Contacts of the helix formed by residues 184 - 199 (chain B) in PDB entry 3GUC
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 ASN 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B THR* 5.7 0.3 - - - +
182B VAL* 3.3 7.0 - - - +
183B ASP* 1.3 90.0 + - - +
185B PHE* 1.3 67.7 + - - +
186B GLU* 3.5 10.4 + - - +
187B ALA* 3.1 36.4 + - - +
188B ARG* 3.1 30.1 + - - +
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Residues in contact with PHE 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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184B ASN* 1.3 73.2 - - - +
186B GLU* 1.3 63.1 + - + +
188B ARG* 3.1 13.0 + - - +
189B MET* 2.8 61.5 + - + +
227B PHE* 3.9 26.5 - + - -
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Residues in contact with GLU 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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152B THR* 3.9 31.7 + - + +
184B ASN* 3.4 9.2 + - - +
185B PHE* 1.3 85.2 - - + +
187B ALA* 1.3 50.3 + - - +
189B MET* 3.3 4.0 + - - +
190B THR* 2.6 41.8 + - - +
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Residues in contact with ALA 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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151B ILE* 4.9 10.6 - - + +
152B THR* 4.1 11.1 - - + +
182B VAL* 3.4 32.3 - - + -
184B ASN* 3.1 18.8 + - - +
186B GLU* 1.3 74.7 - - - +
188B ARG* 1.3 58.8 + - - +
190B THR* 3.3 8.4 + - - -
191B ILE* 2.9 35.4 + - + +
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Residues in contact with ARG 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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180B SER* 3.9 10.3 - - - +
182B VAL* 3.0 32.3 + - + -
183B ASP* 3.7 21.8 + - - +
184B ASN* 3.1 18.3 + - - +
185B PHE* 3.1 11.4 + - - +
187B ALA* 1.3 75.5 - - - +
189B MET* 1.3 58.2 + - - +
191B ILE* 3.3 10.7 + - - +
192B ASN* 3.0 26.2 + - - +
202B TRP* 3.8 7.3 - - + -
204B GLU* 3.2 22.2 + - - -
205B SER 3.2 18.8 + - - -
206B GLY* 4.0 9.7 - - - -
215B HIS* 5.1 2.4 - - - -
227B PHE* 3.8 29.1 - - + -
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Residues in contact with MET 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 PHE* 2.8 50.5 + - + +
186B GLU* 3.8 3.8 - - - +
188B ARG* 1.3 73.9 - - - +
190B THR* 1.3 61.3 + - - +
192B ASN* 3.2 25.5 + - - +
193B THR* 2.8 39.4 + - - +
227B PHE* 3.9 22.2 - - + +
228B ALA* 3.8 24.5 - - + -
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Residues in contact with THR 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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151B ILE* 3.3 44.0 - - + +
152B THR* 3.4 16.7 + - - +
157B PHE* 3.5 18.5 - - + -
160B PHE* 5.3 1.1 - - + -
186B GLU* 2.6 28.6 + - - +
187B ALA* 3.3 9.4 - - - -
189B MET* 1.3 76.7 - - - +
191B ILE* 1.3 61.2 + - - -
193B THR* 3.2 8.5 + - - -
194B ALA* 3.0 17.5 + - - -
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Residues in contact with ILE 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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79B VAL* 3.8 29.6 - - + -
151B ILE* 5.3 3.8 - - + -
160B PHE* 4.1 25.4 - - + -
178B VAL* 4.0 19.1 - - + -
180B SER* 3.4 27.6 - - - +
182B VAL* 4.7 3.4 - - + -
187B ALA* 2.9 27.4 + - + +
188B ARG* 3.6 6.1 - - - +
190B THR* 1.3 67.8 - - - +
192B ASN* 1.3 60.9 + - - +
194B ALA* 3.1 2.1 + - - +
195B CYS* 2.9 31.7 + - - -
202B TRP* 3.5 29.4 - - + -
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Residues in contact with ASN 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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188B ARG 3.0 12.6 + - - +
