 + - - -
142A GLY* 3.0 19.8 + - - -
143A ARG* 3.0 17.5 + - - +
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Residues in contact with VAL 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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139A ASP* 1.3 75.7 + - - +
141A THR* 1.3 63.2 + - - +
143A ARG* 3.3 26.4 + - - +
144A ILE* 3.1 28.0 + - + +
177A VAL* 4.2 8.3 - - + -
178A GLY 4.8 3.6 - - - +
179A CYS* 3.8 38.1 - - + -
183A THR* 4.4 13.0 - - + -
187A ILE* 4.9 3.6 - - + -
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Residues in contact with THR 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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139A ASP* 3.0 17.0 + - - -
140A VAL* 1.3 78.6 - - - +
142A GLY* 1.3 62.6 + - - +
144A ILE* 3.2 4.5 + - - +
145A ALA* 3.1 22.2 + - + +
187A ILE* 3.1 42.2 - - + +
190A MET* 5.1 15.2 - - + +
191A LEU* 4.0 18.8 - - + +
194A GLN* 5.4 4.3 - - - +
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Residues in contact with GLY 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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138A LEU* 3.7 20.3 - - - +
139A ASP* 3.0 16.0 + - - -
141A THR* 1.3 76.2 - - - +
143A ARG* 1.3 62.9 + - - +
145A ALA* 3.2 6.8 + - - +
146A GLN* 3.0 26.2 + - - +
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Residues in contact with ARG 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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134A ASN 3.7 16.4 - - - +
135A LEU* 3.0 28.7 + - - +
138A LEU* 2.6 43.3 + - + +
139A ASP* 3.0 20.8 + - - +
140A VAL* 3.5 21.0 - - - +
141A THR 3.3 0.2 - - - -
142A GLY* 1.3 74.7 - - - +
144A ILE* 1.3 57.2 + - - +
147A THR* 2.8 33.4 + - - -
177A VAL* 3.2 42.5 + - + -
178A GLY 4.5 8.1 + - - -
303A GOL 3.3 25.4 + - - +
135B LEU 4.0 14.5 + - - -
136B ALA* 4.5 4.6 + - - +
143B ARG* 4.3 4.8 - - - +
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Residues in contact with ILE 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 VAL* 3.1 20.8 + - + +
141A THR 3.2 7.6 + - - +
143A ARG* 1.3 76.3 - - - +
145A ALA* 1.3 57.4 + - - +
147A THR* 3.3 2.6 + - - -
148A LEU* 3.1 31.0 + - + +
173A ILE* 4.0 22.7 - - + -
177A VAL* 3.7 22.4 - - + -
184A VAL* 4.2 18.8 - - + -
187A ILE* 3.7 33.0 - - + -
188A LEU* 4.3 15.0 - - + -
191A LEU* 3.8 18.8 - - + -
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Residues in contact with ALA 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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141A THR* 3.1 15.6 + - + +
142A GLY* 3.8 7.2 - - - +
144A ILE* 1.3 76.0 - - - +
146A GLN* 1.3 62.9 + - - +
148A LEU* 3.7 6.5 + - - +
149A LEU* 3.4 26.2 + - - +
191A LEU* 4.4 22.7 - - + -
196A LEU* 5.0 10.1 - - + -
206A VAL* 5.6 0.2 - - - +
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Residues in contact with GLN 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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130A GLU* 4.6 9.4 + - - +
134A ASN* 3.4 20.4 - - - +
138A LEU* 4.6 7.2 - - + +
142A GLY 3.0 16.8 + - - +
145A ALA* 1.3 76.1 - - - +
147A THR* 1.3 63.7 + - - +
149A LEU* 3.3 22.0 + - - +
150A ASN* 3.1 55.2 + - - +
303A GOL 3.3 17.3 - - - +
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Residues in contact with THR 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 ARG 2.8 27.2 + - - -
144A ILE* 3.3 6.0 + - - -
146A GLN* 1.3 72.3 - - - +
148A LEU* 1.3 59.4 + - + +
150A ASN* 3.3 7.6 + - + +
151A LEU* 2.8 40.6 + - + +
173A ILE* 5.1 9.2 - - + -
176A ILE* 3.7 34.3 - - + +
177A VAL* 3.2 19.6 - - + +
303A GOL 3.2 19.3 + - - -
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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 ILE* 3.1 19.1 + - + +
145A ALA* 4.1 6.3 - - - +
146A GLN 3.3 0.4 - - - -
147A THR* 1.3 76.9 - - + +
149A LEU* 1.3 59.2 + - - +
151A LEU* 3.5 9.0 + - + +
152A ALA* 3.1 26.3 + - - +
166A ILE* 4.1 18.8 - - + -
173A ILE* 4.0 29.8 - - + -
188A LEU* 4.1 19.3 - - + -
191A LEU* 4.2 12.3 - - + -
197A ILE* 4.0 26.2 - - + -
204A ILE* 4.5 9.4 - - + -
206A VAL* 3.8 23.1 - - + +
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Residues in contact with LEU 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 ALA 3.4 16.6 - - - +
146A GLN* 3.3 29.6 + - - +
147A THR 3.3 0.4 - - - -
148A LEU* 1.3 74.0 - - - +
150A ASN* 1.3 67.8 + - - +
152A ALA* 2.9 22.4 + - + +
153A LYS* 3.5 13.1 + - - +
206A VAL* 3.8 20.2 - - + -
207A TYR 5.7 6.1 - - - -
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Residues in contact with ASN 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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130A GLU* 4.7 8.9 + - - +
134A ASN* 4.8 0.7 - - - +
146A GLN* 3.1 38.0 + - - +
147A THR* 3.6 8.4 - - + +
149A LEU* 1.3 75.9 - - - +
151A LEU* 1.3 63.3 - - + +
153A LYS* 3.2 40.5 + - - +
154A GLN* 3.8 7.7 + - - +
303A GOL 3.9 18.7 + - - -
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Residues in contact with LEU 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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64A TYR* 4.0 27.8 - - + -
90A LYS* 6.1 0.9 - - - +
147A THR* 2.8 40.8 + - + +
148A LEU* 3.6 10.5 - - + +
149A LEU 3.2 0.2 - - - -
150A ASN* 1.3 68.6 - - + +
152A ALA* 1.3 58.5 + - - +
153A LYS 3.0 10.5 + - - -
154A GLN* 3.1 30.6 + - + +
157A ALA* 3.2 11.8 - - - +
166A ILE* 3.6 29.8 - - + +
168A ILE* 3.9 28.3 - - + -
173A ILE* 4.9 1.6 - - + -
176A ILE* 4.5 5.6 - - + -
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Residues in contact with ALA 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 3.1 13.0 + - - +
149A LEU* 2.9 15.8 + - + +
151A LEU* 1.3 76.3 - - - +
153A LYS* 1.3 56.5 + - - +
157A ALA* 3.5 17.1 - - - +
164A MET* 3.4 48.5 - - + +
166A ILE* 3.9 3.8 - - - -
206A VAL* 4.3 12.8 - - + -
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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