Contacts of the helix formed by residues 153 - 162 (chain B) in PDB entry 3IO6
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 GLU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ASN* 3.4 25.6 + - - +
151B LEU 4.6 1.1 - - - -
152B GLN* 1.3 94.3 - - - +
154B PRO* 1.3 72.4 - - + +
155B TYR* 4.5 5.4 - - + +
156B PHE* 3.1 35.3 + - + +
157B THR* 3.4 10.8 + - - +
344B ARG* 2.8 40.4 + - - -
347B VAL* 6.0 0.4 - - - -
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Residues in contact with PRO 154 (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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152B GLN 4.1 1.1 - - - +
153B GLU* 1.3 82.5 - - + +
155B TYR* 1.3 61.2 + - + +
156B PHE 3.0 2.7 - - - -
157B THR* 3.4 11.2 - - - +
158B TRP* 2.7 39.1 + - + +
340B TRP* 4.0 23.1 - - + +
343B VAL* 3.8 23.3 - - + +
344B ARG* 3.5 47.1 - - + +
347B VAL* 5.0 3.6 - - + -
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Residues in contact with TYR 155 (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 GLU* 4.9 3.3 + - - +
112B ALA* 4.7 3.3 - - - -
113B LEU* 3.3 41.6 + - + +
153B GLU* 3.2 4.0 - - + -
154B PRO* 1.3 80.7 - - + +
156B PHE* 1.3 79.5 + + + +
158B TRP* 4.3 2.4 - - - +
159B PRO* 3.6 8.5 - - - +
230B TRP* 3.9 33.4 - + - -
258B PHE* 3.7 34.7 + + + -
260B GLY 5.5 1.7 + - - -
330B MET* 3.7 31.3 - - + +
340B TRP* 4.1 17.9 - + + -
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Residues in contact with PHE 156 (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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113B LEU* 3.9 23.4 - - + +
149B PHE* 3.7 15.4 - + + -
150B ASN* 3.2 43.3 - - + +
153B GLU* 3.1 23.4 + - + +
154B PRO 3.0 0.4 - - - -
155B TYR* 1.3 93.5 - + + +
157B THR* 1.3 63.3 + - - +
158B TRP 3.3 0.4 - - - -
159B PRO* 3.4 17.2 - - - +
210B TYR* 3.8 27.4 - + - -
226B ILE* 3.7 31.5 - - + +
227B ASN* 4.0 11.4 - - - -
230B TRP* 4.5 11.2 - + - -
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Residues in contact with THR 157 (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 PHE* 3.8 19.7 - - + -
150B ASN 3.9 1.8 - - - +
151B LEU* 3.7 39.7 - - + +
153B GLU 3.4 1.3 + - - +
154B PRO* 3.4 18.4 - - - +
156B PHE* 1.3 74.0 - - - +
158B TRP* 1.3 65.7 + - - +
159B PRO 3.5 0.4 - - - -
160B LEU* 3.2 17.5 + - - +
161B ILE* 3.5 15.8 + - - +
195B LEU* 4.0 24.2 - - + +
347B VAL* 3.8 16.2 - - + +
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Residues in contact with TRP 158 (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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154B PRO* 2.7 22.9 + - + +
155B TYR 4.3 2.0 - - - +
157B THR* 1.3 67.6 + - - +
159B PRO* 1.3 74.2 - - + +
160B LEU 2.8 4.5 + - - -
161B ILE* 2.8 46.3 + - + -
162B ALA* 2.8 31.4 + - + +
166B GLY 4.1 0.9 - - - -
167B TYR* 3.9 28.3 - - - -
168B ALA 4.0 0.7 - - - -
182B GLY 4.4 6.3 - - - -
183B VAL* 4.3 13.5 - - + -
256B LYS 3.9 10.3 - - - -
258B PHE* 3.1 36.1 - + + -
328B GLU* 3.2 18.8 + - - -
339B PHE* 3.5 33.9 - + - -
343B VAL* 4.1 19.7 - - + -
361B LEU* 6.0 0.9 - - + -
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Residues in contact with PRO 159 (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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113B LEU* 4.2 8.5 - - + -
129B TRP* 5.9 2.7 - - + -
155B TYR 3.6 9.9 - - - +
156B PHE 3.4 16.6 - - - +
158B TRP* 1.3 93.1 - - + +
160B LEU* 1.3 57.0 + - + +
163B ALA* 3.3 17.0 + - - +
226B ILE* 5.3 5.4 - - + -
247B LEU* 4.4 11.4 - - + -
255B SER* 3.3 34.5 + - - +
256B LYS 3.4 14.7 + - - +
257B PRO* 3.8 29.6 - - + -
258B PHE 5.1 0.7 - - - +
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Residues in contact with LEU 160 (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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129B TRP* 3.7 50.5 - - + -
149B PHE* 5.9 1.1 - - + -
157B THR* 3.2 10.6 + - - +
158B TRP 2.8 4.4 + - - -
159B PRO* 1.3 76.6 - - - +
161B ILE* 1.3 64.9 + - + +
162B ALA 3.4 0.2 - - - -
163B ALA* 3.5 12.0 - - - +
164B ASP 4.5 0.2 + - - -
191B GLY* 3.7 18.4 - - - +
194B PHE* 4.1 12.8 - - + -
195B LEU* 3.9 31.6 - - + +
198B LEU* 5.2 0.2 - - + -
250B PHE* 3.7 39.7 - - + -
255B SER* 4.4 1.8 - - - -
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Residues in contact with ILE 161 (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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154B PRO 5.4 0.2 - - - +
157B THR* 3.6 22.7 - - - +
158B TRP* 2.8 47.1 + - + +
160B LEU* 1.3 73.6 - - + +
162B ALA* 1.3 60.4 + - - +
163B ALA 3.4 0.5 + - - -
164B ASP 4.1 0.7 + - - -
166B GLY 4.1 0.5 + - - -
187B GLY 3.6 7.1 - - - +
188B ALA* 3.4 46.5 + - + +
191B GLY* 4.3 7.4 - - - -
192B LEU* 4.4 21.1 - - + +
195B LEU* 5.6 2.2 - - + -
343B VAL* 4.6 3.1 - - + -
347B VAL* 3.8 28.3 - - + -
361B LEU* 5.0 9.9 - - + -
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Residues in contact with ALA 162 (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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158B TRP* 2.8 39.6 + - + +
161B ILE* 1.3 75.9 - - - +
163B ALA* 1.3 65.5 + - - +
164B ASP 3.1 3.0 + - - -
165B GLY* 3.1 12.2 + - - -
166B GLY* 3.3 27.7 - - - +
256B LYS* 4.0 27.3 - - + +
328B GLU* 4.6 2.5 - - - +
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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