Contacts of the helix formed by residues 180 - 194 (chain B) in PDB entry 4O9U
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 ILE 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ALA* 5.0 1.8 - - + -
104B LEU* 3.9 30.3 - - + +
105B LEU* 3.7 35.0 - - + -
171B LEU* 3.8 22.0 - - + -
175B ASP* 4.2 11.0 - - + +
176B ALA 3.6 20.6 - - - +
177B THR* 3.9 13.0 - - + -
178B ALA 3.5 0.6 - - - +
179B SER* 1.3 77.6 - - - +
181B VAL* 1.3 65.6 + - + +
182B LEU 3.3 0.9 - - - -
183B PHE* 3.1 7.3 + - - +
184B PHE* 2.8 52.8 + - + -
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Residues in contact with VAL 181 (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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101B ALA* 6.4 1.6 - - + -
105B LEU* 6.2 2.2 - - + -
177B THR 4.7 13.5 - - - +
178B ALA* 5.0 7.0 - - - +
180B ILE* 1.3 79.0 - - + +
182B LEU* 1.3 58.3 + - + +
184B PHE* 3.5 11.6 - - + +
185B LEU* 2.6 49.9 + - + +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 6.1 3.1 - - + -
167B ILE* 3.7 25.1 - - + -
178B ALA 4.2 18.1 + - - +
179B SER* 4.6 1.6 - - - -
180B ILE 3.3 0.8 - - - +
181B VAL* 1.3 79.3 - - + +
183B PHE* 1.3 58.1 + - - +
185B LEU* 4.5 9.6 - - + +
186B LEU* 3.1 42.8 + - + +
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Residues in contact with PHE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 5.1 0.4 - - + -
119B ILE* 3.3 42.2 - - + -
122B GLY 4.6 0.4 - - - -
123B LEU* 3.6 33.0 - - + -
164B THR* 3.1 32.8 - - + +
167B ILE* 3.6 17.8 - - + +
168B GLY* 3.5 17.0 - - - -
171B LEU* 4.1 12.6 - - + -
179B SER 3.5 16.6 + - - +
180B ILE 3.1 15.5 + - - +
182B LEU* 1.3 78.0 - - - +
184B PHE* 1.3 83.0 + + - +
186B LEU* 3.7 0.6 + - - -
187B ALA* 3.3 17.8 + - - +
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Residues in contact with PHE 184 (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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97B ALA* 3.2 42.4 - - + -
100B ALA* 4.0 9.0 - - + -
101B ALA* 3.7 29.4 - - + -
104B LEU* 4.3 4.0 - - + -
122B GLY* 3.8 13.0 - - - -
126B SER* 3.3 20.4 - - - -
180B ILE* 2.8 40.2 + - + +
181B VAL* 3.1 15.2 + - + +
183B PHE* 1.3 91.5 - + - +
185B LEU* 1.3 60.6 + - + +
187B ALA* 3.4 5.2 + - - +
188B LEU* 2.9 37.3 + - + +
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Residues in contact with LEU 185 (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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181B VAL* 2.6 34.2 + - + +
182B LEU* 4.5 9.4 - - + +
184B PHE* 1.3 71.0 - - + +
186B LEU* 1.3 55.2 + - - +
187B ALA 3.2 0.4 - - - -
188B LEU* 3.4 25.5 - - + +
189B LEU* 2.6 35.8 + - - +
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Residues in contact with LEU 186 (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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160B VAL* 3.3 41.3 - - + +
163B LEU* 3.9 24.2 - - + -
164B THR* 3.2 33.0 + - + +
167B ILE* 3.8 19.7 - - + -
182B LEU* 3.1 33.8 + - + +
183B PHE 3.7 1.3 - - - +
185B LEU* 1.3 77.7 - - - +
187B ALA* 1.3 52.6 + - - +
189B LEU* 3.7 8.0 - - + +
190B PHE* 2.8 32.7 + - - +
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Residues in contact with ALA 187 (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 GLY 4.9 0.2 - - - +
123B LEU* 3.5 31.2 - - + +
126B SER* 3.7 13.0 - - - -
127B VAL* 3.4 21.1 - - + +
164B THR* 3.6 12.3 - - + +
183B PHE* 3.3 11.2 + - + +
