Contacts of the helix formed by residues 182 - 198 (chain G) in PDB entry 3MQT
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 182 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181G VAL* 1.3 76.4 - - - +
183G ASP* 1.3 64.0 + - - +
184G LYS* 3.4 10.7 + - - +
185G GLU* 2.9 36.3 + - - +
186G ILE* 3.0 20.1 + - - +
210G ARG* 3.6 2.5 - - - +
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Residues in contact with ASP 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G SER* 1.3 69.3 - - - +
184G LYS* 1.3 60.4 + - - +
186G ILE* 3.0 9.1 + - - +
187G VAL* 2.9 32.6 + - - +
210G ARG* 3.0 32.2 + - - -
211G TRP* 2.9 27.8 + - - -
216G LYS* 3.0 36.6 + - - +
219G TRP* 4.0 13.6 - - + -
220G THR* 3.6 15.8 + - - +
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Residues in contact with LYS 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G SER* 3.4 10.0 + - - +
183G ASP* 1.3 78.0 - - - +
185G GLU* 1.3 61.1 + - + +
187G VAL* 3.4 20.4 + - + +
188G ALA* 3.3 20.0 + - + +
191G ARG* 5.4 2.2 - - - +
219G TRP* 3.6 38.9 - - + -
223G GLN* 4.5 8.3 + - - +
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Residues in contact with GLU 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G LEU* 3.8 9.2 - - + +
180G LYS 4.4 2.8 - - - +
181G VAL* 3.2 27.0 - - + +
182G SER* 2.9 43.8 + - - +
184G LYS* 1.3 75.8 - - + +
186G ILE* 1.3 58.3 + - - +
188G ALA* 3.4 7.6 + - - +
189G TYR* 3.0 28.1 + - - +
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Residues in contact with ILE 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G LEU* 4.3 12.6 - - + -
175G ILE* 3.7 46.0 - - + -
181G VAL* 3.5 25.4 - - + -
182G SER 3.0 16.0 + - - +
183G ASP* 3.0 9.4 + - - +
185G GLU* 1.3 72.5 - - - +
187G VAL* 1.3 67.8 + - - +
189G TYR* 3.2 7.7 + - + +
190G LEU* 2.9 35.6 + - + +
210G ARG* 3.7 24.5 - - - +
211G TRP* 4.3 11.0 - - + -
220G THR* 4.5 4.5 - - + -
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Residues in contact with VAL 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G ASP 2.9 16.3 + - - +
184G LYS* 3.6 21.3 - - + +
185G GLU 3.3 0.2 - - - -
186G ILE* 1.3 77.2 - - - +
188G ALA* 1.3 62.8 + - - +
190G LEU 3.4 0.2 + - - -
191G ARG* 3.0 59.6 + - - +
219G TRP* 4.0 11.4 - - + -
220G THR* 3.8 33.2 - - + +
223G GLN* 3.9 14.1 - - + -
224G LEU* 3.6 16.7 - - + +
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Residues in contact with ALA 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G LYS* 3.3 11.8 + - + +
185G GLU* 3.7 9.6 - - - +
186G ILE 3.3 0.2 - - - -
187G VAL* 1.3 80.4 - - - +
189G TYR* 1.3 57.8 + - - +
191G ARG* 3.2 10.1 + - - +
192G GLU* 2.9 31.6 + - - +
195V GLU* 4.4 20.0 - - - +
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Residues in contact with TYR 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G LEU* 3.9 37.5 - - + -
152G ILE* 3.4 29.6 - - + +
153G VAL* 3.6 28.7 - - + -
156G TYR* 3.6 8.8 - - - -
174G CYS 2.7 27.9 + - - -
175G ILE* 4.3 13.1 - - + -
176G ILE 4.8 1.9 + - - -
185G GLU 3.0 15.2 + - - +
186G ILE* 3.2 18.8 + - + +
188G ALA* 1.3 76.6 - - - +
190G LEU* 1.3 75.1 + - + +
192G GLU* 3.3 10.3 + - - +
193G LEU* 3.0 41.9 + - + +
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Residues in contact with LEU 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G VAL* 4.5 3.8 - - + -
174G CYS 5.4 0.4 - - - +
175G ILE* 4.5 5.6 - - + -
186G ILE* 2.9 34.8 + - + +
187G VAL 4.1 2.9 - - - +
189G TYR* 1.3 93.4 - - + +
191G ARG* 1.3 60.8 + - - +
193G LEU* 3.3 11.2 + - + +
194G ARG 3.0 21.3 + - - -
203G MET* 3.6 7.0 - - + +
