Contacts of the helix formed by residues 175 - 190 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 4.1 5.8 - - + +
174B TYR* 1.3 74.2 - - - +
176B SER* 1.3 67.5 + - - +
177B TRP* 3.3 33.7 - - + +
178B GLU* 2.7 29.3 + - - +
179B VAL* 3.0 12.2 + - - +
358B TYR* 3.8 3.8 - - - -
359B PHE* 3.5 28.9 - - + +
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Residues in contact with SER 176 (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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176A SER* 3.5 9.2 + - - -
177A TRP* 3.6 7.3 - - - +
211A GLU* 2.8 16.8 + - - -
174B TYR 3.7 0.8 + - - -
175B ALA* 1.3 72.0 - - - +
177B TRP* 1.3 58.1 + - - +
179B VAL* 3.3 5.1 + - - +
180B ALA 3.0 23.2 + - - -
211B GLU* 3.6 17.5 + - - +
212B LEU* 3.7 34.1 - - - -
215B CYS* 3.5 14.5 - - - -
358B TYR* 2.9 20.1 + - - -
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Residues in contact with TRP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.4 34.8 - - - +
177A TRP* 3.6 9.4 - - - +
180A ALA* 3.2 13.2 - - + +
211A GLU* 3.6 27.3 + - + +
214A PRO* 3.9 23.4 - - + +
215A CYS* 3.7 20.6 - - + +
218A HIS* 3.9 42.6 - + + -
219A PHE* 4.0 9.0 - + - -
146B HIS* 6.3 1.1 - + - -
175B ALA* 3.3 26.1 - - + +
176B SER* 1.3 80.3 + - - +
178B GLU* 1.3 85.7 + - + +
180B ALA 3.5 0.2 + - - -
181B GLU* 3.1 30.1 + - - +
359B PHE* 6.1 0.8 - - - -
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Residues in contact with GLU 178 (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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144B PRO* 4.1 8.9 - - - +
146B HIS* 3.3 28.7 + - - -
174B TYR* 3.5 23.0 - - + -
175B ALA* 2.7 38.4 + - - +
177B TRP* 1.3 111.6 - - + +
179B VAL* 1.3 63.6 + - - +
181B GLU* 3.6 9.8 - - - +
182B ILE* 3.0 32.9 + - + +
359B PHE* 4.8 0.9 - - - +
360B ARG 4.5 4.0 - - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.8 26.9 - - + -
174B TYR* 4.0 4.9 - - + +
175B ALA 3.0 14.9 + - - +
176B SER* 3.4 8.1 - - - +
178B GLU* 1.3 77.2 - - - +
180B ALA* 1.3 57.6 + - - +
182B ILE* 3.3 2.1 + - - +
183B CYS* 2.9 37.6 + - - -
197B TYR* 3.7 30.1 - - + -
212B LEU* 4.3 5.2 - - + -
215B CYS* 4.1 14.4 - - - -
216B LEU* 4.1 15.0 - - + -
219B PHE* 5.2 0.4 - - + -
221B LEU* 4.2 11.7 - - + -
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Residues in contact with ALA 180 (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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177A TRP* 3.2 31.9 - - + +
181A GLU* 4.4 5.4 - - + +
176B SER 3.0 15.0 + - - +
177B TRP 3.7 4.3 - - - +
178B GLU 3.3 0.2 - - - -
179B VAL* 1.3 74.6 - - - +
181B GLU* 1.3 61.9 + - - +
183B CYS* 3.4 1.2 + - - +
184B THR* 2.6 35.2 + - - -
215B CYS* 4.1 0.9 - - - -
219B PHE* 3.8 28.0 - - + -
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Residues in contact with GLU 181 (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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180A ALA* 4.4 3.1 - - + +
184A THR* 3.7 22.7 + - + +
187A LYS* 4.7 5.4 + - - -
218A HIS* 3.5 26.4 + - - -
219A PHE* 3.8 20.6 - - + -
150B VAL* 4.1 19.2 - - + +
177B TRP* 3.1 26.0 + - + +
178B GLU* 3.6 10.1 - - - +
179B VAL 3.3 0.2 - - - -
180B ALA* 1.3 75.6 - - - +
182B ILE* 1.3 58.7 - - - +
184B THR* 3.3 2.2 + - - -
185B LEU* 2.8 48.2 + - + +
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Residues in contact with ILE 182 (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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141B LEU* 5.5 0.2 - - + -
150B VAL* 3.7 33.0 - - + -
154B LEU* 3.8 30.3 - - + -
171B LEU* 3.9 18.6 - - + -
174B TYR* 3.7 30.3 - - + -