184B PHE* 3.7 4.5 - - - +
185B LEU 3.2 0.2 - - - -
186B LEU* 1.3 74.8 - - - +
188B LEU* 1.3 61.5 + - - +
189B LEU 3.1 1.6 - - - -
190B PHE* 4.3 0.9 - - - +
191B GLY* 2.8 23.7 + - - -
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Residues in contact with LEU 188 (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 SER* 3.6 23.1 - - - +
129B PHE* 3.5 34.1 - - + -
130B THR* 3.0 36.7 + - + +
184B PHE* 2.9 30.8 + - + +
185B LEU* 3.4 31.4 - - + +
187B ALA* 1.3 75.9 - - - +
189B LEU* 1.3 57.6 + - - +
192B VAL* 3.4 11.3 + - - +
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Residues in contact with LEU 189 (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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160B VAL* 3.5 32.3 - - + -
185B LEU 2.6 20.9 + - - +
186B LEU* 3.7 9.4 - - + +
188B LEU* 1.3 73.8 - - - +
190B PHE* 1.3 59.6 + - - +
191B GLY 3.0 1.6 - - - -
192B VAL* 2.9 28.8 + - + +
193B LEU* 3.0 29.6 + - + -
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Residues in contact with PHE 190 (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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127B VAL* 4.0 21.4 - - + +
157B ASN* 3.3 44.2 - - + -
160B VAL* 3.9 12.3 - - + -
161B LEU* 3.7 46.2 - - + -
164B THR* 4.7 3.8 - - + +
186B LEU 2.8 23.1 + - - +
187B ALA* 4.3 4.5 - - - +
189B LEU* 1.3 69.1 - - - +
191B GLY* 1.3 64.6 + - - +
193B LEU* 3.9 6.7 - - + -
194B MET* 3.2 58.6 + - + +
213B PHE* 6.3 1.1 - + - -
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Residues in contact with GLY 191 (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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127B VAL* 3.7 20.9 - - - -
130B THR* 3.4 17.9 - - - -
131B GLY* 3.2 12.6 - - - -
187B ALA 2.8 13.9 + - - -
189B LEU 3.0 0.6 - - - -
190B PHE* 1.3 79.4 - - - +
192B VAL* 1.3 49.5 + - - +
195B THR* 2.7 33.0 + - - +
210B TYR* 3.9 2.6 + - - -
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Residues in contact with VAL 192 (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 THR* 4.0 12.1 - - + -
134B ILE* 3.8 34.8 - - + -
188B LEU 3.4 16.4 - - - +
189B LEU* 2.9 16.5 + - + +
191B GLY* 1.3 75.9 - - - +
193B LEU* 1.3 65.2 + - + +
195B THR* 3.3 10.2 + - - +
196B LEU* 3.1 36.9 - - + +
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Residues in contact with LEU 193 (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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150B PHE* 4.0 29.2 - - + -
153B GLN* 4.4 1.6 - - - +
156B VAL* 3.9 10.5 - - + +
157B ASN* 3.4 34.2 + - - +
160B VAL* 3.8 24.5 - - + -
189B LEU* 3.0 40.4 + - + +
190B PHE* 4.1 6.1 - - + +
191B GLY 3.5 0.2 - - - -
192B VAL* 1.3 77.4 - - + +
194B MET* 1.3 61.3 + - - +
196B LEU* 3.4 30.7 + - + +
197B PRO* 3.5 6.4 - - - +
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Residues in contact with MET 194 (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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127B VAL* 5.2 3.8 - - + -
157B ASN* 4.0 13.9 - - + +
190B PHE* 3.2 50.0 + - + +
193B LEU* 1.3 77.7 - - - +
195B THR* 1.3 57.0 + - - +
196B LEU 3.4 1.6 - - - -
197B PRO* 3.5 9.9 - - + +
198B ILE* 3.5 19.3 - - + +
209B PHE* 4.9 17.5 - - + -
210B TYR* 3.4 33.4 - - + +
213B PHE* 5.4 6.1 - - + -
260B LEU* 4.6 17.5 - - + +
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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