Contacts of the helix formed by residues 175 - 190 (chain C) in PDB entry 2BP1
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 ALA 175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TYR* 1.3 75.6 - - - +
176C SER* 1.3 68.4 + - - +
177C TRP* 3.6 28.5 - - + +
178C GLU* 2.9 29.7 + - + +
179C VAL* 3.0 12.2 + - - +
358C TYR* 3.8 3.1 - - - -
359C PHE* 3.5 30.1 - - + +
211D GLU* 3.9 5.8 - - + +
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Residues in contact with SER 176 (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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174C TYR 3.8 0.4 + - - -
175C ALA* 1.3 72.4 - - - +
177C TRP* 1.3 56.8 + - - +
179C VAL* 3.3 1.9 + - - -
180C ALA 3.0 22.7 + - - -
211C GLU* 3.6 28.2 + - - -
212C LEU* 3.8 19.3 - - - -
215C CYS* 3.4 13.2 - - - -
358C TYR* 2.8 20.5 + - - -
176D SER* 3.5 6.4 + - - -
177D TRP* 3.4 15.6 - - - +
211D GLU* 2.7 16.6 + - - -
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Residues in contact with TRP 177 (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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146C HIS* 6.3 0.2 - + - -
175C ALA* 3.6 12.3 - - + +
176C SER* 1.3 78.8 + - - +
178C GLU* 1.3 87.1 + - + +
180C ALA 3.6 0.2 + - - -
181C GLU* 3.1 29.7 + - - +
359C PHE* 6.3 0.4 - - - -
176D SER* 3.5 30.1 - - - +
177D TRP* 3.6 9.4 - - - +
180D ALA* 3.2 15.1 - - + +
211D GLU* 3.5 41.0 + - + +
214D PRO* 4.2 13.1 - - + +
215D CYS* 3.8 21.7 - - + +
218D HIS* 4.1 41.5 - + + -
219D PHE* 4.0 18.4 - + - -
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Residues in contact with GLU 178 (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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144C PRO* 3.9 9.0 - - - +
146C HIS* 3.2 28.3 + - - -
174C TYR* 3.7 24.8 - - + -
175C ALA* 2.9 33.2 + - + +
177C TRP* 1.3 112.2 - - + +
179C VAL* 1.3 65.5 + - - +
181C GLU* 3.3 9.8 + - - +
182C ILE* 3.0 31.5 + - + +
359C PHE* 5.0 0.3 - - - +
360C ARG 4.3 3.3 - - - +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.9 23.8 - - + -
174C TYR* 4.0 3.8 - - + -
175C ALA 3.0 16.8 + - - +
176C SER 3.5 7.2 - - - +
178C GLU* 1.3 73.8 - - - +
180C ALA* 1.3 60.9 + - - +
182C ILE* 3.3 2.4 + - - +
183C CYS* 2.9 44.3 + - - -
197C TYR* 3.6 33.4 - - + -
212C LEU* 4.3 5.8 - - + -
215C CYS* 4.2 14.4 - - - -
216C LEU* 4.2 14.6 - - + -
219C PHE* 5.2 0.9 - - + -
221C LEU* 4.3 6.5 - - + -
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Residues in contact with ALA 180 (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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176C SER 3.0 16.1 + - - +
177C TRP 3.8 4.9 - - - +
178C GLU 3.3 0.2 - - - -
179C VAL* 1.3 77.0 - - - +
181C GLU* 1.3 58.0 + - - +
183C CYS* 3.3 1.0 + - - +
184C THR* 2.7 35.0 + - - -
215C CYS* 4.2 1.3 - - - -
219C PHE* 3.9 27.3 - - + -
177D TRP* 3.1 33.7 - - + +
181D GLU* 4.4 5.2 - - + +
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Residues in contact with GLU 181 (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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150C VAL* 4.3 20.1 - - + +
177C TRP* 3.1 22.7 + - + +
178C GLU* 3.6 12.1 - - - +
179C VAL 3.2 0.2 - - - -
180C ALA* 1.3 77.7 - - - +
182C ILE* 1.3 57.5 + - - +
184C THR* 3.4 3.4 + - - -
185C LEU* 2.9 43.1 + - + +
180D ALA* 4.5 8.2 - - + +
184D THR* 3.7 23.1 - - + +
187D LYS* 4.3 9.7 + - - -
218D HIS* 4.3 14.8 - - - -
219D PHE* 4.1 21.7 - - + -
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Residues in contact with ILE 182 (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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141C LEU* 5.2 0.2 - - + -
150C VAL* 3.6 36.3 - - + -
154C LEU* 3.8 28.3 - - + -
171C LEU* 3.9 20.0 - - + -
