Contacts of the helix formed by residues 184 - 198 (chain B) in PDB entry 3GA5
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LYS* 4.7 12.4 + - - +
13B ASP 5.4 3.6 - - - +
15B ASN* 5.8 0.7 - - - -
181B ALA 2.9 15.0 + - - +
182B MET 4.1 4.3 - - - +
183B TRP* 1.3 77.9 - - - +
185B THR* 1.3 67.1 + - - +
186B ALA* 3.1 14.6 + - - +
187B GLN* 2.9 43.8 + - + +
188B ALA* 3.2 23.6 + - - +
213B ALA 4.4 0.2 - - - -
214B MET* 3.6 4.7 - - - +
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Residues in contact with THR 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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15B ASN* 4.4 7.9 + - - -
183B TRP 4.1 1.6 + - - -
184B ASP* 1.3 73.6 + - - +
186B ALA* 1.3 63.2 + - - +
188B ALA* 3.1 3.5 + - - +
189B LYS* 2.9 26.2 + - + +
213B ALA* 2.7 38.1 + - - +
216B MET* 4.2 16.3 - - + +
217B GLY* 3.6 18.2 - - - +
220B GLU* 3.8 17.3 - - - +
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Residues in contact with ALA 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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184B ASP* 3.1 11.7 + - - +
185B THR* 1.3 80.1 - - - +
187B GLN* 1.3 62.8 + - + +
189B LYS* 3.3 9.8 + - - +
190B ASP* 3.1 28.3 + - - +
220B GLU* 6.1 0.2 - - - -
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Residues in contact with GLN 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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180B THR 4.5 2.3 - - - +
181B ALA* 3.5 25.6 - - + +
182B MET* 3.5 30.8 - - - +
184B ASP* 2.9 29.2 + - + +
185B THR 3.3 0.2 - - - -
186B ALA* 1.3 76.7 - - + +
188B ALA* 1.3 57.7 + - - +
190B ASP* 3.3 9.1 + - - +
191B LYS* 3.0 37.2 + - + +
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Residues in contact with ALA 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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146B LEU* 4.1 11.0 - - + +
181B ALA* 3.5 12.3 - - + +
184B ASP 3.2 17.6 + - - +
185B THR 3.1 4.2 + - - +
187B GLN* 1.3 77.7 - - - +
189B LYS* 1.3 66.4 + - - +
191B LYS* 3.3 1.0 + - - +
192B MET* 2.9 27.0 + - - +
214B MET* 3.3 40.2 - - + +
217B GLY* 4.3 2.5 - - - -
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Residues in contact with LYS 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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185B THR 2.9 12.8 + - - +
186B ALA* 3.5 12.3 - - - +
188B ALA* 1.3 75.4 - - - +
190B ASP* 1.3 63.7 + - - +
192B MET 3.3 0.2 + - - -
193B ASP* 2.8 40.7 + - + +
217B GLY* 3.3 26.6 - - - +
220B GLU* 3.6 45.7 + - + +
221B ALA* 3.6 9.3 - - + +
224B ALA* 5.5 6.2 - - - +
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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
----------------------------------------------------------
186B ALA* 3.1 14.3 + - - +
187B GLN* 3.7 9.7 - - - +
188B ALA 3.2 0.4 - - - -
189B LYS* 1.3 85.7 - - - +
191B LYS* 1.3 63.4 + - + +
193B ASP* 3.6 9.3 - - - +
194B ALA* 3.0 24.1 + - - +
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Residues in contact with LYS 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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146B LEU* 3.7 22.9 - - + -
179B ASP* 3.1 32.6 + - + +
180B THR 3.7 22.2 - - - +
181B ALA* 4.6 1.6 - - + +
187B GLN* 3.0 28.3 + - - +
190B ASP* 1.3 77.5 - - + +
192B MET* 1.3 62.3 + - - +
194B ALA* 3.5 7.8 + - + +
195B TRP* 3.2 37.3 + - + +
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Residues in contact with MET 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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144B VAL* 4.1 5.4 - - + -
146B LEU* 4.7 2.7 - - + +
188B ALA 2.9 17.4 + - - +
191B LYS* 1.3 74.3 - - - +
193B ASP* 1.3 60.2 + - - +
195B TRP* 3.2 22.8 + - + +
196B LEU* 2.9 64.9 + - + +
204B ILE* 4.1 18.4 - - + -
207B VAL* 3.6 40.6 - - + -
218B ALA* 3.8 22.7 - - + +
221B ALA* 3.7 20.0 - - + -
222B LEU* 4.4 4.3 - - + -
230B ILE* 5.7 0.7 - - + -
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Residues in contact with ASP 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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189B LYS* 2.8 27.7 + - + +
190B ASP* 3.6 11.1 - - - +
192B MET* 1.3 76.4 - - - +
194B ALA* 1.3 58.5 + - - +
196B LEU 3.2 2.3 + - - -
197B SER* 2.7 38.5 + - - -
221B ALA* 3.5 12.9 - - + +
224B ALA* 5.8 3.3 - - - +
225B HIS* 2.7 33.9 + - - -
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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 ASP 3.0 14.4 + - - +
191B LYS* 3.5 12.8 - - + +
192B MET 3.3 0.2 - - - -
193B ASP* 1.3 76.1 - - - +
195B TRP* 1.3 67.8 + - + +
197B SER* 2.8 18.1 + - - -
198B GLY* 3.0 11.1 + - - -
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Residues in contact with TRP 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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144B VAL* 3.7 34.1 - - + -
145B LEU 3.6 22.0 - - - -
146B LEU* 3.7 34.1 - - + -
177B ALA* 3.4 30.1 - - + +
178B LEU 4.2 0.7 - - - -
179B ASP* 3.9 27.1 - - + +
191B LYS* 3.2 21.4 + - + -
192B MET* 3.2 17.5 + - + +
194B ALA* 1.3 82.3 - - + +
196B LEU* 1.3 62.1 + - - +
197B SER 3.2 0.9 + - - -
198B GLY* 3.3 12.0 + - - +
200B ASN* 4.7 1.2 - - - +
201B ALA* 3.6 16.3 + - - +
204B ILE* 4.0 17.3 - - + +
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Residues in contact with LEU 196 (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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192B MET* 2.9 37.7 + - + +
193B ASP 3.7 0.7 - - - +
194B ALA 3.2 0.2 - - - -
195B TRP* 1.3 75.3 - - - +
197B SER* 1.3 60.3 + - - +
198B GLY 3.4 0.4 - - - +
201B ALA* 3.3 23.1 - - + +
204B ILE* 4.4 9.9 - - + -
221B ALA* 3.7 28.0 - - + +
222B LEU* 3.7 34.8 - - + +
225B HIS* 3.6 31.7 + - + -
227B LYS* 4.3 17.0 - - + -
230B ILE* 4.4 6.5 - - + -
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Residues in contact with SER 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP* 2.7 25.9 + - - -
194B ALA* 2.8 9.2 + - - -
196B LEU* 1.3 77.0 - - - +
198B GLY* 1.3 61.0 + - - +
225B HIS* 3.0 19.7 - - - -
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Residues in contact with GLY 198 (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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194B ALA 3.0 10.4 + - - -
195B TRP* 3.3 5.8 + - - -
197B SER* 1.3 83.1 - - - +
199B PRO* 1.3 70.4 - - - +
200B ASN 3.1 10.2 + - - -
201B ALA* 3.2 17.4 + - - +
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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