178B GLU* 3.0 22.5 + - + +
179B VAL 3.5 4.3 - - - +
181B GLU* 1.3 77.7 - - + +
183B CYS* 1.3 58.9 + - - +
185B LEU* 3.3 4.3 + - - +
186B CYS* 2.9 34.5 + - - -
194B PRO* 4.0 26.5 - - + -
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Residues in contact with CYS 183 (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 VAL* 2.9 27.3 + - - +
180B ALA 4.0 0.2 - - - +
182B ILE* 1.3 73.9 - - - +
184B THR* 1.3 59.1 + - - +
186B CYS* 3.4 2.5 + - - +
187B LYS* 3.0 34.9 + - - +
193B LEU* 4.0 16.3 - - + +
194B PRO* 4.0 20.2 - - - -
219B PHE* 3.5 44.4 - - + -
221B LEU* 4.0 16.4 - - - -
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Residues in contact with THR 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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181A GLU* 3.9 21.0 + - + +
184A THR* 3.8 25.1 - - + -
185A LEU* 4.1 32.1 - - + +
188A SER* 6.1 0.7 - - - +
180B ALA 2.6 23.3 + - - -
181B GLU 3.7 3.4 - - - -
183B CYS* 1.3 74.7 - - - +
185B LEU* 1.3 63.9 + - - +
187B LYS* 3.5 14.3 + - + +
188B SER* 3.1 24.0 + - - -
219B PHE* 4.1 6.9 - - - -
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Residues in contact with LEU 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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184A THR* 3.7 20.4 - - + -
188A SER* 6.0 4.0 - - - -
150B VAL* 3.8 29.6 - - + -
151B GLU* 4.4 31.4 - - + +
154B LEU* 4.6 8.3 - - + -
181B GLU* 2.8 31.9 + - + +
182B ILE* 3.3 4.5 + - - +
184B THR* 1.3 76.8 - - - +
186B CYS* 1.3 56.2 + - - +
188B SER* 3.0 9.4 + - - +
189B ASN* 3.0 38.9 + - - +
191B TRP* 5.0 3.6 - - + -
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Residues in contact with CYS 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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154B LEU* 4.0 24.5 - - - -
182B ILE* 2.9 34.8 + - - +
183B CYS 3.7 4.7 - - - +
185B LEU* 1.3 73.1 - - - +
187B LYS* 1.3 59.9 + - - +
190B GLY* 2.9 9.9 + - - -
191B TRP* 2.8 58.8 + - + +
192B ILE 3.5 19.1 - - - +
193B LEU* 3.9 8.1 - - + -
194B PRO* 4.4 6.3 - - - -
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Residues in contact with LYS 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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181A GLU* 4.7 6.4 + - - -
185A LEU* 6.5 0.7 - - - -
183B CYS 3.0 22.3 + - - +
184B THR* 3.8 13.9 - - - +
186B CYS* 1.3 75.3 - - - +
188B SER* 1.3 63.9 + - - +
190B GLY* 3.2 12.1 + - - -
193B LEU* 3.9 25.1 - - + +
218B HIS* 5.7 2.6 - - - -
219B PHE* 3.6 31.7 - - - -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 6.1 0.2 - - - +
185A LEU* 6.5 0.9 - - - -
188A SER* 4.3 25.6 - - - -
184B THR* 3.1 13.4 + - - -
185B LEU* 3.0 17.3 + - - +
187B LYS* 1.3 79.1 - - - +
189B ASN* 1.3 70.8 + - - +
190B GLY 3.5 0.7 + - - -
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Residues in contact with ASN 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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151B GLU* 3.1 27.2 + - - +
185B LEU* 3.0 25.7 + - - +
186B CYS 4.2 0.2 - - - +
188B SER* 1.3 84.6 + - - +
190B GLY* 1.3 61.1 + - - +
191B TRP* 3.5 46.5 + - + +
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Residues in contact with GLY 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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158B GLN* 3.7 10.0 + - - -
186B CYS 2.9 5.0 + - - -
187B LYS* 3.2 11.4 + - - -
188B SER 3.3 1.4 + - - -
189B ASN* 1.3 79.4 - - - +
191B TRP* 1.3 62.3 + - - +
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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