Contacts of the helix formed by residues 213 - 224 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E TRP* 4.4 1.8 - - - +
212E THR* 1.3 79.9 + - - +
214E TRP* 1.3 67.0 + - - +
215E GLN* 2.9 22.9 + - - +
216E LYS* 3.0 25.5 + - + +
217E ALA 3.3 8.1 + - - -
236E LEU* 3.8 3.7 - - - +
230F TYR* 4.3 1.2 + - - -
254F ARG* 2.8 34.4 + - - -
277F SER* 5.9 0.3 - - - -
303F ASN* 4.0 8.0 + - - +
305F GLN* 3.2 27.6 - - + +
329F ILE 5.7 2.0 - - - +
331F GLU* 5.0 1.9 - - + +
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Residues in contact with TRP 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E THR 3.7 0.6 + - - -
213E ASP* 1.3 72.5 + - - +
215E GLN* 1.3 82.9 + - + +
217E ALA* 3.3 3.8 + - - +
218E ARG* 2.7 75.0 + - + +
236E LEU* 3.6 17.7 - - + +
243E GLY* 3.4 19.7 - - - +
246E LYS* 3.5 52.8 - - + +
247E LEU* 3.6 19.0 - - + +
250E ALA* 3.9 7.9 - - + -
277F SER* 4.2 8.3 + - - -
303F ASN* 2.9 47.2 + - + +
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Residues in contact with GLN 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ASP* 2.9 13.6 + - - +
214E TRP* 1.3 107.2 - - + +
216E LYS* 1.3 59.5 - - - +
218E ARG* 3.2 31.5 + - - +
219E TRP* 3.1 25.8 + - - +
253F THR* 3.6 26.3 + - + -
254F ARG* 3.5 37.1 + - + +
255F LEU 5.1 0.2 - - - +
277F SER* 2.7 28.6 + - - +
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Residues in contact with LYS 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASP* 3.3 29.6 - - - +
211E TRP* 3.8 13.5 - - + -
213E ASP* 3.0 19.5 + - + +
215E GLN* 1.3 76.1 - - - +
217E ALA* 1.3 63.5 + - - +
219E TRP* 3.4 9.5 + - + +
220E THR* 3.2 24.1 + - - -
202F ASP* 6.1 0.7 - - - -
230F TYR* 5.8 1.6 - - + -
254F ARG* 3.5 14.7 - - - +
331F GLU* 2.3 45.3 + - - +
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Residues in contact with ALA 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E TRP* 3.8 24.2 - - + +
213E ASP 3.3 5.6 + - - +
214E TRP 3.5 10.3 - - - +
216E LYS* 1.3 78.1 - - - +
218E ARG* 1.3 62.4 + - - +
220E THR* 3.1 2.7 + - - -
221E PHE* 3.0 29.5 + - + +
235E CYS* 3.6 30.5 - - - -
236E LEU* 4.3 3.4 - - + -
247E LEU* 3.9 13.7 - - + -
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Residues in contact with ARG 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TRP* 2.7 44.8 + - + +
215E GLN* 3.2 33.9 + - - +
217E ALA* 1.3 73.5 - - - +
219E TRP* 1.3 62.2 + - - +
221E PHE 3.5 0.5 + - - -
222E ARG* 3.0 47.1 + - + +
247E LEU* 3.6 14.1 - - + +
250E ALA* 3.7 26.1 + - + +
251E ILE* 5.3 5.3 - - + +
248F ALA 5.5 2.6 + - - -
249F ALA 5.6 1.6 + - - -
251F ILE 3.5 18.4 + - - -
252F ASN* 3.6 26.6 + - - +
253F THR 4.1 2.4 + - - +
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Residues in contact with TRP 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASP* 3.9 31.2 - - + -
184E LYS* 3.5 41.7 - - + -
187E VAL* 4.1 4.5 - - + -
215E GLN 3.1 14.4 + - - +
216E LYS* 3.6 12.3 - - + +
217E ALA 3.3 0.2 - - - -
218E ARG* 1.3 76.8 - - - +
220E THR* 1.3 84.9 + - - +
222E ARG* 3.4 19.1 + - - +
223E GLN* 3.2 62.3 + - + +
228F ASP* 2.7 40.3 + - - -
254F ARG* 6.0 0.7 - - - +
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Residues in contact with THR 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASP* 3.5 21.1 - - - +
186E ILE* 4.7 4.9 - - + -
187E VAL* 3.8 15.7 - - + +
211E TRP* 3.3 36.9 - - + -
216E LYS 3.2 10.8 + - - -
217E ALA 3.1 9.2 + - - -
219E TRP* 1.3 87.5 - - - +
221E PHE* 1.3 63.6 + - + +
223E GLN* 3.2 19.6 + - - +
224E LEU* 3.3 24.2 + - + +
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Residues in contact with PHE 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ILE* 5.1 0.7 - - + -
190E LEU* 4.2 10.3 - - + -
205E VAL* 5.1 2.9 - - + -
207E CYS* 3.7 21.8 - - - -
211E TRP* 3.6 32.5 - + - -
217E ALA 3.0 25.9 + - - +
218E ARG 3.9 0.4 - - - +
220E THR* 1.3 74.6 - - + +
222E ARG* 1.3 64.4 + - - +
224E LEU* 3.3 21.4 + - + +
225E GLU* 3.3 24.0 + - - +
229E LEU* 3.8 31.0 - - + -
232E ILE* 3.7 28.9 - - + -
235E CYS* 3.9 16.6 - - - -
247E LEU* 5.5 3.6 - - + -
251E ILE* 4.6 15.3 - - + -
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Residues in contact with ARG 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ARG* 3.0 45.5 + - + +
219E TRP* 3.7 33.5 - - - +
221E PHE* 1.3 74.7 - - - +
223E GLN* 1.3 73.5 + - - +
224E LEU 3.2 0.3 + - - -
225E GLU* 3.4 35.4 + - - +
251E ILE* 5.9 0.4 - - - +
228F ASP* 4.5 5.9 + - - -
252F ASN* 3.1 56.4 + - - +
253F THR* 5.5 4.6 + - - +
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Residues in contact with GLN 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LYS* 4.7 6.6 + - - +
187E VAL* 3.8 13.9 - - + -
191E ARG* 3.2 34.1 + - - +
219E TRP* 3.2 68.3 + - + +
220E THR 3.2 8.0 + - - +
222E ARG* 1.3 91.5 - - - +
224E LEU* 1.3 56.8 + - - +
225E GLU 3.3 2.5 + - - -
226E ASP* 3.7 6.2 + - - +
228F ASP* 5.0 1.0 + - - -
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E VAL* 3.5 39.5 - - + +
190E LEU* 3.6 30.3 - - + -
191E ARG* 4.0 12.8 - - + +
220E THR* 3.3 26.0 + - + +
221E PHE* 3.3 27.7 + - + +
222E ARG 3.1 1.2 - - - -
223E GLN* 1.3 77.2 - - - +
225E GLU* 1.3 64.3 + - - +
226E ASP* 3.1 4.3 - - - -
227E ILE* 3.1 41.2 + - + +
228E ASP 3.8 2.1 + - - -
229E LEU* 4.6 7.1 + - + +
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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