Contacts of the helix formed by residues 175 - 190 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 1.3 74.7 - - - +
176A SER* 1.3 67.0 + - - +
177A TRP* 3.6 30.7 - - + +
178A GLU* 2.9 31.4 + - + +
179A VAL* 3.0 11.9 + - - +
358A TYR* 3.7 5.4 - - - -
359A PHE* 3.5 26.3 - - + +
211B GLU* 3.7 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR 3.8 0.2 + - - -
175A ALA* 1.3 70.7 - - - +
177A TRP* 1.3 56.7 + - - +
179A VAL* 3.3 2.3 + - - -
180A ALA 3.1 22.5 + - - -
211A GLU* 3.6 32.1 + - - +
212A LEU* 3.8 17.0 - - - -
215A CYS* 3.4 13.8 - - - -
358A TYR* 2.8 19.8 + - - -
176B SER* 3.5 9.9 + - - -
177B TRP* 3.4 11.0 - - - +
211B GLU* 2.7 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 3.6 19.2 - - + +
176A SER* 1.3 81.1 + - - +
178A GLU* 1.3 84.9 + - + +
180A ALA 3.6 0.2 + - - -
181A GLU* 3.1 29.7 + - - +
359A PHE* 6.2 0.8 - - - -
176B SER* 3.6 33.0 - - - +
177B TRP* 3.6 8.7 - - - +
180B ALA* 3.2 13.7 - - + +
211B GLU* 3.5 29.7 + - + +
214B PRO* 4.0 15.2 - - + +
215B CYS* 3.7 20.0 - - + -
218B HIS* 3.9 44.4 - + + -
219B PHE* 4.0 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 3.9 8.7 - - - +
146A HIS* 3.1 30.1 + - - -
174A TYR* 3.7 23.5 - - + -
175A ALA* 2.9 34.8 + - + +
177A TRP* 1.3 113.2 - - + +
179A VAL* 1.3 63.1 + - - +
181A GLU* 3.5 9.9 + - - +
182A ILE* 3.1 31.4 + - + +
359A PHE* 5.0 0.5 - - - +
360A ARG 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.9 21.1 - - + -
174A TYR* 3.8 9.6 - - + +
175A ALA 3.0 14.5 + - - +
176A SER* 3.6 8.1 - - - +
178A GLU* 1.3 77.2 - - - +
180A ALA* 1.3 56.3 + - - +
182A ILE* 3.3 2.6 + - - +
183A CYS* 2.9 41.1 + - - -
197A TYR* 3.5 32.1 - - + -
212A LEU* 4.3 3.8 - - + -
215A CYS* 4.3 8.3 - - - -
216A LEU* 4.1 20.6 - - + -
219A PHE* 5.3 0.9 - - + -
221A LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER 3.1 16.9 + - - +
177A TRP 3.7 4.0 - - - +
179A VAL* 1.3 76.5 - - - +
181A GLU* 1.3 59.9 + - - +
183A CYS* 3.3 1.7 + - - +
184A THR* 2.7 33.9 + - - -
215A CYS* 4.1 0.4 - - - -
219A PHE* 3.6 29.4 - - + -
177B TRP* 3.2 32.1 - - + +
181B GLU 4.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.3 19.1 - - + +
177A TRP* 3.1 23.7 + - - +
178A GLU* 3.7 10.2 - - - +
179A VAL 3.4 0.2 - - - -
180A ALA* 1.3 78.8 - - - +
182A ILE* 1.3 57.5 + - - +
184A THR* 3.7 3.1 - - - -
185A LEU* 2.9 42.8 + - + +
180B ALA* 4.4 7.7 - - + +
184B THR* 3.9 22.7 + - + +
187B LYS* 4.7 5.7 + - - -
218B HIS* 4.1 17.5 - - - -
219B PHE* 3.7 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.5 36.6 - - + -
154A LEU* 3.9 26.9 - - + -
171A LEU* 4.0 19.1 - - + -
174A TYR* 3.7 27.1 - - + -
178A GLU* 3.1 21.2 + - + +
179A VAL 3.4 4.5 - - - +
181A GLU* 1.3 78.0 - - + +
183A CYS* 1.3 62.5 + - - +
185A LEU* 3.3 4.6 + - - +
186A CYS* 3.0 29.0 + - - -
194A PRO* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 2.9 24.1 + - - +
180A ALA 3.8 0.9 - - - +
182A ILE* 1.3 75.4 - - - +
184A THR* 1.3 57.5 + - - +
186A CYS* 3.4 7.2 + - - +
187A LYS* 3.0 35.3 + - - +
193A LEU* 4.1 11.5 - - + +
194A PRO* 3.9 26.9 - - - -
219A PHE* 3.4 45.1 - - + -
221A LEU* 4.0 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA 2.7 21.9 + - - -
181A GLU 3.7 3.6 - - - -
183A CYS* 1.3 73.8 - - - +
185A LEU* 1.3 64.2 + - - +
187A LYS* 3.5 11.5 + - - +
188A SER* 3.2 23.4 + - - -
219A PHE* 4.0 6.1 - - - -
181B GLU* 3.7 21.6 + - + +
184B THR* 3.8 24.0 - - + -
185B LEU* 3.7 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.7 29.8 - - + -
151A GLU* 3.9 37.9 - - + +
154A LEU* 4.4 11.4 - - + -
181A GLU* 2.9 29.8 + - + +
182A ILE 3.3 3.8 + - - +
184A THR* 1.3 76.6 - - - +
186A CYS* 1.3 57.5 + - - +
188A SER* 3.2 10.7 + - - +
189A ASN* 3.0 37.7 + - - +
191A TRP* 5.5 0.7 - - + -
184B THR* 4.1 18.3 - - + +
187B LYS* 6.5 0.7 - - - -
188B SER* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.9 26.0 - - - -
182A ILE* 3.0 32.9 + - - +
183A CYS 3.6 5.2 - - - +
185A LEU* 1.3 72.9 - - - +
187A LYS* 1.3 67.1 + - - +
189A ASN 3.5 0.2 + - - -
190A GLY* 2.9 3.8 + - - -
191A TRP* 2.7 52.4 + - + +
192A ILE 3.5 16.2 - - - +
193A LEU* 3.6 17.0 - - + -
194A PRO* 4.5 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A CYS 3.0 20.1 + - - +
184A THR* 3.7 9.4 - - + +
186A CYS* 1.3 74.7 - - - +
188A SER* 1.3 63.8 + - - +
190A GLY* 3.2 12.9 + - - -
193A LEU* 3.9 23.6 - - + -
218A HIS* 4.9 6.9 + - - -
219A PHE* 3.9 34.9 - - - -
181B GLU* 4.7 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 3.2 13.8 + - - -
185A LEU* 3.2 15.3 + - - +
187A LYS* 1.3 80.8 - - - +
189A ASN* 1.3 68.7 + - - +
190A GLY 3.6 0.3 + - - -
184B THR* 6.1 0.5 - - - +
185B LEU* 6.0 4.0 - - - -
188B SER* 4.3 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 2.8 28.8 + - - +
185A LEU* 3.0 21.1 + - - +
188A SER* 1.3 83.6 + - - +
190A GLY* 1.3 61.1 + - - +
191A TRP* 3.1 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 4.1 7.4 + - - -
186A CYS 2.9 5.7 + - - -
187A LYS 3.2 11.5 + - - -
188A SER 3.3 1.0 + - - -
189A ASN* 1.3 79.1 - - - +
191A TRP* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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