Contacts of the helix formed by residues 166 - 177 (chain B) in PDB entry 1DXX
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 GLY 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B TRP 3.1 7.3 + - - -
164B SER 2.8 12.5 + - - -
165B ASP* 1.3 70.8 + - - +
167B LEU* 1.3 59.1 + - - +
168B ALA 3.7 2.0 - - - -
169B LEU* 3.8 4.9 + - - +
170B ASN* 2.7 32.5 + - - -
195B ARG* 3.8 13.6 - - - -
196B LEU* 3.7 24.9 - - - -
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Residues in contact with LEU 167 (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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153B GLN* 4.1 25.8 - - + +
154B VAL* 3.7 16.2 - - + -
165B ASP* 2.9 31.0 + - - +
166B GLY* 1.3 68.5 - - - +
168B ALA* 1.3 55.4 + - - +
170B ASN* 3.0 2.6 + - - -
171B ALA* 2.5 37.1 + - - +
183B TRP* 3.5 14.1 - - + -
186B VAL* 3.9 14.1 - - + -
187B VAL* 4.2 13.0 - - + -
195B ARG* 3.4 47.1 - - - +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 5.5 0.2 - - + -
148B THR* 4.3 2.1 - - - +
154B VAL* 3.7 17.2 - - + +
155B ASN 5.7 0.2 - - - +
156B VAL* 3.3 34.8 - - + -
162B SER 3.8 15.0 - - - +
163B TRP* 3.8 16.1 - - + +
165B ASP* 4.2 2.2 + - - -
166B GLY 3.7 0.6 - - - +
167B LEU* 1.3 77.1 - - - +
169B LEU* 1.3 59.1 + - - +
171B ALA* 3.8 0.5 - - - +
172B LEU* 2.8 32.1 + - - +
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Residues in contact with LEU 169 (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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163B TRP* 3.6 19.4 - - + +
166B GLY 3.8 7.9 + - - +
167B LEU 3.2 0.8 - - - -
168B ALA* 1.3 80.1 - - - +
170B ASN* 1.3 64.0 + - - +
172B LEU* 3.5 1.9 + - + +
173B ILE* 3.2 22.4 + - + +
196B LEU* 4.2 14.1 - - + -
199B ALA* 3.5 17.5 - - + -
200B PHE* 3.3 40.4 - - + -
213B LEU* 5.8 0.2 - - + -
218B VAL* 6.2 0.7 - - + -
231B TYR* 4.0 11.2 - - + +
232B ILE* 4.2 10.8 - - + -
235B LEU* 3.4 32.3 - - + -
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Residues in contact with ASN 170 (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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166B GLY 2.7 22.4 + - - +
167B LEU 3.0 6.5 + - - +
169B LEU* 1.3 74.6 - - - +
171B ALA* 1.3 67.5 + - - +
173B ILE* 3.0 6.3 + - - +
174B HIS* 2.9 23.2 + - - +
181B PHE* 3.7 9.5 - - + -
183B TRP* 3.8 5.8 - - + -
186B VAL* 3.6 28.3 - - + +
195B ARG* 2.9 26.3 + - - +
198B HIS* 2.6 35.9 + - - -
199B ALA* 3.5 13.6 - - - +
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Residues in contact with ALA 171 (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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148B THR* 3.8 12.3 - - + -
151B TYR* 3.4 31.8 - - + -
154B VAL* 3.6 15.7 - - + -
167B LEU 2.5 21.0 + - - +
168B ALA 3.9 0.4 - - - +
170B ASN* 1.3 71.2 - - - +
172B LEU* 1.3 55.9 + - - +
174B HIS* 3.1 1.2 + - - +
175B SER* 2.7 33.4 + - - -
183B TRP* 3.2 14.8 - - + -
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Residues in contact with LEU 172 (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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143B TRP* 3.6 43.3 - - + -
144B VAL* 4.1 20.4 - - + +
147B SER* 3.6 26.7 - - - +
148B THR* 3.6 10.6 - - + +
163B TRP* 4.2 14.4 - - + -
168B ALA 2.8 20.9 + - - +
169B LEU* 3.8 2.5 - - + +
171B ALA* 1.3 72.7 - - - +
173B ILE* 1.4 62.9 + - - +
175B SER* 3.1 16.5 + - - -
176B HIS* 3.2 15.5 - - - +
232B ILE* 4.2 4.5 - - + -
235B LEU* 3.8 28.3 - - + -
239B LEU* 4.4 2.0 - - + +
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Residues in contact with ILE 173 (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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169B LEU* 3.2 19.9 + - + +
170B ASN* 3.0 7.1 + - - +
172B LEU* 1.4 77.4 - - - +
174B HIS* 1.3 52.5 + - - +
176B HIS* 3.1 4.9 + - - +
177B ARG* 2.7 33.6 + - + +
180B LEU* 4.1 11.4 - - + -
181B PHE* 4.5 8.1 - - + -
199B ALA* 3.9 33.4 - - + +
202B ILE* 4.0 23.1 - - + -
203B ALA* 4.2 15.7 - - + -
207B LEU* 4.0 24.5 - - + -
235B LEU* 4.4 14.8 - - + -
239B LEU* 4.7 8.1 - - + -
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Residues in contact with HIS 174 (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 TYR* 2.7 34.9 + + + +
170B ASN 2.9 12.8 + - - +
171B ALA* 3.4 7.6 - - - +
173B ILE* 1.3 74.6 - - - +
175B SER* 1.3 65.9 + - - +
177B ARG 4.0 6.7 - - - -
178B PRO* 3.1 53.9 + - + +
181B PHE* 2.9 51.9 + + + -
182B ASP* 4.3 0.2 - - - -
183B TRP* 3.6 25.3 + + + +
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Residues in contact with SER 175 (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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147B SER* 3.0 32.1 + - - -
151B TYR* 3.1 17.1 + - - -
171B ALA 2.7 18.1 + - - -
172B LEU 3.1 4.5 + - - -
174B HIS* 1.3 75.6 - - - +
176B HIS* 1.3 84.8 + - - +
178B PRO* 4.3 4.5 - - - +
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Residues in contact with HIS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 3.9 10.6 + + - -
147B SER* 2.7 30.4 + - - -
172B LEU* 3.2 14.1 - - + -
173B ILE 3.1 4.3 + - - +
175B SER* 1.3 101.9 + - - +
177B ARG* 1.3 68.7 + - + +
178B PRO* 3.3 8.3 - - - +
239B LEU* 3.7 33.4 - - + -
240B PRO* 3.3 51.0 - - + +
242B GLN* 5.8 1.6 - - + -
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Residues in contact with ARG 177 (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 ILE* 2.7 16.7 + - + +
174B HIS* 3.3 13.0 - - - +
176B HIS* 1.3 82.4 - - - +
178B PRO* 1.3 62.4 - - - +
179B ASP* 2.5 36.9 + - - -
180B LEU* 3.0 56.0 + - + +
181B PHE* 5.1 0.3 - - - -
206B GLN* 5.3 4.0 + - - +
207B LEU* 3.9 19.2 - - + +
239B LEU* 4.4 17.7 - - + +
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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