Contacts of the helix formed by residues 206 - 216 (chain A) in PDB entry 2RKX
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 LYS 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLY* 1.3 77.8 - - - +
207A MET* 1.3 64.9 + - - +
208A GLU* 3.4 32.6 - - - +
209A HIS* 3.2 50.3 + - + +
210A PHE* 3.7 6.2 - - - -
212A GLU* 5.9 1.3 - - - -
232A ILE* 3.4 13.8 - - - +
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 1.3 74.6 - - - +
208A GLU* 1.3 70.1 + - - +
210A PHE* 3.2 21.0 + - - +
211A LEU 3.6 3.3 + - - -
232A ILE* 3.6 18.8 - - + +
233A ASP 5.9 0.4 - - - -
236A GLU* 3.8 14.6 - - + +
237A LEU* 3.7 45.9 - - + +
240A TYR* 3.7 44.1 - - + -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LYS* 3.4 35.2 + - + +
207A MET* 1.3 81.4 + - - +
209A HIS* 1.3 58.5 + - - +
211A LEU* 3.2 6.2 + - + +
212A GLU* 3.0 41.9 + - + +
240A TYR* 3.4 31.6 - - + +
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Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS 3.3 26.0 - - - -
180A SER 3.7 6.0 + - - -
181A GLY* 3.4 32.8 + - - -
182A TYR* 3.4 22.7 - - + +
204A ALA* 4.5 0.7 - - - -
205A GLY* 2.9 24.2 + - - +
206A LYS* 3.2 43.4 + - + +
208A GLU* 1.3 75.7 - - - +
210A PHE* 1.3 58.6 + - + +
212A GLU* 3.4 21.5 + - - +
213A ALA 2.9 24.4 + - - -
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Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.1 11.0 - - + -
182A TYR* 3.5 26.2 - + - -
204A ALA* 4.0 13.2 - - + -
206A LYS 3.7 11.2 - - - -
207A MET 3.2 6.9 + - - +
209A HIS* 1.3 75.5 - - - +
211A LEU* 1.3 65.3 + - - +
213A ALA* 3.2 3.5 + - - +
214A PHE* 3.0 31.9 + + + -
221A ALA* 3.5 29.4 - - + -
223A ALA* 4.0 9.6 - - + -
227A PHE* 3.8 25.1 - + - -
232A ILE* 3.7 24.2 - - + -
237A LEU* 3.7 34.3 - - + -
241A LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A MET 3.6 2.4 + - - -
208A GLU* 3.2 9.0 + - + +
210A PHE* 1.3 77.1 - - - +
212A GLU* 1.3 64.6 + - + +
214A PHE* 3.2 5.4 + - + +
215A LEU* 3.0 47.8 + - + +
240A TYR* 3.4 33.0 - - + +
241A LEU* 3.6 9.5 - - + +
244A HIS* 4.1 31.2 - - + +
246A VAL* 3.7 25.4 - - + -
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLY* 5.2 2.4 - - - -
182A TYR 5.4 1.6 + - - +
184A THR* 3.5 23.8 - - + +
188A ARG* 4.8 1.6 + - - -
206A LYS* 5.9 1.2 - - - -
208A GLU* 3.0 27.4 + - + +
209A HIS* 3.5 28.6 - - - +
211A LEU* 1.3 78.6 - - + +
213A ALA* 1.3 60.5 + - - +
215A LEU* 3.3 14.3 + - + +
216A ALA* 3.1 17.8 + - - +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.4 42.2 - - + -
184A THR* 3.9 9.3 - - - +
187A ILE* 4.2 8.3 - - + -
200A ALA* 4.2 8.3 - - + -
209A HIS 2.9 8.0 + - - +
210A PHE* 3.2 4.5 + - - +
212A GLU* 1.3 75.2 - - - +
214A PHE* 1.3 62.6 + - + +
216A ALA* 3.3 12.0 + - - +
218A ALA* 3.1 25.1 + - + +
221A ALA* 5.0 4.0 - - + -
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.7 38.3 + - + -
5A ARG 3.6 18.4 - - - -
6A ILE* 3.8 18.8 - - + -
210A PHE* 3.0 32.8 + - + +
211A LEU 3.2 3.6 + - - +
213A ALA* 1.3 75.4 - - - +
215A LEU* 1.3 63.9 + - - +
217A GLY* 3.1 13.5 + - - -
218A ALA* 3.2 21.5 + - + +
220A ALA* 3.6 30.7 - - - -
221A ALA* 3.7 14.6 - - + -
241A LEU* 4.0 15.3 - - + -
246A VAL* 3.9 23.8 - - + -
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.7 23.0 + - - +
211A LEU* 3.0 39.6 + - + +
212A GLU* 3.3 15.7 + - + +
214A PHE* 1.3 76.0 - - - +
216A ALA* 1.3 62.2 + - - +
217A GLY* 3.3 1.4 + - - -
246A VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A THR* 3.8 19.5 - - + +
187A ILE* 3.7 21.2 - - + +
188A ARG* 3.6 44.9 + - + +
191A ARG* 4.0 7.4 - - - +
212A GLU 3.1 13.9 + - - +
213A ALA 3.4 12.1 - - - +
214A PHE 3.2 0.4 - - - -
215A LEU* 1.3 76.5 - - - +
217A GLY* 1.3 54.8 + - - +
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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