Contacts of the helix formed by residues 184 - 201 (chain B) in PDB entry 3GUU
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 4.3 8.7 - - - -
183B TYR* 1.3 82.1 - - - +
185B GLY* 1.3 62.8 + - - -
187B ALA* 3.0 8.8 + - - +
188B HIS 3.2 0.2 + - - -
212B GLY 3.1 12.3 + - - -
213B GLY 3.3 16.4 - - - -
215B PRO* 3.2 20.6 - - - +
366B HIS* 2.9 29.5 + - - -
431B PHE* 3.6 11.6 - - - -
442B 1PE 2.7 23.0 + - - -
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL 4.3 1.9 - - - +
93B TYR* 3.8 7.0 - - - +
94B GLU 5.5 0.2 - - - -
95B ASP* 3.3 21.5 - - - -
142B HIS* 4.6 3.1 + - - -
149B PHE* 4.5 9.1 - - - -
150B ILE* 5.2 1.1 - - - +
155B GLU* 4.8 3.3 - - - +
183B TYR 3.3 0.2 + - - -
184B SER* 1.3 78.5 - - - +
186B GLY* 1.3 59.8 + - - +
188B HIS* 3.5 9.9 + - - +
189B ALA* 3.3 19.6 + - - +
442B 1PE 3.0 15.3 + - - -
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 3.3 27.6 - - - +
92B VAL 3.7 10.3 - - - -
93B TYR* 3.7 5.5 - - - +
182B GLY 4.0 0.4 - - - -
183B TYR 2.8 16.7 + - - -
185B GLY* 1.3 74.5 - - - +
187B ALA* 1.3 54.6 + - - +
189B ALA* 3.5 1.7 + - - -
190B THR* 2.7 36.5 + - - -
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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
----------------------------------------------------------
182B GLY 3.7 13.2 - - - +
183B TYR 3.4 3.8 - - - -
184B SER 3.0 10.0 + - - +
186B GLY* 1.3 75.2 - - - +
188B HIS* 1.3 59.2 + - - +
190B THR* 3.7 0.3 - - - -
191B VAL* 2.8 32.4 + - - +
211B HIS* 3.7 11.4 + - + -
212B GLY 3.0 28.7 - - - +
214B THR* 3.6 22.5 - - - +
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Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 3.1 58.4 + - + +
152B GLY* 3.8 4.9 - - - -
155B GLU* 2.6 29.6 + - - -
184B SER 3.2 5.9 + - - -
185B GLY 3.6 9.6 - - - +
187B ALA* 1.3 77.2 - - - +
189B ALA* 1.3 61.4 + - - +
191B VAL* 3.4 3.6 - - - +
192B TRP* 3.1 63.1 + + - -
215B PRO* 3.3 41.7 - - + +
216B VAL* 5.4 2.5 - - - -
217B SER 6.2 0.4 - - - -
218B ALA* 5.9 5.0 + - - +
308B GLU* 5.1 4.2 + - - -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 4.0 4.9 - - + -
142B HIS* 3.7 24.7 - - + +
155B GLU* 3.3 21.3 - - - +
156B GLY* 4.6 0.3 - - - -
159B ILE* 3.4 29.7 - - + +
185B GLY 3.3 7.1 + - - +
186B GLY 3.8 7.4 - - - +
187B ALA 3.2 0.6 - - - -
188B HIS* 1.3 79.1 - - - +
190B THR* 1.3 58.1 + - - +
192B TRP* 3.3 3.5 + - - +
193B ALA 2.9 23.7 + - - -
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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
----------------------------------------------------------
91B GLN* 3.0 23.6 + - - +
180B LEU* 3.8 35.0 - - + +
181B GLU 3.6 8.3 + - - +
182B GLY 3.7 0.3 + - - -
186B GLY 2.7 22.3 + - - -
187B ALA* 3.3 7.4 + - - -
189B ALA* 1.3 73.8 - - - +
191B VAL* 1.3 66.3 + - - +
193B ALA* 3.1 6.6 + - - +
194B THR* 3.0 30.9 + - + +
209B ALA* 4.4 0.9 - - + -
210B SER 4.4 0.2 - - - +
211B HIS* 3.9 24.0 - - + -
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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
----------------------------------------------------------
187B ALA 2.8 19.4 + - - +
188B HIS* 3.4 14.4 - - - +
190B THR* 1.3 72.7 - - - +
192B TRP* 1.3 68.2 + - + +
194B THR* 2.8 17.6 + - - +
195B SER* 2.8 27.1 + - - +
211B HIS* 3.8 27.3 - - + +
214B THR* 3.9 15.5 - - + -
215B PRO 4.6 3.1 - - - +
310B VAL* 4.4 15.0 - - + -
345B TYR* 3.3 38.6 - - + +
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Residues in contact with TRP 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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152B GLY* 3.4 32.5 - - - +
153B TYR* 3.5 34.1 - + - -
156B GLY* 3.9 5.2 - - - +
188B HIS* 3.1 59.8 + + - +
189B ALA* 3.7 5.8 - - - +
191B VAL* 1.3 82.5 - - + +
193B ALA* 1.3 62.8 + - - +
195B SER* 3.3 5.0 + - - -
196B LEU* 3.1 46.5 + - + +
216B VAL 5.0 5.3 + - - -
307B GLN 3.4 20.2 - - - -
308B GLU* 4.0 7.8 - - - -
309B THR 3.6 29.4 - - - +
