Contacts of the helix formed by residues 213 - 224 (chain M) 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 ASP 213 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211M TRP* 4.4 2.3 - - - +
212M THR* 1.3 80.5 + - - +
214M TRP* 1.3 69.9 + - - +
215M GLN* 2.9 18.8 + - - +
216M LYS* 3.1 29.4 + - + +
217M ALA* 3.2 9.2 + - - +
236M LEU* 3.8 5.0 - - - +
230N TYR* 4.2 1.6 + - - -
254N ARG* 2.9 33.4 + - - -
277N SER* 6.0 0.2 - - - -
303N ASN* 4.1 8.3 + - - +
305N GLN* 3.3 24.4 - - + +
329N ILE 6.0 0.4 - - - +
331N GLU* 5.1 0.7 - - - +
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Residues in contact with TRP 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M THR 3.7 0.4 + - - -
213M ASP* 1.3 73.4 + - - +
215M GLN* 1.3 86.8 + - + +
217M ALA* 3.4 3.9 + - - +
218M ARG* 2.9 58.3 + - + +
236M LEU* 3.7 17.2 - - + +
243M GLY* 3.6 17.5 - - - +
246M LYS* 3.4 56.6 - - + +
247M LEU* 3.6 19.2 - - + +
250M ALA* 3.8 16.2 - - + -
275N GLY 6.1 1.1 - - - -
277N SER* 3.9 9.5 + - - -
303N ASN* 2.8 47.2 + - - +
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Residues in contact with GLN 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M ASP* 2.9 12.4 + - - +
214M TRP* 1.3 106.0 - - + +
216M LYS* 1.3 61.0 + - - +
218M ARG* 3.2 31.4 + - - +
219M TRP* 3.2 24.6 + - - +
252N ASN 4.2 0.2 - - - +
253N THR* 3.4 30.6 + - + +
254N ARG* 3.6 37.9 + - + +
277N SER* 2.9 23.4 + - - +
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Residues in contact with LYS 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M ASP* 3.3 28.9 + - - +
211M TRP* 3.9 10.7 - - + -
213M ASP* 3.1 19.9 + - + +
215M GLN* 1.3 77.1 - - - +
217M ALA* 1.3 65.8 + - - +
219M TRP* 3.5 8.2 + - + +
220M THR* 3.3 22.3 + - - -
202N ASP* 5.8 2.2 - - - -
230N TYR* 5.6 2.2 - - + -
254N ARG* 3.5 14.3 - - - +
331N GLU* 2.9 38.8 + - - +
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Residues in contact with ALA 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M TRP* 3.7 24.7 - - + +
213M ASP 3.2 9.2 + - - +
214M TRP 3.6 8.3 - - - +
216M LYS* 1.3 78.5 - - - +
218M ARG* 1.3 62.6 + - - +
220M THR* 3.1 2.1 + - - -
221M PHE* 3.0 30.6 + - + -
235M CYS* 3.6 30.7 - - - -
236M LEU* 4.3 2.5 - - + -
247M LEU* 3.9 11.4 - - + -
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Residues in contact with ARG 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M TRP* 2.9 37.5 + - + +
215M GLN* 3.2 36.3 + - - +
216M LYS 3.3 0.2 - - - -
217M ALA* 1.3 74.4 - - - +
219M TRP* 1.3 65.1 + - - +
220M THR 3.2 0.2 + - - -
221M PHE* 3.9 1.8 - - - +
222M ARG* 2.9 37.5 + - + +
247M LEU* 3.7 14.1 - - + +
250M ALA* 3.6 31.9 + - + +
251M ILE* 5.4 3.0 - - + +
248N ALA 5.5 2.2 + - - -
249N ALA 5.5 1.6 + - - -
251N ILE 3.5 18.6 + - - -
252N ASN* 3.5 34.4 + - - +
253N THR 4.0 1.6 + - - +
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Residues in contact with TRP 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M ASP* 4.0 11.4 - - + -
184M LYS* 2.9 61.9 - - + -
187M VAL* 4.1 5.4 - - + -
215M GLN 3.2 11.2 + - - +
216M LYS* 3.6 10.8 - - + +
217M ALA 3.3 0.2 - - - -
218M ARG* 1.3 78.3 - - - +
220M THR* 1.3 73.0 + - - +
222M ARG* 3.4 21.4 + - - +
223M GLN* 3.0 61.2 + - + +
228N ASP* 2.8 42.0 + - - -
253N THR* 6.4 1.3 - - + -
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Residues in contact with THR 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183M ASP* 3.4 27.3 + - - +
186M ILE* 4.8 7.9 - - + -
187M VAL* 3.8 13.9 - - + +
211M TRP* 3.5 27.6 - - + -
216M LYS 3.3 10.8 + - - -
217M ALA 3.1 8.6 + - - -
219M TRP* 1.3 87.2 - - - +
221M PHE* 1.3 70.4 + - + +
223M GLN* 3.2 13.5 + - - +
224M LEU* 3.3 23.9 + - + +
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Residues in contact with PHE 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M ILE* 5.1 0.4 - - + -
190M LEU* 4.3 9.2 - - + -
205M VAL* 5.1 1.3 - - + -
207M CYS* 3.7 20.9 - - - -
211M TRP* 3.6 33.2 - + - -
217M ALA* 3.0 26.8 + - + +
218M ARG 4.5 0.2 - - - +
220M THR* 1.3 77.3 - - + +
222M ARG* 1.3 64.3 + - - +
224M LEU* 3.2 35.7 + - + +
225M GLU* 3.3 15.9 + - - +
229M LEU* 3.8 18.6 - - + -
232M ILE* 3.8 34.8 - - + -
235M CYS* 3.9 15.7 - - - -
247M LEU* 5.6 2.7 - - + -
251M ILE* 4.5 18.4 - - + -
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Residues in contact with ARG 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218M ARG* 2.9 41.6 + - + +
219M TRP* 3.5 33.2 - - - +
221M PHE* 1.3 72.7 - - - +
223M GLN* 1.3 76.0 + - - +
224M LEU 3.0 2.6 + - - -
225M GLU* 3.2 37.3 + - - +
251M ILE* 5.7 0.8 - - - +
228N ASP* 4.8 4.0 + - - +
252N ASN* 3.2 57.0 + - - +
253N THR* 5.2 5.7 - - - +
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Residues in contact with GLN 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M LYS* 4.2 7.9 + - - +
187M VAL* 3.8 19.1 - - + -
191M ARG* 2.7 33.4 + - - +
219M TRP* 3.0 75.6 + - + +
220M THR 3.2 6.5 + - - +
222M ARG* 1.3 93.3 - - - +
224M LEU* 1.3 57.9 + - - +
225M GLU 3.4 1.0 + - - -
226M ASP* 3.9 3.5 - - - +
228N ASP* 5.2 0.6 + - - -
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Residues in contact with LEU 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M VAL* 3.5 39.7 - - + +
190M LEU* 3.5 32.3 - - + -
191M ARG* 4.0 10.5 - - + -
220M THR* 3.3 23.3 + - + +
221M PHE* 3.2 30.2 + - + +
222M ARG 3.0 1.2 - - - -
223M GLN* 1.3 77.6 - - - +
225M GLU* 1.3 63.2 + - - +
226M ASP* 3.1 5.2 - - - -
227M ILE* 3.1 37.7 + - + +
228M ASP 3.9 1.9 + - - -
229M LEU* 4.6 8.7 + - + +
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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