Contacts of the helix formed by residues 178 - 192 (chain B) in PDB entry 2HXO
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 ASP 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ASN 5.2 5.9 - - - +
179B ARG* 1.3 65.5 + - - +
180B ASP* 3.2 10.1 + - - +
181B GLU* 3.3 32.5 + - - +
182B PHE* 2.8 30.8 + - - +
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Residues in contact with ARG 179 (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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115A LEU 3.9 6.3 + - - -
166B ASN* 3.1 45.6 - - + +
178B ASP* 1.3 82.3 + - - +
180B ASP* 1.3 63.8 + - - +
182B PHE* 3.3 37.2 - - - +
183B LEU* 2.9 62.7 + - + +
211B HIS* 5.0 1.0 + - - -
213B ASP* 2.6 53.2 + - - +
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Residues in contact with ASP 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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178B ASP 3.2 5.1 + - - +
179B ARG* 1.3 83.8 - - - +
181B GLU* 1.3 59.5 + - + +
183B LEU* 3.8 11.5 + - - +
184B ASP* 3.1 26.2 + - - +
209B ARG 4.7 6.7 - - - +
211B HIS 5.3 2.1 - - - +
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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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178B ASP* 3.3 31.5 + - - +
179B ARG 3.1 0.4 - - - -
180B ASP* 1.3 80.7 - - + +
182B PHE* 1.3 63.6 + - - +
184B ASP* 3.3 5.6 + - - +
185B THR* 3.0 31.9 + - + +
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Residues in contact with PHE 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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114A GLN 5.1 0.2 - - - -
115A LEU* 3.5 19.3 - - - -
116A SER 3.2 30.3 - - - -
117A ARG* 3.9 2.2 - - - -
118A THR 4.4 2.9 - - - -
119A PRO* 3.3 39.3 - - + -
178B ASP* 2.8 21.6 + - - +
179B ARG* 3.3 41.1 - - - +
181B GLU* 1.3 78.4 - - - +
183B LEU* 1.3 62.5 + - + +
185B THR* 2.7 19.9 + - - -
186B VAL* 3.0 39.1 + - + +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 6.4 0.7 - - + -
179B ARG* 2.9 63.2 + - - +
180B ASP* 4.1 7.9 - - - +
182B PHE* 1.3 82.5 - - + +
184B ASP* 1.3 58.3 + - - +
186B VAL* 4.4 4.0 - - + -
187B SER* 2.9 28.8 + - - -
208B VAL* 3.6 38.0 - - + +
209B ARG* 3.8 11.4 - - - +
211B HIS* 3.1 35.7 - - + +
213B ASP* 5.0 0.2 - - - +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP 3.1 19.3 + - - +
181B GLU* 3.7 7.6 - - - +
182B PHE 3.2 0.4 - - - -
183B LEU* 1.3 76.7 - - - +
185B THR* 1.3 63.1 + - - +
187B SER* 4.4 4.3 - - - -
188B THR* 2.8 38.5 + - - -
209B ARG* 2.9 35.4 + - + +
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Residues in contact with THR 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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119A PRO* 3.6 23.0 - - + +
120A TRP* 4.8 19.9 - - + -
181B GLU* 3.0 16.3 + - + +
182B PHE* 2.7 25.0 + - - -
184B ASP* 1.3 80.5 - - - +
186B VAL* 1.3 58.4 + - - +
188B THR* 3.4 6.6 + - - +
189B ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 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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119A PRO* 3.9 22.4 - - + +
182B PHE* 3.0 50.5 + - + +
183B LEU* 3.8 5.6 - - + +
184B ASP 3.3 0.2 - - - -
185B THR* 1.3 74.3 + - - +
187B SER* 1.3 67.1 + - - +
189B ALA 3.2 1.2 + - - -
190B TRP* 2.9 59.0 + - + +
208B VAL* 4.0 16.6 - - + -
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Residues in contact with SER 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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183B LEU 2.9 18.4 + - - -
184B ASP 3.8 0.7 - - - -
185B THR 3.4 0.2 - - - -
186B VAL* 1.3 78.0 - - - +
188B THR* 1.3 56.8 + - - +
190B TRP* 3.4 3.5 + - - +
191B GLU* 2.9 36.3 + - - +
205B ALA* 2.6 28.5 + - - +
206B ASP* 4.0 0.7 - - - -
208B VAL* 4.1 4.9 - - - +
209B ARG* 3.1 45.8 + - - -
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Residues in contact with THR 188 (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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120A TRP* 5.5 8.5 - - + +
184B ASP* 2.8 25.3 + - - -
185B THR* 3.6 7.6 - - - -
186B VAL 3.2 0.2 - - - -
187B SER* 1.3 78.3 - - - +
189B ALA* 1.3 63.9 + - - +
191B GLU* 3.1 19.2 + - - +
192B GLY* 3.3 8.7 + - - -
209B ARG* 3.0 15.6 + - - +
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Residues in contact with ALA 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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119A PRO 3.7 15.9 - - - +
120A TRP* 3.4 40.2 - - + +
185B THR 2.9 17.3 + - - +
186B VAL 3.6 4.0 - - - +
188B THR* 1.3 77.1 - - - +
190B TRP* 1.3 65.6 + - + +
192B GLY* 3.2 13.7 + - - -
193B LEU* 3.8 9.4 + - - +
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Residues in contact with TRP 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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119A PRO 4.5 6.6 + - - -
121A GLY 5.0 0.9 + - - -
124A ALA* 4.4 9.4 - - + +
125A PRO* 3.8 41.1 - - + +
128A PHE* 4.0 30.3 - + + -
146A PHE* 4.3 14.6 - + - -
186B VAL* 2.9 40.1 + - + +
187B SER 3.9 0.4 - - - +
189B ALA* 1.3 81.4 - - + +
191B GLU* 1.3 62.7 + - - +
192B GLY 2.9 4.9 - - - -
193B LEU* 3.1 24.1 + - + +
201B THR* 3.3 32.3 - - + -
202B ARG* 3.3 13.5 - - - +
204B VAL* 4.5 6.5 - - + -
205B ALA* 3.8 16.9 - - + +
208B VAL* 3.9 25.4 - - + -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 2.9 24.1 + - - +
188B THR* 3.1 9.4 + - - +
190B TRP* 1.3 76.2 - - - +
192B GLY* 1.3 56.8 + - - +
193B LEU 3.3 1.3 - - - -
202B ARG* 2.6 40.6 + - - +
205B ALA* 3.5 15.9 - - + -
206B ASP* 4.2 15.9 + - - +
209B ARG* 3.2 36.4 + - - -
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Residues in contact with GLY 192 (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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188B THR 3.3 6.8 + - - -
189B ALA 3.2 12.3 + - - -
190B TRP 2.9 1.4 - - - -
191B GLU* 1.3 79.4 - - - +
193B LEU* 1.3 60.4 + - - +
194B ASP 3.9 1.0 + - - -
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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