205G VAL* 4.1 40.8 - - + -
221G PHE* 4.4 8.3 - - + -
224G LEU* 3.5 24.0 - - + -
227G ILE* 3.6 22.8 - - + +
229G LEU* 5.1 0.9 - - + -
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Residues in contact with ARG 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G LYS* 5.4 2.6 - - - +
187G VAL* 3.0 38.3 + - - +
188G ALA* 3.5 11.0 - - - +
190G LEU* 1.3 72.1 - - - +
192G GLU* 1.3 66.6 + - - +
194G ARG* 3.3 4.2 + - - +
195G GLU* 3.1 27.3 + - + +
223G GLN* 2.8 30.2 + - - +
224G LEU* 3.8 9.1 - - + +
226G ASP* 2.5 38.5 + - - -
227G ILE* 4.1 15.0 - - + +
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Residues in contact with GLU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G SER* 5.3 5.8 + - - -
153G VAL* 3.4 38.6 - - + +
154G GLU* 4.5 6.9 - - - +
157G LYS* 4.6 6.1 + - - -
188G ALA 2.9 16.5 + - - +
189G TYR* 3.3 8.4 + - - +
191G ARG* 1.3 78.0 - - - +
193G LEU* 1.3 61.8 + - - +
195G GLU* 3.3 22.2 + - - +
196G VAL* 3.1 30.5 + - + +
150V SER* 5.0 6.1 + - - -
192V GLU* 5.4 10.0 - - - +
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Residues in contact with LEU 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G VAL* 4.1 22.2 - - + -
156G TYR* 4.0 31.0 - - + -
160G ILE* 4.4 9.6 - - + -
173G VAL* 3.9 24.2 - - + -
189G TYR* 3.0 52.7 + - + +
190G LEU* 3.8 10.1 - - + +
191G ARG 3.2 0.6 - - - -
192G GLU* 1.3 72.1 - - - +
194G ARG* 1.3 65.8 + - - +
196G VAL* 3.2 5.6 + - + +
197G ILE* 2.9 34.2 + - + +
203G MET* 3.8 9.6 - - + -
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Residues in contact with ARG 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G LEU 3.0 9.1 + - - +
191G ARG 3.3 7.8 + - - +
193G LEU* 1.3 75.3 - - - +
195G GLU* 1.3 55.3 + - + +
197G ILE* 3.1 5.2 + - - +
198G GLY* 2.7 56.5 + - - -
199G TRP* 3.6 44.6 + - + +
201G MET 3.1 21.2 + - - -
202G ASP* 5.2 1.2 + - - +
203G MET* 3.6 43.6 - - - +
227G ILE* 2.8 45.4 + - + -
228G ASP* 3.1 20.4 + - - +
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Residues in contact with GLU 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G LYS* 5.5 0.2 + - - -
191G ARG* 3.1 18.9 + - + +
192G GLU* 3.3 27.1 + - + +
194G ARG* 1.3 77.8 - - + +
196G VAL* 1.3 63.7 + - + +
198G GLY* 3.6 8.8 + - - -
199G TRP* 5.7 3.6 - - - +
188V ALA* 5.1 13.7 - - - +
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Residues in contact with VAL 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G VAL* 4.6 9.4 - - + -
156G TYR* 6.0 0.2 - - + -
157G LYS* 3.9 45.8 - - + +
160G ILE* 3.8 29.8 - - + +
164G LYS* 3.0 23.7 + - - -
192G GLU* 3.1 20.4 + - + +
193G LEU* 3.2 8.2 + - + +
195G GLU* 1.3 78.0 - - + +
197G ILE* 1.3 58.1 + - - +
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Residues in contact with ILE 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G ILE* 3.9 28.0 - - + -
164G LYS* 3.2 18.9 - - - -
171G VAL* 4.0 19.7 - - + -
173G VAL* 4.2 15.7 - - + -
193G LEU* 2.9 21.5 + - + +
194G ARG* 3.7 15.0 - - - +
196G VAL* 1.3 75.5 - - - +
198G GLY* 1.3 70.9 + - - +
200G ASP* 4.9 1.6 + - - +
201G MET* 3.8 31.6 + - + +
203G MET* 3.7 31.4 - - + -
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Residues in contact with GLY 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G LYS* 4.9 2.9 - - - -
194G ARG* 2.7 43.3 + - - -
195G GLU* 3.6 7.4 + - - -
196G VAL 3.4 2.4 - - - -
197G ILE* 1.3 80.0 - - - +
199G TRP* 1.3 72.6 + - - -
200G ASP 3.5 1.0 + - - -
201G MET 4.1 0.2 - - - +
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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