310B VAL* 3.9 14.0 - - + +
317B TYR* 3.5 15.5 - + - -
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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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156B GLY* 3.8 14.7 - - - +
159B ILE* 3.6 35.4 - - + -
160B LEU* 3.6 14.8 - - + +
180B LEU* 3.8 12.3 - - + -
189B ALA 2.9 12.9 + - - +
190B THR* 3.1 7.6 + - - +
192B TRP* 1.3 75.0 - - - +
194B THR* 1.3 63.9 + - - +
196B LEU 3.6 0.3 + - - -
197B ALA* 3.2 20.6 + - - +
206B ILE* 5.0 0.6 - - - +
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.4 10.8 - - + -
190B THR* 3.0 22.3 + - + +
191B VAL* 2.8 29.0 + - - +
193B ALA* 1.3 76.5 - - - +
195B SER* 1.3 60.0 + - - +
197B ALA* 3.5 16.6 - - - +
198B GLU 4.6 1.2 + - - -
206B ILE* 5.2 2.2 - - - -
209B ALA* 3.6 30.7 - - + -
211B HIS* 4.9 2.6 + - + -
320B SER* 4.8 1.2 + - - -
322B PRO* 3.7 22.4 - - - +
324B PHE* 3.9 22.9 - - + -
326B ARG* 4.5 6.5 + - - -
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL 2.8 20.9 + - - -
192B TRP* 3.7 10.1 - - - -
193B ALA 3.2 0.2 - - - -
194B THR* 1.3 77.1 + - - +
196B LEU* 1.3 68.8 + - - +
197B ALA 3.2 1.0 + - - -
198B GLU* 4.3 4.0 + - - +
199B SER* 4.9 1.4 + - - -
310B VAL* 3.8 23.5 - - - +
317B TYR* 6.1 0.2 - - - -
319B VAL* 4.8 6.1 - - - +
320B SER* 3.1 38.9 + - - -
322B PRO* 4.7 2.5 - - - +
345B TYR* 4.4 9.2 + - - -
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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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152B GLY 4.1 7.0 - - - +
153B TYR* 3.9 57.0 - - + +
157B MET* 4.2 17.5 - - + +
160B LEU* 3.9 15.0 - - + -
192B TRP* 3.1 24.9 + - + +
195B SER* 1.3 80.2 - - - +
197B ALA* 1.3 56.6 + - - +
198B GLU 3.4 0.4 - - - -
199B SER* 3.2 13.6 + - - +
200B TYR* 2.7 40.7 + - + +
317B TYR* 6.2 2.7 - - + -
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Residues in contact with ALA 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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160B LEU* 3.9 11.4 - - + -
193B ALA 3.2 10.7 + - - +
194B THR 3.5 14.4 - - - +
195B SER 3.2 1.6 - - - -
196B LEU* 1.3 76.2 - - - +
198B GLU* 1.3 64.7 + - - +
201B ALA 2.9 35.9 + - - +
202B PRO* 3.5 1.5 - - - +
204B LEU 6.0 0.4 - - - +
206B ILE* 3.6 30.1 - - + -
324B PHE* 5.4 4.0 - - + -
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Residues in contact with GLU 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 THR 4.6 1.6 + - - -
195B SER 4.3 2.5 + - - +
196B LEU 3.4 0.8 - - - -
197B ALA* 1.3 80.2 - - - +
199B SER* 1.3 64.7 + - - +
202B PRO* 3.4 24.0 - - - +
320B SER* 2.7 36.5 + - - +
321B VAL 4.3 4.9 + - - +
323B LYS* 5.9 0.7 + - - -
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Residues in contact with SER 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 SER 4.9 0.9 + - - -
196B LEU* 3.2 21.6 + - - +
198B GLU* 1.3 86.8 - - - +
200B TYR* 1.3 64.0 + - - +
201B ALA 3.7 0.2 - - - -
202B PRO* 3.8 5.9 - - - +
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Residues in contact with TYR 200 (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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33B LYS* 3.4 35.5 + - + +
62B THR* 2.9 22.2 + - + -
157B MET* 3.6 46.0 - - + -
160B LEU* 4.1 17.5 - - + -
161B ASP* 2.6 39.9 + - - -
164B ARG* 2.9 22.6 + - - -
196B LEU* 2.7 28.2 + - + +
199B SER* 1.3 77.0 + - - +
201B ALA* 1.3 56.3 + - - +
202B PRO* 3.4 3.4 - - - +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 4.2 17.5 - - + -
164B ARG* 3.3 26.5 - - - +
196B LEU 3.9 0.2 + - - -
197B ALA* 2.9 20.5 + - - +
200B TYR* 1.3 73.9 - - - +
202B PRO* 1.3 64.9 - - - +
203B GLU 3.1 5.3 + - - -
204B LEU* 3.2 38.6 + - + +
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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
------------------------------------------------------------
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