Contacts of the helix formed by residues 183 - 195 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C LEU 3.1 10.1 + - - -
179C ALA 3.1 18.5 + - - -
182C ILE* 1.3 76.8 - - - +
184C ILE* 1.3 63.5 + - - +
186C PHE* 2.9 38.9 + - - -
187C PHE* 2.9 16.9 + - - -
225C LEU* 3.9 4.7 - - - -
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LYS* 3.4 40.8 - - + -
102C PRO* 4.0 19.5 - - + -
128C LEU* 5.1 4.3 - - + -
179C ALA 3.3 3.1 + - - -
180C THR* 3.1 22.5 + - + +
181C ASN 4.4 0.9 - - - +
182C ILE 3.1 1.4 + - - -
183C GLY* 1.3 76.6 - - - +
185C HIS* 1.3 67.2 + - - +
187C PHE* 4.4 4.3 - - + -
188C ASP* 2.9 30.2 + - + +
285C ALA* 3.6 41.1 - - + +
286C ILE* 3.9 13.9 - - + +
289C ALA* 4.1 13.7 - - + -
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Residues in contact with HIS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LYS* 3.6 25.0 - - + +
127C VAL 5.2 0.2 - - - -
128C LEU* 5.2 7.7 - - - +
129C GLN* 3.4 34.8 + - - -
130C LEU* 3.6 24.0 + - + +
156C TYR* 3.6 26.5 - - + +
182C ILE 3.4 17.2 + - - +
183C GLY 3.0 0.4 + - - -
184C ILE* 1.3 81.3 - - + +
186C PHE* 1.3 58.3 + - - +
188C ASP* 3.6 4.3 + - - +
189C LEU* 3.0 24.9 + - - +
260C PHE* 3.8 7.4 - + - -
311C NAD 3.7 7.4 + - - -
312C AKG 2.8 33.0 + - + -
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Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 4.8 0.9 - - - -
154C LEU* 3.6 35.2 - - + -
156C TYR* 3.8 32.1 - + + -
183C GLY* 2.9 30.5 + - - -
185C HIS* 1.3 75.6 - - - +
187C PHE* 1.3 100.3 + + - +
188C ASP 3.1 1.6 - - - -
189C LEU* 3.6 8.4 - - + +
190C LEU* 2.9 37.3 + - + +
223C TRP* 3.6 38.8 - + + -
224C PHE 5.1 0.4 - - - -
225C LEU* 3.8 24.2 - - + -
256C PHE* 5.4 0.2 - - + -
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Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ALA* 3.5 24.7 - - + -
183C GLY* 2.9 28.2 + - - +
184C ILE* 4.2 4.0 - - - +
186C PHE* 1.3 111.3 - + - +
188C ASP* 1.3 57.7 + - - +
190C LEU* 3.4 4.1 + - + +
191C ALA* 3.0 28.6 + - - +
214C LEU* 4.0 25.8 - - + -
223C TRP* 3.9 17.7 - + - -
285C ALA* 3.7 21.3 - - + +
288C VAL* 4.0 18.7 - - + +
289C ALA* 4.9 5.8 - - + -
292C LEU* 3.4 30.5 - - + -
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Residues in contact with ASP 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C LEU* 3.6 32.2 - - + +
130C LEU* 6.0 1.2 - - - +
131C ARG* 2.8 47.6 + - - +
184C ILE* 2.9 20.4 + - + +
185C HIS 3.7 3.4 - - - +
187C PHE* 1.3 75.0 - - - +
189C LEU* 1.3 60.9 + - - +
191C ALA* 3.3 2.3 + - - +
192C TRP* 2.8 29.6 + - - +
281C GLU 3.8 5.9 - - - +
282C ALA* 4.3 3.1 - - - -
285C ALA* 3.4 18.9 + - + +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 4.3 9.2 - - + -
131C ARG* 5.9 0.4 - - - -
136C LEU* 4.0 26.7 - - + -
154C LEU* 4.4 9.6 - - + -
185C HIS 3.0 18.4 + - - +
186C PHE* 3.6 6.3 - - - +
188C ASP* 1.3 78.9 + - - +
190C LEU* 1.3 62.6 + - + +
192C TRP* 3.3 32.7 + - + +
193C LEU* 3.0 45.6 + - + +
247C ILE* 4.3 16.6 - - + -
256C PHE* 4.1 29.8 - - + -
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL* 4.3 3.6 - - + -
154C LEU* 4.4 10.3 - - + -
186C PHE* 2.9 39.3 + - + +
187C PHE* 3.8 5.4 - - - +
189C LEU* 1.3 78.9 - - + +
191C ALA* 1.3 57.7 + - - +
193C LEU 3.3 0.3 + - - -
194C PHE* 2.8 58.6 + - + +
214C LEU* 3.9 19.7 - - + -
216C LEU* 3.4 14.2 - - + +
221C VAL* 3.7 35.0 - - + -
247C ILE* 4.3 16.8 - - + -
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ARG* 5.5 2.0 - - - +
187C PHE 3.0 17.8 + - - +
188C ASP* 3.8 6.3 - - - +
190C LEU* 1.3 72.7 - - - +
192C TRP* 1.3 63.4 + - - +
195C GLY* 2.9 35.5 + - - +
216C LEU* 4.1 1.9 - - + +
281C GLU 5.9 0.9 - - - +
284C GLU* 3.6 36.1 - - + -
285C ALA* 4.5 4.9 - - - +
288C VAL* 6.2 0.7 - - + -
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Residues in contact with TRP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU 4.0 5.8 - - - -
131C ARG* 3.5 83.5 - - + +
136C LEU* 4.3 15.5 - - + -
137C LEU* 3.9 19.5 - - + -
140C LYS* 3.3 47.0 - - + +
188C ASP 2.8 17.3 + - - +
189C LEU* 3.5 32.3 - - + +
191C ALA* 1.3 78.0 - - - +
193C LEU* 1.3 65.2 + - + +
195C GLY 5.0 0.2 + - - -
277C PHE* 6.0 0.6 - - - -
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU 5.0 1.3 - - - +
139C LEU* 4.7 5.4 - - + -
140C LYS* 3.6 48.4 - - + +
143C LEU* 4.3 11.7 - - + -
189C LEU* 3.0 38.5 + - + +
190C LEU* 5.0 0.2 - - - -
192C TRP* 1.3 87.0 - - + +
194C PHE* 1.3 97.6 + - + +
195C GLY 3.8 0.2 - - - -
247C ILE* 3.8 17.9 - - + -
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Residues in contact with PHE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.9 23.6 - - + -
150C LYS* 4.0 22.4 - - + -
152C VAL* 3.7 27.1 - - + -
190C LEU* 2.8 39.8 + - + +
193C LEU* 1.3 106.4 - - + +
195C GLY* 1.3 63.6 + - - +
216C LEU* 3.7 10.5 - - + +
217C GLU* 3.6 5.9 + - - +
218C GLY* 2.8 39.4 + - - -
219C ALA* 3.5 24.7 - - + +
221C VAL* 5.0 0.9 - - + -
247C ILE* 4.5 3.6 - - + -
249C VAL* 4.4 4.9 - - + -
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ALA* 2.9 28.4 + - - +
192C TRP 5.0 0.2 + - - -
193C LEU 3.8 0.4 - - - -
194C PHE* 1.3 79.6 - - - +
196C ARG* 1.3 63.1 + - - -
197C ALA 3.8 0.3 + - - -
216C LEU* 3.3 15.2 - - - +
217C GLU* 3.5 9.4 - - - -
284C GLU* 4.2 4.2 - - - +
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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