Contacts of the helix formed by residues 184 - 194 (chain A) in PDB entry 2O8C
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 PHE 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A MET* 4.4 10.8 - - - -
159A ARG* 4.7 9.0 - - - -
161A VAL* 4.7 5.8 - - + -
180A ASP* 3.8 25.4 - - + +
181A ASN 3.3 18.5 + - - +
182A ASP 3.9 11.7 - - - -
183A GLN* 1.3 86.4 - - - +
185A SER* 1.3 64.6 + - - +
186A ASN 3.4 2.6 + - - -
187A LEU* 3.7 25.2 + - + +
188A GLU* 3.9 13.9 - - - +
209A ASP* 3.8 32.3 - - + -
212A LYS* 4.2 16.4 - - + -
213A LEU* 3.6 45.5 - - + -
216A ILE* 4.2 8.1 - - + +
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Residues in contact with SER 185 (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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181A ASN* 3.6 32.0 - - - +
183A GLN 3.6 1.3 - - - -
184A PHE* 1.3 74.8 - - - +
186A ASN* 1.3 68.9 + - - +
187A LEU 3.5 0.7 + - - -
188A GLU* 3.6 25.2 + - - +
189A ALA* 3.7 5.7 + - - +
301A LYS* 5.8 1.9 - - - +
302A LEU 5.5 0.3 - - - +
303A ASP* 5.3 4.2 + - - -
734A SER* 3.9 21.5 + - - -
738A SER* 3.5 17.7 + - - -
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Residues in contact with ASN 186 (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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178A PHE* 3.7 13.7 - - + +
179A PRO* 3.0 26.8 + - - +
180A ASP* 3.2 15.7 + - - +
181A ASN* 5.2 7.1 + - - +
184A PHE 3.4 0.6 - - - -
185A SER* 1.3 83.2 + - - +
187A LEU* 1.3 64.0 + - - +
189A ALA* 3.4 8.2 - - - +
190A LEU* 3.2 25.6 + - - +
296A PHE* 4.1 20.9 - - + -
301A LYS* 3.3 25.2 + - - +
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Residues in contact with LEU 187 (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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150A VAL* 4.3 18.2 - - + -
161A VAL* 4.3 5.2 - - + -
163A VAL* 3.8 20.6 - - + -
178A PHE* 3.7 19.7 - - + -
180A ASP* 3.4 21.7 + - - +
184A PHE* 3.7 16.1 + - + +
185A SER 3.3 0.8 - - - -
186A ASN* 1.3 75.3 - - - +
188A GLU* 1.3 55.1 + - - +
190A LEU* 3.0 6.4 + - + +
191A LEU* 2.8 52.2 + - + +
213A LEU* 3.7 31.2 - - + -
216A ILE* 5.3 5.8 - - + -
217A ILE* 5.4 7.6 - - + -
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Residues in contact with GLU 188 (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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183A GLN 4.9 2.3 - - - +
184A PHE 3.9 13.6 - - - +
185A SER* 3.6 13.8 + - - +
187A LEU* 1.3 76.6 - - - +
189A ALA* 1.3 63.6 + - - +
191A LEU* 3.2 8.5 + - - +
192A ILE* 2.9 33.7 + - + +
216A ILE* 4.0 17.6 - - + +
219A ARG* 4.2 12.0 + - - -
302A LEU 4.2 6.5 - - - +
303A ASP* 3.5 30.7 - - - +
304A ILE* 3.5 36.6 + - + +
734A SER* 5.6 3.5 + - - -
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Residues in contact with ALA 189 (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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185A SER 3.7 5.6 + - - +
186A ASN* 3.4 15.2 + - - +
187A LEU 3.2 0.6 - - - -
188A GLU* 1.3 78.8 - - - +
190A LEU* 1.3 59.1 + - - +
192A ILE* 3.8 2.5 + - - +
193A GLN* 3.1 34.7 + - - +
296A PHE* 4.8 7.2 - - + -
301A LYS* 3.8 39.7 - - + +
302A LEU 4.2 13.4 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 4.7 15.0 - - + -
165A TYR* 6.1 2.2 - - + -
176A CYS* 3.8 22.0 - - + -
178A PHE* 3.6 34.8 - - + -
186A ASN 3.2 23.6 + - - +
187A LEU* 3.0 9.1 + - + +
189A ALA* 1.3 73.4 - - - +
191A LEU* 1.3 62.2 + - + +
192A ILE 3.0 4.9 - - - -
193A GLN* 3.0 8.3 + - - +
194A ILE* 2.9 49.1 + - + +
296A PHE* 3.7 35.2 - - + -
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Residues in contact with LEU 191 (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 VAL* 4.5 13.0 - - + -
150A VAL* 5.0 11.2 - - + -
163A VAL* 5.6 3.6 - - + -
187A LEU* 2.8 39.7 + - + +
188A GLU* 3.7 7.4 - - - +
190A LEU* 1.3 73.6 - - + +
192A ILE* 1.3 58.6 + - + +
194A ILE* 5.3 4.5 - - + -
195A GLY* 3.4 20.1 - - - -
196A PRO* 3.4 28.0 - - + +
199A CYS* 5.7 1.1 - - - -
216A ILE* 4.9 6.3 - - + +
217A ILE* 4.0 37.9 - - + -
222A ILE* 4.7 18.1 - - + +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A GLU* 2.9 18.3 + - - +
189A ALA* 4.2 4.0 - - - +
191A LEU* 1.3 80.8 - - + +
193A GLN* 1.3 64.4 + - + +
195A GLY* 3.7 2.0 + - - -
302A LEU* 3.4 44.6 - - + +
303A ASP 3.4 23.1 - - - +
304A ILE* 4.1 13.9 - - + +
307A VAL* 3.8 22.2 - - + -
312A LEU* 5.6 0.9 - - + -
313A PHE* 6.3 1.6 - - + -
347A LYS* 3.4 32.2 - - + +
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Residues in contact with GLN 193 (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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189A ALA* 3.1 26.2 + - - +
190A LEU* 3.0 7.5 + - - +
192A ILE* 1.3 78.5 - - + +
194A ILE* 1.3 62.7 + - + +
296A PHE* 3.6 25.5 + - - +
299A TYR* 3.3 37.1 - - + +
300A MET 3.2 27.7 + - - +
301A LYS* 4.2 4.4 - - - +
344A GLN* 5.3 1.2 + - - -
347A LYS* 3.3 39.2 - - - +
348A GLN* 3.3 23.6 + - + +
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Residues in contact with ILE 194 (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 ILE* 3.9 25.2 - - + +
148A VAL* 3.8 27.1 - - + -
163A VAL* 5.0 8.3 - - + -
165A TYR* 4.1 38.4 - - + +
190A LEU* 2.9 38.9 + - + +
191A LEU* 5.3 2.5 - - + -
193A GLN* 1.3 77.1 - - + +
195A GLY* 1.3 66.8 + - - +
196A PRO* 3.6 10.3 - - + -
344A GLN* 6.1 0.7 - - - +
347A LYS* 3.5 8.3 + - - -
348A GLN* 4.6 10.1 - - - +
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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