Contacts of the helix formed by residues 212 - 221 (chain D) in PDB entry 5MR4
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 PRO 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D ASN* 5.8 0.7 - - - +
173D ASN* 4.3 8.5 - - - +
210D ARG 4.2 4.5 - - - +
211D VAL* 1.3 93.4 - - + +
213D SER* 1.3 58.6 - - - +
214D GLU* 3.9 27.8 - - + +
215D TYR* 2.9 33.4 + - + +
216D THR* 3.2 8.4 + - - -
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Residues in contact with SER 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL 3.5 2.0 + - - -
212D PRO* 1.3 71.5 - - - +
214D GLU* 1.3 63.9 + - - +
216D THR* 3.5 11.4 - - - -
217D TYR* 3.0 65.6 + - - +
218D ARG 4.1 0.2 + - - -
291D GLN* 4.6 6.6 + - - -
355D PHE* 4.8 1.3 - - - -
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Residues in contact with GLU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D PRO* 3.1 18.6 + - + +
213D SER* 1.3 81.1 + - - +
215D TYR* 1.3 91.6 + - + +
218D ARG* 3.5 21.8 - - - +
355D PHE* 5.5 4.4 - - - -
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Residues in contact with TYR 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA* 5.1 1.7 - - - +
167D ALA* 3.7 41.3 - - + -
168D CYS* 4.2 6.5 - - + -
171D ASN* 3.1 35.0 + - + +
174D CYS* 3.9 11.7 - - + -
211D VAL* 3.8 14.4 - - + -
212D PRO* 2.9 29.6 + - + +
214D GLU* 1.3 106.2 + - + +
216D THR* 1.3 63.1 + - - +
218D ARG* 3.4 7.4 + - - +
219D MET* 3.3 26.5 + - - +
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Residues in contact with THR 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D PHE* 3.6 35.6 - - + +
208D PHE* 3.8 24.0 + - + -
211D VAL* 3.6 34.8 + - + +
212D PRO 3.2 3.9 + - - +
213D SER* 3.5 9.0 - - - -
215D TYR* 1.3 72.6 - - - +
217D TYR* 1.3 81.3 + - - +
219D MET* 3.2 6.6 + - - +
220D LEU* 3.0 28.2 + - - +
236D THR* 5.7 0.2 - - - +
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Residues in contact with TYR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 5.3 3.1 - + - -
213D SER* 3.0 37.1 + - - +
216D THR* 1.3 91.0 + - - +
218D ARG* 1.3 60.7 + - - +
220D LEU* 3.7 1.3 - - - +
221D PHE* 2.8 56.4 + + + +
291D GLN* 4.0 24.3 + - - -
294D LEU* 4.1 13.7 - - + -
295D GLY* 3.0 30.0 + - - -
298D ALA* 4.3 19.9 - - + +
355D PHE* 3.5 29.0 - + + -
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Residues in contact with ARG 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D HIS 4.7 3.5 + - - +
163D ASP* 3.6 32.9 + - - +
164D ALA* 3.4 20.7 - - + +
167D ALA* 3.5 25.5 - - - +
213D SER 4.1 0.6 + - - -
214D GLU 3.5 21.5 - - - +
215D TYR* 3.6 5.8 - - - +
216D THR 3.2 0.6 - - - -
217D TYR* 1.3 79.7 - - - +
219D MET* 1.3 58.0 + - - +
222D CYS* 3.2 31.0 + - + +
355D PHE* 3.7 17.1 - - + -
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Residues in contact with MET 219 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B TYR* 6.2 0.4 - - - +
161D CYS* 5.2 1.9 - - - +
164D ALA* 3.7 22.9 - - + +
165D ALA* 4.4 7.2 - - + +
168D CYS* 3.8 24.2 - - - -
174D CYS* 4.5 0.7 - - - -
178D ARG* 3.7 38.4 - - + +
181D TYR* 4.5 8.3 - - - +
207D PHE* 3.8 23.3 - - + -
215D TYR 3.4 13.5 - - - +
216D THR* 3.2 7.1 + - - +
217D TYR 3.2 0.4 - - - -
218D ARG* 1.3 79.8 - - - +
220D LEU* 1.3 58.2 + - - +
222D CYS* 3.2 21.0 - - - -
233D ARG* 4.3 1.9 - - - +
236D THR* 3.6 27.2 + - + +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PHE* 3.8 18.8 - - + -
216D THR 3.0 15.0 + - - +
217D TYR* 4.2 2.7 - - + +
219D MET* 1.3 76.5 - - - +
221D PHE* 1.3 85.0 + - + +
222D CYS 3.6 0.2 - - - -
233D ARG* 3.6 5.0 - - - +
236D THR* 4.5 13.0 - - + -
237D ILE* 4.3 16.8 - - + -
297D TYR* 4.7 4.7 - - + -
298D ALA* 4.1 7.0 - - + -
301D ILE* 3.5 33.9 - - + -
308D ASN* 5.1 4.5 - - - +
309D TYR* 2.6 47.7 + - + -
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Residues in contact with PHE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D TYR* 2.8 60.6 + + + +
220D LEU* 1.3 100.4 - - + +
222D CYS* 1.3 66.3 + - - +
223D SER* 3.6 1.0 + - - -
294D LEU* 3.8 39.0 - - + -
297D TYR* 3.8 29.4 - + - -
309D TYR* 3.7 14.1 - - - -
352D ILE* 3.7 34.6 - - + +
355D PHE* 3.8 18.2 - + + -
356D GLY* 3.7 16.1 + - - -
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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