Contacts of the helix formed by residues 180 - 193 (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 SER 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B THR 3.6 2.2 + - - -
179B PHE* 1.3 76.2 - - - +
181B GLN* 1.3 63.6 + - - +
182B ALA* 4.0 7.5 + - - +
183B GLN* 3.0 47.9 + - - +
184B ARG* 3.3 12.6 + - - +
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Residues in contact with GLN 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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172B GLN* 3.5 29.6 - - - +
180B SER* 1.3 70.1 - - - +
182B ALA* 1.3 68.2 + - - +
183B GLN 3.0 0.9 - - - -
184B ARG* 2.8 47.4 + - - +
185B ASP* 2.8 34.2 + - - +
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Residues in contact with ALA 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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180B SER* 4.2 6.7 - - - +
181B GLN* 1.3 77.8 - - - +
183B GLN* 1.3 52.2 + - - +
185B ASP* 3.5 11.1 + - - +
186B LYS* 2.8 45.1 + - + +
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Residues in contact with GLN 183 (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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179B PHE* 2.8 60.6 - - + -
180B SER* 3.0 38.3 + - - +
181B GLN 3.0 0.2 - - - -
182B ALA* 1.3 72.4 - - - +
184B ARG* 1.3 60.8 + - - +
186B LYS* 3.7 4.4 - - - +
187B ARG* 2.8 32.6 + - - +
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Residues in contact with ARG 184 (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* 6.3 1.1 - - - -
171B ALA* 4.8 5.6 - - + -
172B GLN* 3.8 32.4 + - + +
175B LEU* 3.5 52.4 + - + +
176B PRO 3.6 9.7 + - - -
177B ARG 4.0 9.3 + - - -
179B PHE* 3.2 27.4 + - + +
180B SER 3.5 8.6 + - - +
181B GLN* 2.8 43.1 + - - +
183B GLN* 1.3 71.3 - - - +
185B ASP* 1.3 59.0 + - - +
187B ARG* 3.0 2.6 + - - +
188B VAL* 2.8 40.7 + - + +
397B GLN* 3.8 22.4 - - - +
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Residues in contact with ASP 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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164B ARG* 4.7 5.9 + - - +
168B ALA* 6.2 0.3 - - - +
181B GLN* 2.8 33.3 + - - +
182B ALA* 3.5 10.8 - - - +
184B ARG* 1.3 80.7 - - - +
186B LYS* 1.3 63.6 + - + +
188B VAL* 3.5 8.9 - - - +
189B GLU* 3.3 19.9 + - - +
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Residues in contact with LYS 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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182B ALA* 2.8 27.7 + - + +
183B GLN* 4.0 3.8 - - - +
185B ASP* 1.3 74.8 - - + +
187B ARG* 1.3 59.8 + - - +
189B GLU* 3.9 7.0 - - + +
190B ASP* 2.8 43.8 + - - +
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Residues in contact with ARG 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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175B LEU* 3.6 20.2 - - + +
179B PHE* 4.2 24.7 - - + -
183B GLN 2.8 19.6 + - - +
184B ARG* 3.4 7.0 - - - +
186B LYS* 1.3 75.3 - - - +
188B VAL* 1.3 67.0 + - + +
190B ASP* 3.1 13.1 + - - +
191B VAL* 2.8 33.5 + - - +
227B LEU 4.9 0.4 - - - -
228B LEU* 2.9 49.1 + - + +
229B TRP* 3.9 5.5 - - - +
230B ASN* 3.3 34.7 - - - +
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Residues in contact with VAL 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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164B ARG* 4.3 21.8 - - + +
167B LEU* 4.1 18.2 - - + +
168B ALA* 3.8 32.8 - - + +
171B ALA* 4.4 9.4 - - + -
184B ARG* 2.8 17.4 + - + +
185B ASP* 3.5 11.0 - - - +
186B LYS 3.4 0.2 - - - -
187B ARG* 1.3 75.9 - - - +
189B GLU* 1.3 59.4 + - - +
191B VAL* 2.9 7.1 + - - +
192B ILE* 2.8 46.6 + - + +
228B LEU* 4.6 8.7 - - + -
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Residues in contact with GLU 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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164B ARG* 3.6 27.2 + - - +
185B ASP 3.3 10.3 + - - +
186B LYS* 3.9 10.1 - - + +
187B ARG 3.3 0.4 - - - -
188B VAL* 1.3 79.6 - - - +
190B ASP* 1.3 59.5 + - - +
191B VAL 3.0 0.2 + - - -
192B ILE* 3.0 16.2 + - - +
193B ALA* 2.8 53.3 + - + +
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Residues in contact with ASP 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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28B PHE* 3.8 27.8 - - - +
29B SER* 4.2 7.0 - - - +
186B LYS* 2.8 38.0 + - - +
187B ARG* 3.1 15.2 + - - +
189B GLU* 1.3 73.8 - - - +
191B VAL* 1.3 58.5 + - - +
193B ALA* 4.4 3.4 - - - -
194B GLU* 3.7 18.8 + - - +
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Residues in contact with VAL 191 (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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29B SER* 5.6 3.1 - - - +
167B LEU* 4.8 9.0 - - + -
187B ARG* 2.8 21.5 + - - +
188B VAL 3.3 6.5 - - - +
190B ASP* 1.3 75.9 - - - +
192B ILE* 1.3 70.5 + - - +
193B ALA 3.0 1.6 - - - -
194B GLU* 2.8 17.5 + - - +
195B LEU* 2.8 34.0 + - + +
197B LEU* 6.0 0.9 - - + -
224B GLY* 4.0 17.9 - - - +
227B LEU* 3.6 32.1 - - + +
228B LEU* 3.8 17.0 - - + -
230B ASN* 5.0 3.4 - - - +
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Residues in contact with ILE 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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163B VAL* 4.7 2.2 - - + -
164B ARG* 4.5 24.5 - - + +
167B LEU* 3.9 20.0 - - + -
188B VAL* 2.8 37.6 + - + +
189B GLU* 3.6 23.3 - - - +
191B VAL* 1.3 74.5 - - - +
193B ALA* 1.3 52.9 + - - +
195B LEU* 3.4 1.4 + - - +
196B ARG 2.8 13.0 + - - -
197B LEU* 2.8 68.7 + - + +
198B ARG* 4.9 4.3 - - - +
201B ALA* 4.8 11.9 - - + -
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Residues in contact with ALA 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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28B PHE* 3.0 39.8 - - + -
189B GLU* 2.8 39.1 + - + +
190B ASP* 5.1 1.3 - - - -
192B ILE* 1.3 73.2 - - + +
194B GLU* 1.3 62.7 + - - +
196B ARG* 3.7 19.2 + - - +
198B ARG* 6.1 2.0 - - - +
257B ARG* 5.1 0.5 + - - -
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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