Contacts of the helix formed by residues 168 - 182 (chain B) in PDB entry 1O0W
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 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B MET* 4.2 14.4 - - + +
100B LYS* 6.2 3.8 - - - +
167B PHE* 1.3 73.1 - - - +
169B TYR* 1.3 64.3 + - - +
170B LYS* 3.4 10.0 + - - +
171B THR* 2.7 41.3 + - + +
172B ALA* 3.1 20.6 + - - +
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Residues in contact with TYR 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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155B PHE* 4.3 17.7 - + - -
159B LYS* 3.5 15.8 - - - +
165B MET 2.8 28.9 + - - -
166B LEU* 3.4 22.8 - - + +
167B PHE* 2.8 51.7 + + - -
168B ASP* 1.3 71.5 + - - +
170B LYS* 1.3 55.1 + - - +
172B ALA* 3.0 3.6 + - - +
173B LEU* 2.8 35.9 + - - +
225B LYS* 3.4 27.8 - - + +
228B ALA* 3.7 20.3 - - + +
229B ARG* 3.5 37.3 - - + +
232B TYR* 4.9 2.5 - - + -
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASP* 3.4 7.9 + - - +
169B TYR* 1.3 75.9 - - - +
171B THR* 1.3 59.2 + - - +
173B LEU* 3.3 1.4 + - - +
174B GLN* 2.9 31.4 + - - +
187B TYR* 3.9 32.1 + - + +
221B LYS* 3.5 25.5 + - - +
224B GLU* 3.3 41.8 + - - +
225B LYS* 3.4 29.1 - - + +
228B ALA* 3.9 8.7 - - + -
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Residues in contact with THR 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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168B ASP* 2.7 36.4 + - + +
170B LYS* 1.3 76.4 - - - +
172B ALA* 1.3 63.2 + - - +
174B GLN* 3.6 7.7 - - + +
175B GLU* 3.3 39.8 + - + +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 3.7 24.5 - - + -
168B ASP 3.1 17.4 + - - +
169B TYR 3.0 5.8 + - - +
171B THR* 1.3 77.3 - - - +
173B LEU* 1.3 64.1 + - - +
175B GLU* 3.6 9.3 + - - +
176B ILE* 3.4 15.2 + - - +
232B TYR* 3.5 24.0 - - + +
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Residues in contact with LEU 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 TYR 2.8 20.3 + - - +
170B LYS 3.8 2.7 - - - +
172B ALA* 1.3 71.5 - - - +
174B GLN* 1.3 67.0 + - - +
176B ILE* 3.0 13.7 + - + +
177B VAL* 2.8 42.7 + - + +
185B PRO* 4.4 5.8 - - + -
187B TYR* 3.6 20.9 - - - +
205B VAL* 3.8 14.8 - - + -
212B ILE* 5.3 1.8 - - + -
228B ALA* 3.8 13.7 - - - +
231B ALA* 3.8 20.9 - - + -
232B TYR* 3.8 29.1 - - + +
235B LEU* 4.0 11.2 - - + -
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Residues in contact with GLN 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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170B LYS 2.9 17.9 + - - +
171B THR* 3.6 10.5 - - + +
173B LEU* 1.3 76.8 - - - +
175B GLU* 1.3 62.7 + - + +
177B VAL* 4.2 0.3 - - - +
178B GLN* 2.9 67.1 + - - +
184B PRO* 3.4 21.3 - - - +
185B PRO* 3.7 17.5 - - + +
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Residues in contact with GLU 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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171B THR* 3.3 32.9 + - + +
172B ALA* 3.8 8.5 - - - +
173B LEU 3.2 0.4 - - - -
174B GLN* 1.3 85.9 - - + +
176B ILE* 1.3 61.5 + - - +
178B GLN* 4.1 3.7 - - - +
179B SER* 3.1 27.2 + - - -
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Residues in contact with ILE 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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172B ALA 3.4 6.7 + - - +
173B LEU* 3.0 37.6 + - + +
175B GLU* 1.3 76.9 - - - +
177B VAL* 1.3 71.5 + - + +
179B SER* 3.4 5.3 + - - -
180B GLU* 2.8 55.5 + - + +
232B TYR* 4.4 13.7 - - + +
235B LEU* 4.3 22.7 - - + +
236B LEU* 6.1 2.9 - - + -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 2.8 46.9 + - + +
176B ILE* 1.3 71.9 - - - +
178B GLN* 1.3 66.2 + - - +
179B SER 3.2 0.2 + - - -
180B GLU* 3.2 0.8 + - - -
181B HIS* 2.8 33.0 + - + +
183B VAL 3.3 16.6 - - - +
185B PRO* 3.9 18.2 - - + -
207B VAL* 3.6 41.3 - - + -
212B ILE* 4.5 1.1 - - + -
235B LEU* 4.1 14.1 - - + -
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Residues in contact with GLN 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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174B GLN* 2.9 43.1 + - - +
175B GLU* 4.1 3.8 - - - +
177B VAL* 1.3 76.9 - - - +
179B SER* 1.3 59.9 + - - +
182B LYS* 2.8 61.8 + - - +
183B VAL* 3.4 9.9 + - - +
184B PRO* 3.5 19.2 - - - +
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Residues in contact with SER 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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175B GLU 3.1 18.2 + - - -
176B ILE* 3.7 7.2 - - - -
177B VAL 3.1 0.8 - - - -
178B GLN* 1.3 81.7 - - - +
180B GLU* 1.3 62.0 + - - +
182B LYS* 3.8 20.8 + - - +
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 2.8 41.2 + - + +
177B VAL* 5.5 0.2 - - - -
179B SER* 1.3 79.5 - - - +
181B HIS* 1.3 85.5 + - + +
182B LYS* 4.5 4.4 - - - +
235B LEU* 4.9 9.2 - - - +
237B LYS* 4.6 15.8 + - - -
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Residues in contact with HIS 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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177B VAL* 2.8 26.4 + - + +
180B GLU* 1.3 100.0 + - + +
182B LYS* 1.3 72.1 + - - +
183B VAL* 3.1 26.3 + - + +
207B VAL* 3.9 25.5 - - + +
208B ASN* 4.5 11.5 + - - +
212B ILE* 6.2 0.6 - - - +
235B LEU* 6.1 2.5 - - + +
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Residues in contact with LYS 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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178B GLN* 2.8 40.3 + - - +
179B SER* 3.8 23.3 + - - +
180B GLU 4.5 3.4 - - - +
181B HIS* 1.3 76.9 - - - +
183B VAL* 1.3 63.1 + - + +
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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