Contacts of the helix formed by residues 186 - 197 (chain B) in PDB entry 1H5Y
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 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TRP* 5.5 0.3 - - - +
141B TYR* 2.9 36.1 + - - -
175B SER* 3.9 29.5 + - - +
177B ASP* 4.8 5.5 - - - +
178B ARG* 4.1 17.9 - - + +
184B GLY 3.8 0.6 + - - -
185B TYR* 1.3 71.6 - - - +
187B VAL* 1.3 61.6 + - - +
188B GLU* 3.2 15.6 + - - +
189B LEU* 3.5 9.2 - - + +
190B ILE* 3.1 24.7 + - - +
205B GLY 4.4 1.8 + - - -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.2 18.9 + - + +
186B ASP* 1.3 72.7 + - - +
188B GLU* 1.3 61.5 + - + +
190B ILE* 3.8 7.6 - - - -
191B ARG* 2.9 30.3 + - - +
212B HIS 5.7 0.2 - - - +
215B GLU* 3.9 35.2 - - + +
216B ALA* 4.6 2.7 - - - +
219B ALA* 3.6 14.0 - - + +
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Residues in contact with GLU 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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141B TYR* 3.5 20.9 - - + +
186B ASP* 3.2 4.8 + - - +
187B VAL* 1.3 80.8 - - + +
189B LEU* 1.3 65.3 + - - +
191B ARG* 2.9 35.9 + - - +
192B ARG* 2.8 63.2 + - - +
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Residues in contact with LEU 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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134B ALA* 4.1 15.9 - - + +
141B TYR* 3.7 43.8 + - + -
156B ALA* 4.5 1.6 - - + -
157B VAL* 6.1 0.7 - - + -
173B LEU* 3.8 31.0 - - + -
174B THR 4.0 4.0 - - - +
175B SER* 3.9 35.4 - - - +
186B ASP* 3.2 22.0 + - + +
188B GLU* 1.3 75.7 - - - +
190B ILE* 1.3 70.0 + - + +
192B ARG* 3.4 2.0 + - + +
193B VAL* 3.1 32.8 + - + +
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Residues in contact with ILE 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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173B LEU* 3.8 18.1 - - + +
185B TYR* 3.7 22.2 - - + -
186B ASP 3.1 19.1 + - - +
187B VAL* 3.8 8.5 - - - +
188B GLU 3.3 0.2 - - - -
189B LEU* 1.3 80.5 - - + +
191B ARG* 1.3 55.5 + - - +
193B VAL* 3.8 0.9 - - - +
194B ALA* 2.7 39.4 + - + +
201B VAL* 5.0 5.1 - - + +
203B ALA* 3.6 28.3 - - + -
216B ALA* 4.1 12.6 - - + +
219B ALA* 3.7 19.5 - - + +
220B GLY 4.3 0.7 - - - -
221B ALA* 3.7 25.6 - - + +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL 2.9 19.9 + - - +
188B GLU* 2.9 38.2 + - - +
190B ILE* 1.3 76.3 - - - +
192B ARG* 1.3 69.3 + - - +
194B ALA* 3.8 0.5 - - - +
195B ASP* 2.9 57.6 + - - +
219B ALA* 3.3 23.1 - - + +
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Residues in contact with ARG 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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136B TRP* 3.8 30.3 - - - -
139B GLU 5.0 1.8 + - - -
140B TYR* 5.0 4.9 - - - +
141B TYR* 4.1 22.1 - - + +
157B VAL* 3.9 21.6 - - + +
188B GLU* 2.8 49.5 + - - +
189B LEU* 3.9 4.0 - - - +
191B ARG* 1.3 86.1 - - - +
193B VAL* 1.3 62.5 + - + +
195B ASP* 3.7 6.9 + - - +
196B SER* 3.1 23.6 + - - -
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Residues in contact with VAL 193 (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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132B ILE* 5.7 0.7 - - + -
156B ALA 4.4 17.5 - - - +
157B VAL* 4.4 11.2 - - + -
160B ALA* 4.0 18.4 - - + -
171B ILE* 4.2 11.0 - - + -
173B LEU* 3.7 31.0 - - + -
189B LEU* 3.1 26.9 + - + +
192B ARG* 1.3 74.2 - - - +
194B ALA* 1.3 62.2 - - - +
196B SER* 2.8 28.5 + - - -
197B VAL* 3.4 7.1 + - - +
201B VAL* 4.0 19.3 - - + -
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Residues in contact with ALA 194 (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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190B ILE* 2.7 23.9 + - + +
191B ARG 3.9 2.5 - - - +
193B VAL* 1.3 72.8 - - - +
195B ASP* 1.3 60.0 + - - +
197B VAL* 3.0 24.9 - - - +
201B VAL* 4.1 18.1 - - + +
219B ALA 4.1 5.4 - - - +
220B GLY* 3.7 32.1 - - - +
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Residues in contact with ASP 195 (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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191B ARG* 2.9 47.8 + - - +
192B ARG* 3.9 6.9 - - - +
193B VAL 3.2 0.2 - - - -
194B ALA* 1.3 77.5 - - - +
196B SER* 1.3 59.5 + - - +
197B VAL 3.7 1.4 + - - +
219B ALA 5.4 0.9 - - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 2.7 36.5 - - - +
160B ALA* 4.9 0.2 - - - -
161B LYS* 3.2 37.3 + - - +
164B GLU* 4.2 3.1 - - - +
192B ARG 3.1 7.1 + - - -
193B VAL* 2.8 15.4 + - - -
195B ASP* 1.3 80.5 - - - +
197B VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 3.6 39.7 - - + +
161B LYS* 3.7 4.5 - - - +
164B GLU* 3.5 23.3 - - + +
171B ILE* 4.1 12.8 - - + -
193B VAL 3.4 12.8 + - - +
194B ALA 3.0 17.1 - - - +
195B ASP 4.5 1.4 - - - +
196B SER* 1.3 85.1 - - - +
198B ARG* 1.3 64.1 + - - +
199B ILE* 3.7 26.0 - - + +
201B VAL* 4.1 7.9 - - + -
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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