Contacts of the helix formed by residues 139 - 153 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B PHE 4.4 0.2 + - - -
138B LEU* 1.3 72.7 - - - +
140B VAL* 1.3 58.6 + - + +
141B THR* 3.1 12.9 + - - -
142B GLY* 2.9 21.0 + - - +
143B ARG* 2.7 41.2 + - - +
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Residues in contact with VAL 140 (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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139B ASP* 1.3 76.4 - - + +
141B THR* 1.3 66.8 + - - +
143B ARG* 3.7 18.4 - - - +
144B ILE* 3.0 33.9 + - + +
177B VAL* 4.9 4.0 - - + -
179B CYS* 4.2 13.7 - - + -
183B THR* 4.1 15.3 - - + -
187B ILE* 3.8 24.2 - - + -
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Residues in contact with THR 141 (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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139B ASP* 3.1 11.8 + - - -
140B VAL* 1.3 82.4 - - - +
142B GLY* 1.3 58.1 + - - +
144B ILE* 3.3 3.5 + - - +
145B ALA* 2.9 29.0 + - + +
187B ILE* 3.9 23.3 - - + +
190B MET* 3.4 36.1 - - + +
191B LEU* 4.5 11.6 - - + +
194B GLN* 5.8 0.4 - - - +
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Residues in contact with GLY 142 (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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138B LEU* 3.8 20.9 - - - +
139B ASP* 2.9 17.5 + - - -
141B THR* 1.3 73.5 - - - +
143B ARG* 1.3 57.4 + - - +
145B ALA* 3.7 6.2 - - - +
146B GLN* 2.8 33.3 + - - +
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Residues in contact with ARG 143 (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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135A LEU 3.2 17.8 + - - -
136A ALA* 3.8 20.2 + - - +
143A ARG* 4.3 7.5 - - - +
134B ASN* 4.5 5.2 - - + +
135B LEU* 2.7 54.5 + - + +
138B LEU* 2.8 33.2 + - + +
139B ASP* 2.7 26.4 + - - +
140B VAL* 3.7 15.3 - - - +
142B GLY* 1.3 71.5 - - - +
144B ILE* 1.3 58.9 + - - +
146B GLN* 3.9 1.8 - - - +
147B THR* 2.9 32.9 + - - -
177B VAL* 3.8 28.9 + - + -
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Residues in contact with ILE 144 (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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140B VAL* 3.0 18.6 + - + +
141B THR 3.9 2.9 - - - +
143B ARG* 1.3 78.6 - - - +
145B ALA* 1.3 62.6 + - - +
147B THR* 3.2 4.4 + - - -
148B LEU* 3.0 39.1 + - + +
173B ILE* 4.0 15.5 - - + -
177B VAL* 3.9 20.2 - - + -
179B CYS* 4.0 22.4 - - - -
184B VAL* 4.1 13.2 - - + -
187B ILE* 3.9 41.5 - - + -
188B LEU* 4.2 13.0 - - + -
191B LEU* 4.2 1.6 - - + -
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Residues in contact with ALA 145 (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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141B THR* 2.9 17.7 + - + +
142B GLY* 3.7 7.9 - - - +
144B ILE* 1.3 78.4 - - - +
146B GLN* 1.3 56.5 + - - +
148B LEU* 3.5 6.8 + - - +
149B LEU* 3.1 36.4 + - + +
191B LEU* 4.4 23.5 - - + +
196B LEU* 6.3 0.7 - - + -
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Residues in contact with GLN 146 (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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134B ASN* 5.1 10.3 - - - +
138B LEU* 3.9 22.8 - - + +
142B GLY 2.8 20.5 + - - +
143B ARG 4.1 2.0 - - - +
145B ALA* 1.3 72.9 - - - +
147B THR* 1.3 56.7 + - - +
149B LEU* 4.0 22.1 - - - +
150B ASN* 2.8 65.7 + - - +
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG 2.9 23.7 + - - -
144B ILE* 3.2 8.3 + - - -
146B GLN* 1.3 73.8 - - - +
148B LEU* 1.3 60.7 + - + +
150B ASN* 3.4 6.9 + - + +
151B LEU* 2.9 49.7 + - + +
173B ILE* 4.9 13.9 - - + -
176B ILE* 3.7 32.6 - - + +
177B VAL* 3.5 14.2 - - - +
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Residues in contact with LEU 148 (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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144B ILE* 3.0 22.4 + - + +
145B ALA* 3.8 4.9 - - - +
146B GLN 3.5 0.2 - - - -
147B THR* 1.3 76.8 - - + +
149B LEU* 1.3 58.0 + - + +
151B LEU* 3.4 3.8 + - + +
152B ALA* 3.0 28.8 + - - +
166B ILE* 4.0 21.1 - - + +
168B ILE* 4.9 0.9 - - + -
173B ILE* 3.8 32.3 - - + -
188B LEU* 3.8 22.7 - - + -
191B LEU* 4.1 17.7 - - + -
197B ILE* 4.2 20.2 - - + -
204B ILE* 4.3 9.9 - - + -
206B VAL* 3.8 16.6 - - + +
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Residues in contact with LEU 149 (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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145B ALA* 3.1 24.4 + - + +
146B GLN* 3.7 27.6 - - - +
148B LEU* 1.3 73.9 - - + +
150B ASN* 1.3 66.0 + - - +
152B ALA* 3.2 14.7 + - + +
153B LYS* 3.3 35.2 + - - +
206B VAL* 4.1 20.0 - - + -
207B TYR 5.8 2.0 - - - +
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Residues in contact with ASN 150 (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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134B ASN* 5.3 5.5 + - - -
146B GLN* 2.8 46.8 + - - +
147B THR* 3.6 7.4 - - + +
149B LEU* 1.3 73.2 - - - +
151B LEU* 1.3 63.0 + - + +
153B LYS* 3.2 22.2 + - - +
154B GLN* 3.5 16.9 + - - +
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Residues in contact with LEU 151 (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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147B THR* 2.9 44.4 + - + +
148B LEU* 3.7 7.0 - - + +
149B LEU 3.2 0.2 - - - -
150B ASN* 1.3 74.1 - - + +
152B ALA* 1.3 61.0 + - - +
153B LYS 3.1 0.4 - - - -
154B GLN* 3.2 33.6 + - + +
156B ASP* 5.0 0.3 - - - +
157B ALA* 3.5 7.6 - - - +
166B ILE* 3.7 21.1 - - + +
168B ILE* 4.0 46.0 - - + -
173B ILE* 5.1 0.4 - - + -
176B ILE* 4.7 6.5 - - + -
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Residues in contact with ALA 152 (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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148B LEU 3.0 16.2 + - - +
149B LEU* 3.2 7.1 + - + +
151B LEU* 1.3 75.4 - - - +
153B LYS* 1.3 59.7 + - + +
154B GLN 3.4 0.6 - - - +
157B ALA* 3.3 20.8 - - - +
164B MET* 3.6 36.8 - - + +
166B ILE* 3.9 6.0 - - + +
206B VAL* 4.0 24.2 - - + -
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Residues in contact with LYS 153 (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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149B LEU* 3.5 28.9 + - - +
150B ASN* 3.2 17.6 + - - +
151B LEU 3.1 0.6 - - - -
152B ALA* 1.3 77.8 - - + +
154B GLN* 1.3 65.8 + - - +
155B PRO* 3.8 3.1 - - - +
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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