Contacts of the helix formed by residues 213 - 224 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230K TYR* 4.4 1.0 + - - -
254K ARG* 2.8 37.3 + - - -
277K SER* 5.6 2.4 - - - +
303K ASN* 4.1 9.5 - - - +
305K GLN* 3.4 27.7 - - + +
329K ILE 5.6 2.2 - - - +
331K GLU* 5.0 1.1 - - + +
211L TRP* 4.4 2.3 - - - +
212L THR* 1.3 81.3 + - - +
214L TRP* 1.3 69.1 + - - +
215L GLN* 3.1 20.6 + - - +
216L LYS* 3.0 24.4 + - + +
217L ALA 3.3 8.3 + - - -
236L LEU* 3.9 3.6 - - - +
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Residues in contact with TRP 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K GLY 5.9 1.6 - - - -
277K SER* 4.1 9.2 + - - -
303K ASN* 2.8 50.2 + - + +
212L THR 3.6 0.8 + - - -
213L ASP* 1.3 74.6 + - - +
215L GLN* 1.3 85.2 + - + +
216L LYS 3.1 0.2 - - - -
217L ALA* 3.4 4.1 + - - +
218L ARG* 2.9 67.3 + - + +
236L LEU* 3.5 27.8 - - + -
243L GLY* 3.5 9.2 - - - +
246L LYS* 3.6 51.2 - - + +
247L LEU* 3.7 19.1 - - + +
250L ALA* 3.9 7.4 - - + -
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Residues in contact with GLN 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253K THR* 3.4 31.6 + - - -
254K ARG* 3.5 32.6 + - + +
255K LEU 4.8 0.2 - - - +
277K SER* 2.7 26.5 + - - +
213L ASP* 3.1 13.0 + - - +
214L TRP* 1.3 108.1 - - + +
216L LYS* 1.3 56.9 + - - +
218L ARG* 3.1 36.1 + - - +
219L TRP* 3.0 26.5 + - - +
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Residues in contact with LYS 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K TYR* 5.6 1.3 - - + -
254K ARG* 3.4 13.9 - - - +
331K GLU* 2.8 40.9 + - + +
183L ASP* 3.1 33.9 + - - +
210L ARG* 6.2 0.2 - - - +
211L TRP* 3.8 11.9 - - + +
213L ASP* 3.0 20.2 + - + +
215L GLN* 1.3 76.9 - - - +
217L ALA* 1.3 65.7 + - - +
219L TRP* 3.2 8.8 + - + +
220L THR* 3.1 24.3 + - - -
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Residues in contact with ALA 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L TRP* 3.7 24.9 - - + +
213L ASP 3.3 5.6 + - - +
214L TRP* 3.7 10.1 - - - +
216L LYS* 1.3 80.3 - - - +
218L ARG* 1.3 61.1 + - - +
220L THR* 3.1 2.0 + - - -
221L PHE* 2.9 31.0 + - + +
235L CYS* 3.6 31.4 - - - -
236L LEU* 4.5 1.3 - - + -
247L LEU* 4.0 11.4 - - + -
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Residues in contact with ARG 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K ALA 5.2 3.2 + - - -
249K ALA 5.3 2.8 + - - -
251K ILE 3.4 19.2 + - - -
252K ASN* 3.5 29.9 - - - +
253K THR 4.0 2.4 + - - +
214L TRP* 2.9 37.5 + - + +
215L GLN* 3.1 35.4 + - - +
216L LYS 3.2 0.2 - - - -
217L ALA* 1.3 76.1 - - - +
219L TRP* 1.3 63.2 + - - +
221L PHE* 5.3 0.7 - - - -
222L ARG* 3.0 47.1 + - + +
247L LEU* 3.7 14.0 - - + +
250L ALA* 3.8 31.9 + - + +
251L ILE* 5.3 3.2 - - + +
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Residues in contact with TRP 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ASP* 2.7 41.8 + - - -
253K THR* 6.3 2.0 - - + -
254K ARG* 5.8 1.6 - - - +
183L ASP* 4.1 9.9 - - + -
184L LYS* 3.6 52.0 - - + -
187L VAL* 4.0 13.7 - - + -
215L GLN 3.0 14.4 + - - +
216L LYS* 3.5 12.1 - - + +
218L ARG* 1.3 78.1 - - - +
220L THR* 1.3 72.6 + - - +
222L ARG* 3.8 17.1 - - - +
223L GLN* 3.0 61.4 + - + +
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Residues in contact with THR 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183L ASP* 3.2 36.0 + - - +
186L ILE* 4.8 5.8 - - + -
187L VAL* 3.9 10.2 - - + +
211L TRP* 3.3 30.6 - - + -
216L LYS 3.1 3.4 + - - -
217L ALA 3.1 8.6 + - - -
219L TRP* 1.3 87.1 - - - +
221L PHE* 1.3 63.9 + - + +
223L GLN* 3.1 19.9 + - - +
224L LEU* 3.4 28.0 + - + +
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Residues in contact with PHE 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L LEU* 4.3 9.2 - - + -
205L VAL* 5.3 2.0 - - + -
207L CYS* 3.7 22.2 - - - -
211L TRP* 3.6 31.4 - + - -
217L ALA* 2.9 28.6 + - + +
218L ARG 4.6 0.2 - - - +
220L THR* 1.3 75.5 - - + +
222L ARG* 1.3 63.6 + - - +
224L LEU* 3.3 26.8 + - + +
225L GLU* 3.3 15.6 + - - +
229L LEU* 3.8 25.4 - - + -
232L ILE* 3.6 35.2 - - + -
235L CYS* 3.8 17.9 - - - -
247L LEU* 5.3 3.4 - - + -
251L ILE* 4.5 16.4 - - + -
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Residues in contact with ARG 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ASP* 4.6 6.3 + - - -
252K ASN* 3.2 57.8 + - - +
253K THR* 5.4 4.0 - - - +
218L ARG* 3.0 42.9 + - + +
219L TRP* 3.8 30.3 - - - +
221L PHE* 1.3 72.1 - - - +
223L GLN* 1.3 75.5 + - - +
224L LEU 3.0 2.8 + - - -
225L GLU* 3.3 36.9 + - - +
251L ILE* 5.8 0.6 - - - +
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Residues in contact with GLN 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ASP* 5.0 1.4 + - - -
184L LYS* 4.6 6.0 + - - +
187L VAL* 3.8 18.8 - - + -
191L ARG* 2.9 30.1 + - - +
219L TRP* 3.0 73.2 + - + +
220L THR 3.1 8.1 + - - +
222L ARG* 1.3 93.9 - - - +
224L LEU* 1.3 56.5 + - - +
225L GLU 3.7 0.3 + - - -
226L ASP* 3.6 5.9 + - - +
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Residues in contact with LEU 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L VAL* 3.6 36.3 - - + +
190L LEU* 3.4 32.1 - - + -
191L ARG* 3.9 18.2 - - + +
220L THR* 3.6 24.9 - - + +
221L PHE* 3.3 25.2 + - + +
222L ARG 3.0 1.0 - - - -
223L GLN* 1.3 77.7 - - - +
225L GLU* 1.3 64.9 + - - +
226L ASP* 3.0 4.7 - - - +
227L ILE* 2.9 42.6 + - + +
228L ASP 3.6 2.4 + - - -
229L LEU* 4.7 5.9 + - + +
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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