189B MET* 3.3 16.0 - - - +
191B ILE* 1.3 76.3 - - - +
193B THR* 1.3 57.2 + - - +
195B CYS* 3.3 0.9 + - - +
196B ASN* 2.9 50.9 + - - +
202B TRP* 3.4 27.2 + - + -
226B CYS* 3.2 22.5 - - - +
227B PHE* 2.9 31.5 + - + -
228B ALA* 3.5 17.2 - - - +
305B ASP* 3.9 3.6 + - - -
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Residues in contact with THR 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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157B PHE* 3.8 19.5 - - + -
189B MET* 2.8 28.6 + - - +
190B THR* 3.4 10.8 - - - -
192B ASN* 1.3 74.5 - - - +
194B ALA* 1.3 62.0 + - - +
196B ASN* 4.0 1.2 - - - +
197B GLU* 3.0 25.2 + - - +
305B ASP* 3.7 18.3 + - - +
307B ASN* 5.2 5.1 + - - +
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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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157B PHE* 3.6 25.0 - - + -
160B PHE* 3.7 23.1 - - + -
161B MET* 3.7 18.6 - - + -
164B ILE* 5.5 1.1 - - + -
190B THR 3.0 8.4 + - - +
191B ILE 3.1 7.5 + - - +
193B THR* 1.3 75.2 - - - +
195B CYS* 1.3 60.3 + - - +
197B GLU* 3.1 4.2 + - - +
198B LEU* 2.9 37.1 + - + +
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Residues in contact with CYS 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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160B PHE* 5.9 1.1 - - - -
164B ILE* 5.6 2.9 - - - -
178B VAL* 4.3 8.1 - - - -
191B ILE* 2.9 25.8 + - - +
192B ASN 3.9 0.7 - - - +
194B ALA* 1.3 78.0 - - - +
196B ASN* 1.3 60.5 + - - +
198B LEU* 3.3 0.6 + - - -
199B GLY* 2.8 27.9 + - - -
200B GLN* 3.0 43.4 + - - +
202B TRP* 3.4 42.4 - - + +
221B PRO* 3.7 4.6 - - + +
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Residues in contact with ASN 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 ASN* 2.9 34.7 + - - +
193B THR 4.0 0.9 - - - +
195B CYS* 1.3 77.5 - - - +
197B GLU* 1.3 62.6 + - - +
198B LEU 3.3 0.3 + - - -
202B TRP* 5.6 0.3 + - - -
219B ILE* 5.3 0.2 - - - +
221B PRO* 3.4 25.3 - - - +
226B CYS* 3.3 21.6 - - - +
305B ASP* 2.8 34.4 + - - +
307B ASN* 3.7 7.0 - - + +
308B CYS* 3.7 24.0 - - - +
311B GLN* 3.2 24.9 - - - +
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Residues in contact with GLU 197 (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 PHE* 4.5 6.8 - - - -
161B MET* 3.8 33.0 - - - +
193B THR* 3.0 17.3 + - - +
194B ALA 3.4 9.2 - - - +
196B ASN* 1.3 76.6 - - - +
198B LEU* 1.3 64.8 + - + +
307B ASN* 3.9 29.4 + - - +
311B GLN* 4.2 4.2 - - - +
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Residues in contact with LEU 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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161B MET* 3.9 30.1 - - + +
164B ILE* 3.7 37.0 - - + -
165B SER* 3.6 23.1 - - - +
194B ALA 2.9 21.1 + - - +
195B CYS* 4.1 2.2 - - - +
197B GLU* 1.3 82.5 - - + +
199B GLY* 1.3 62.4 + - - +
200B GLN* 4.1 10.7 - - + +
311B GLN* 4.3 1.8 - - - -
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Residues in contact with GLY 199 (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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195B CYS 2.8 7.7 + - - -
196B ASN 3.5 4.9 + - - -
197B GLU 3.5 0.2 - - - -
198B LEU* 1.3 79.5 - - - +
200B GLN* 1.3 62.0 + - - +
201B THR* 3.9 2.3 + - - -
221B PRO* 4.4 10.3 - - - -
311B GLN* 3.5 25.3 + - - -
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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