Contacts of the helix formed by residues 162 - 175 (chain B) in PDB entry 5DO7
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 THR 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B LEU* 1.3 75.2 - - - +
163B VAL* 1.3 66.7 + - - +
164B ARG* 4.1 3.1 + - - +
165B GLU* 2.7 47.4 + - - +
166B THR* 2.8 21.0 + - - -
201B ALA 4.0 0.9 - - - -
202B ASP* 3.6 39.5 - - + +
203B THR 3.3 13.0 - - - +
204B ARG* 4.2 8.1 - - + +
205B VAL* 3.7 1.1 - - - -
412B ARG* 4.5 7.0 - - - +
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Residues in contact with VAL 163 (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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162B THR* 1.3 70.5 - - - +
164B ARG* 1.3 54.7 - - - +
166B THR* 2.9 4.6 + - - -
167B LEU* 2.8 52.5 + - + +
192B ILE* 4.7 7.0 - - + -
197B LEU* 4.2 13.2 - - + -
200B CYS* 3.5 31.9 - - + +
201B ALA* 3.8 8.0 + - - +
203B THR* 3.4 8.6 + - - +
204B ARG 5.4 0.2 - - - +
205B VAL* 3.5 20.1 - - + +
213B LEU* 5.5 3.8 - - + -
221B VAL* 4.1 30.1 - - + -
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Residues in contact with ARG 164 (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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162B THR* 4.3 4.3 - - - +
163B VAL* 1.3 78.7 - - - +
165B GLU* 1.3 58.2 + - + +
167B LEU* 3.5 2.0 + - - +
168B ALA* 2.8 33.3 + - + +
185B ASP* 4.7 5.1 + - - +
188B VAL* 4.3 27.5 - - + +
189B GLU* 3.6 29.7 + - - +
192B ILE* 4.5 9.9 - - + +
201B ALA* 3.1 27.5 + - - +
202B ASP* 3.2 28.7 + - - +
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Residues in contact with GLU 165 (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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161B LEU* 3.0 32.5 - - + +
162B THR* 2.7 40.3 + - - +
164B ARG* 1.3 73.0 - - + +
166B THR* 1.3 57.0 - - - +
168B ALA* 2.9 7.4 + - - -
169B PHE* 2.8 47.4 + - + +
412B ARG* 3.1 27.7 + - - -
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Residues in contact with THR 166 (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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157B LEU* 4.7 19.3 - - + -
158B LEU* 4.7 19.3 - - + +
161B LEU* 3.7 20.3 - - + +
162B THR 2.8 17.8 + - - -
163B VAL* 2.9 4.5 + - - -
165B GLU* 1.3 71.3 - - - +
167B LEU* 1.3 60.0 + - - +
169B PHE* 4.3 6.2 - - - +
170B ILE* 3.3 22.3 + - - +
205B VAL* 3.5 20.1 - - - +
221B VAL* 5.3 6.3 - - - -
225B VAL* 4.9 7.7 - - + +
405B ARG* 5.6 5.6 - - - +
480B TYR* 6.2 0.4 - - - +
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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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163B VAL* 2.8 30.0 + - + +
164B ARG 3.8 3.1 - - - +
165B GLU 3.0 0.2 + - - -
166B THR* 1.3 74.3 - - - +
168B ALA* 1.3 67.8 + - - +
169B PHE 3.1 1.8 - - - -
170B ILE* 2.8 17.2 + - - +
171B ALA* 2.8 12.8 + - - +
188B VAL* 4.1 20.2 - - + +
191B VAL* 4.8 9.9 - - + -
192B ILE* 3.9 30.7 - - + -
197B LEU* 5.4 4.0 - - + -
221B VAL* 4.3 7.9 - - + +
224B GLY* 3.7 10.1 - - - +
225B VAL* 3.6 39.9 - - + +
228B LEU* 3.7 9.8 - - + +
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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
----------------------------------------------------------
164B ARG* 2.8 24.5 + - + +
165B GLU* 2.9 6.0 + - - +
167B LEU* 1.3 71.5 - - - +
169B PHE* 1.3 54.9 + - + +
171B ALA* 3.2 4.5 + - - +
172B GLN* 2.8 44.2 + - + +
184B ARG* 6.3 1.3 - - + -
185B ASP* 6.2 0.2 - - - +
188B VAL* 3.8 16.7 - - + +