174C TYR* 3.7 27.8 - - + -
178C GLU* 3.0 20.3 + - + +
179C VAL* 3.5 4.5 - - - +
181C GLU* 1.3 76.3 - - - +
183C CYS* 1.3 62.9 + - - +
185C LEU* 3.2 3.8 + - - +
186C CYS* 3.0 28.9 + - - -
194C PRO* 4.0 26.7 - - + -
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Residues in contact with CYS 183 (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 VAL* 2.9 36.1 + - - +
180C ALA 3.9 0.4 - - - +
181C GLU 3.3 0.2 - - - -
182C ILE* 1.3 73.7 - - - +
184C THR* 1.3 57.8 + - - +
186C CYS* 3.4 2.6 + - - +
187C LYS* 3.0 34.3 + - - +
193C LEU* 3.9 15.2 - - + +
194C PRO* 3.7 27.8 - - - -
219C PHE* 3.4 31.0 - - + -
221C LEU* 4.0 16.4 - - - -
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Residues in contact with THR 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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180C ALA 2.7 21.1 + - - -
181C GLU 3.7 3.8 - - - -
183C CYS* 1.3 75.1 - - - +
185C LEU* 1.3 64.1 + - - +
187C LYS* 3.5 6.7 + - - +
188C SER* 3.1 24.7 + - - -
219C PHE* 4.1 7.4 - - - -
181D GLU* 3.7 23.1 + - + +
184D THR* 3.7 24.5 - - + -
185D LEU* 3.8 35.0 - - + +
188D SER* 6.0 0.4 - - - +
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Residues in contact with LEU 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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150C VAL* 4.0 28.0 - - + -
151C GLU* 4.1 41.5 - - + +
154C LEU* 4.3 9.6 - - + -
181C GLU* 2.9 29.9 + - + +
182C ILE 3.6 3.8 - - - +
184C THR* 1.3 75.5 - - - +
186C CYS* 1.3 59.5 + - - +
188C SER* 3.1 9.0 + - - +
189C ASN* 3.0 40.5 + - - +
191C TRP* 5.0 0.4 - - + -
184D THR* 4.1 17.7 - - + +
187D LYS* 5.8 4.3 - - - +
188D SER* 6.4 1.8 - - - -
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Residues in contact with CYS 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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154C LEU* 4.1 23.3 - - - -
182C ILE* 3.0 28.7 + - - +
183C CYS 3.7 5.2 - - - +
185C LEU* 1.3 75.3 - - - +
187C LYS* 1.3 59.7 + - - +
190C GLY* 2.9 10.4 + - - -
191C TRP* 2.8 47.1 + - + +
192C ILE 3.4 21.1 - - - +
193C LEU* 3.8 16.4 - - + -
194C PRO* 4.4 5.8 - - - -
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Residues in contact with LYS 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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183C CYS 3.0 22.7 + - - +
184C THR* 3.8 6.7 - - - +
185C LEU 3.4 0.2 - - - -
186C CYS* 1.3 74.7 - - - +
188C SER* 1.3 63.0 + - - +
190C GLY* 3.2 12.5 + - - -
193C LEU* 3.9 25.8 - - + -
219C PHE* 5.9 3.6 - - + -
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Residues in contact with SER 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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184C THR* 3.1 15.2 + - - -
185C LEU* 3.1 16.3 + - - +
187C LYS* 1.3 80.7 - - - +
189C ASN* 1.3 71.3 + - - +
190C GLY 3.5 0.5 + - - -
184D THR* 6.1 0.5 - - - +
185D LEU* 6.1 2.9 - - - -
188D SER* 4.6 24.8 - - - -
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Residues in contact with ASN 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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151C GLU* 3.2 19.4 + - - +
185C LEU* 3.0 24.1 + - - +
186C CYS 4.2 0.2 - - - +
188C SER* 1.3 83.7 + - - +
190C GLY* 1.3 61.6 + - - +
191C TRP* 3.0 63.5 + - + +
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Residues in contact with GLY 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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158C GLN* 4.0 7.3 + - - -
186C CYS 2.9 6.3 + - - -
187C LYS* 3.2 12.1 + - - -
188C SER 3.3 1.0 + - - -
189C ASN* 1.3 77.8 - - - +
191C TRP* 1.3 65.8 + - - +
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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