Contacts of the helix formed by residues 183 - 195 (chain B) in PDB entry 3O9Z
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 GLY 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B LEU 3.1 8.5 + - - -
179B ALA 3.1 16.5 + - - -
182B ILE* 1.3 78.4 - - - +
184B ILE* 1.3 66.5 + - - +
185B HIS 3.0 0.4 - - - -
186B PHE* 3.0 29.3 + - - -
187B PHE* 3.0 26.1 + - - -
225B LEU* 3.9 5.4 - - - +
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Residues in contact with ILE 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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101B LYS* 3.5 39.7 - - + -
102B PRO* 4.0 19.5 - - + -
128B LEU* 5.1 4.3 - - + -
179B ALA 3.2 2.5 + - - -
180B THR* 3.1 23.0 + - + +
181B ASN 4.4 0.7 - - - +
182B ILE 4.6 0.2 - - - +
183B GLY* 1.3 76.4 - - - +
185B HIS* 1.3 67.4 + - - +
187B PHE* 4.4 3.6 - - + -
188B ASP* 2.9 30.6 + - + +
285B ALA* 3.6 40.2 - - + +
286B ILE* 3.8 17.7 - - + +
289B ALA* 4.1 11.2 - - + -
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Residues in contact with HIS 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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101B LYS* 3.6 24.1 - - + +
128B LEU* 5.2 7.5 - - - +
129B GLN* 3.3 35.4 + - - -
130B LEU* 3.6 24.4 + - + +
156B TYR* 3.6 27.4 - - + +
182B ILE 3.4 15.8 + - - +
183B GLY 3.0 0.6 + - - -
184B ILE* 1.3 83.9 - - + +
186B PHE* 1.3 58.0 + - - +
188B ASP* 3.8 4.3 - - - +
189B LEU* 3.0 24.9 + - - +
260B PHE* 3.8 6.7 - + - -
311B NAD 3.4 8.7 + - - -
312B AKG 2.8 34.3 + - + -
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Residues in contact with PHE 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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130B LEU* 4.9 0.4 - - - -
154B LEU* 3.6 33.7 - - + -
156B TYR* 3.7 36.1 - + + -
183B GLY* 3.0 27.6 + - - -
185B HIS* 1.3 75.8 - - - +
187B PHE* 1.3 106.7 + + - +
188B ASP 3.1 1.3 - - - -
189B LEU* 3.5 9.6 - - + +
190B LEU* 2.9 37.1 + - + +
223B TRP* 3.7 33.4 - + + -
224B PHE 4.9 0.7 - - - -
225B LEU* 3.8 22.0 - - + -
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Residues in contact with PHE 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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179B ALA* 3.5 23.3 - - + -
183B GLY* 3.0 28.9 + - - +
184B ILE* 4.2 3.8 - - - +
186B PHE* 1.3 108.8 - + - +
188B ASP* 1.3 57.3 + - - +
190B LEU* 3.4 4.3 + - - +
191B ALA* 3.0 27.9 + - - +
214B LEU* 4.0 20.4 - - + -
223B TRP* 3.9 24.7 - + - -
285B ALA* 3.6 22.1 - - + +
288B VAL* 3.9 20.7 - - + +
289B ALA* 4.8 6.3 - - + -
292B LEU* 3.4 31.2 - - + -
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Residues in contact with ASP 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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128B LEU* 3.5 33.8 - - + +
130B LEU* 6.0 1.4 - - - +
131B ARG* 2.8 47.3 + - - +
184B ILE* 2.9 20.9 + - + +
185B HIS 3.8 2.8 - - - +
187B PHE* 1.3 74.3 - - - +
189B LEU* 1.3 65.4 + - - +
191B ALA* 3.2 3.0 + - - +
192B TRP* 2.9 24.4 + - - +
281B GLU 3.8 5.9 - - - +
282B ALA* 4.4 2.8 - - - -
285B ALA* 3.4 19.6 + - + +
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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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130B LEU* 4.3 11.9 - - + -