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Residues in contact with PHE 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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161B LEU* 4.4 18.2 - - + -
165B GLU* 2.8 39.5 + - + +
166B THR* 4.5 3.8 - - - +
168B ALA* 1.3 74.7 - - + +
170B ILE* 1.3 60.4 + - - +
172B GLN* 4.0 12.4 + - + -
173B MET* 3.6 7.7 + - - +
401B THR* 3.3 36.0 - - + +
404B ARG* 3.9 26.5 - - + -
405B ARG* 3.7 61.7 - - + -
408B SER* 4.4 7.2 - - - -
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Residues in contact with ILE 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 THR 3.3 15.8 + - - +
167B LEU* 2.8 21.4 + - - +
169B PHE* 1.3 71.0 - - - +
171B ALA* 1.3 66.5 + - - +
172B GLN 3.2 1.3 - - - -
173B MET* 2.8 33.1 + - + -
174B ARG* 2.8 36.0 + - + +
225B VAL* 4.1 35.4 - - + +
228B LEU* 3.4 17.7 - - + -
405B ARG* 5.5 4.2 - - - +
480B TYR* 4.7 16.8 - - + -
485B GLY* 4.7 12.6 - - - -
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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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167B LEU 2.8 12.7 + - - +
168B ALA* 3.3 14.8 - - - +
170B ILE* 1.3 77.3 - - - +
172B GLN* 1.3 58.3 + - - +
174B ARG* 4.5 0.9 - - - +
175B LEU* 2.8 59.3 + - + +
184B ARG* 4.7 7.0 - - + +
188B VAL* 4.4 10.3 - - + -
228B LEU* 3.8 17.5 - - + -
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Residues in contact with GLN 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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168B ALA* 2.8 26.8 + - + +
169B PHE* 4.2 14.2 - - + +
170B ILE 3.2 0.6 - - - -
171B ALA* 1.3 72.5 - - - +
173B MET* 1.3 60.4 + - - +
175B LEU 4.1 7.4 - - - +
181B GLN* 3.5 25.5 + - - +
184B ARG* 3.8 23.2 + - + +
397B GLN* 4.2 36.4 + - - +
401B THR* 4.1 20.3 + - + +
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Residues in contact with MET 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 PHE 3.6 16.8 + - - +
170B ILE* 2.8 30.2 + - + +
172B GLN* 1.3 74.5 - - - +
174B ARG* 1.3 61.4 + - - +
175B LEU 4.3 3.4 - - - +
398B GLN* 4.3 26.5 + - + +
401B THR* 3.8 26.7 - - + +
402B LEU* 3.9 32.5 - - + -
405B ARG* 4.2 16.8 - - - +
480B TYR* 5.7 0.2 - - + -
484B ASP 5.7 0.3 - - - +
485B GLY* 3.7 30.2 - - - +
486B LEU* 4.5 7.2 - - + -
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Residues in contact with ARG 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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145B ARG* 4.5 12.1 + - - +
146B LYS* 6.0 2.2 - - - +
148B VAL 5.5 0.8 + - - -
170B ILE* 2.8 39.7 + - + +
171B ALA* 4.5 2.5 - - - +
173B MET* 1.3 75.3 - - - +
175B LEU* 1.3 63.2 + - - +
176B PRO* 3.7 4.0 - - - +
177B ARG* 5.8 1.0 + - - -
225B VAL 4.9 1.1 + - - -
226B GLN* 5.1 2.0 - - - +
228B LEU* 5.1 9.6 - - + +
229B TRP* 2.8 73.3 - - + +
483B GLU* 2.5 43.9 + - - +
484B ASP* 4.8 11.4 + - - +
485B GLY* 5.1 9.2 - - - +
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Residues in contact with LEU 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 ALA* 2.8 44.4 + - + +
172B GLN 4.1 7.3 - - - +
173B MET 4.3 2.9 - - - +
174B ARG* 1.3 73.3 - - - +
176B PRO* 1.3 73.4 - - + +
177B ARG 3.9 0.3 + - - -
179B PHE* 4.2 20.2 - - + -
184B ARG* 3.5 44.1 + - + +
187B ARG* 3.6 30.1 - - + +
228B LEU* 3.1 26.5 - - + +
229B TRP* 5.2 1.6 - - + -
397B GLN* 5.4 1.4 - - - +
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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