131B ARG* 5.9 0.9 - - - -
136B LEU* 3.9 30.5 - - + -
154B LEU* 4.4 15.3 - - + -
185B HIS 3.0 18.2 + - - +
186B PHE* 3.5 6.5 - - - +
188B ASP* 1.3 77.0 + - - +
190B LEU* 1.3 59.5 + - - +
192B TRP* 3.3 28.7 + - + +
193B LEU* 3.0 50.0 + - + +
247B ILE* 4.5 7.2 - - + -
256B PHE* 3.9 33.7 - - + -
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Residues in contact with LEU 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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152B VAL* 4.3 2.9 - - + -
154B LEU* 4.4 10.8 - - + -
186B PHE* 2.9 39.6 + - + +
187B PHE* 3.8 5.2 - - - +
188B ASP 3.2 0.2 - - - -
189B LEU* 1.3 78.0 - - + +
191B ALA* 1.3 56.9 + - - +
193B LEU* 4.6 0.7 - - - -
194B PHE* 2.8 57.8 + - + +
214B LEU* 3.7 26.7 - - + -
216B LEU* 3.8 13.9 - - + +
221B VAL* 3.8 26.5 - - + -
223B TRP* 5.3 0.2 - - + -
247B ILE* 4.3 16.8 - - + -
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Residues in contact with ALA 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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131B ARG* 5.4 2.2 - - - +
187B PHE 3.0 17.6 + - - +
188B ASP* 3.2 8.7 + - - +
190B LEU* 1.3 78.5 - - - +
192B TRP* 1.3 60.4 + - - +
195B GLY* 2.9 35.3 + - - +
216B LEU* 4.8 1.1 - - - +
281B GLU 5.9 1.6 - - - +
284B GLU* 3.8 32.8 - - + -
285B ALA* 4.6 4.5 - - - +
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Residues in contact with TRP 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 LEU 4.1 4.5 - - - -
131B ARG* 3.5 83.9 - - + +
136B LEU* 4.2 17.3 - - + -
137B LEU* 3.8 21.8 - - + -
140B LYS* 3.5 43.0 - - + +
188B ASP 2.9 17.5 + - - +
189B LEU* 3.5 31.2 - - + +
191B ALA* 1.3 78.1 - - - +
193B LEU* 1.3 70.0 + - + +
195B GLY 4.9 0.2 + - - -
277B PHE* 5.8 1.4 - - - -
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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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136B LEU* 4.7 1.8 - - + +
139B LEU* 4.5 5.6 - - + -
140B LYS* 3.5 47.5 - - + +
143B LEU* 4.4 12.0 - - + +
189B LEU* 3.0 36.7 + - + +
192B TRP* 1.3 89.0 - - + +
194B PHE* 1.3 90.6 + - + +
195B GLY 3.8 0.4 - - - -
247B ILE* 3.8 28.9 - - + -
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Residues in contact with PHE 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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143B LEU* 3.7 33.4 - - + -
150B LYS* 3.9 17.9 - - + -
152B VAL* 3.7 28.0 - - + -
190B LEU* 2.8 39.8 + - + +
193B LEU* 1.3 103.1 - - + +
195B GLY* 1.3 65.1 + - - +
216B LEU* 3.7 13.8 - - + +
217B GLU* 3.4 5.7 + - - +
218B GLY* 2.8 46.7 + - - -
219B ALA* 3.5 15.0 - - + -
247B ILE* 4.4 3.4 - - + -
249B VAL* 4.4 3.6 - - + -
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Residues in contact with GLY 195 (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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191B ALA* 2.9 36.5 + - - +
192B TRP 4.9 0.2 + - - -
193B LEU 3.8 0.4 - - - -
194B PHE* 1.3 80.9 - - - +
196B ARG* 1.3 63.1 + - - +
197B ALA 3.9 1.0 + - - -
216B LEU* 4.2 8.0 - - - +
217B GLU* 3.7 8.3 - - - -
284B GLU* 4.2 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