Contacts of the helix formed by residues 206 - 214 (chain D) in PDB entry 2I6A
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 TYR 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.9 12.0 - - + +
172D LEU* 4.5 7.4 - - + -
173D THR* 3.3 54.6 + - + -
201D PHE* 3.9 21.8 - + - -
202D ILE* 3.0 33.7 + - + +
205D PHE* 1.3 96.1 - + + +
207D LYS* 1.3 64.4 - - - +
208D GLU* 3.2 4.6 + - - -
209D SER* 3.4 14.7 + - - -
210D LEU* 3.0 20.6 + - - +
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Residues in contact with LYS 207 (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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202D ILE 3.5 1.7 + - - -
203D SER* 2.8 22.0 - - - +
204D GLN 3.2 19.7 - - - +
205D PHE 3.7 1.2 - - - -
206D TYR* 1.3 74.9 - - - +
208D GLU* 1.3 58.2 + - - +
210D LEU* 3.9 9.4 - - + -
211D MET* 2.7 43.0 + - + +
230D PHE* 6.5 0.2 - - + -
233D GLU* 2.2 55.6 + - + +
234D GLN* 4.4 13.5 - - - +
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Residues in contact with GLU 208 (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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206D TYR* 3.2 1.3 - - - -
207D LYS* 1.3 78.8 - - - +
209D SER* 1.3 58.3 + - - +
211D MET* 3.7 3.1 - - - +
212D LYS* 2.9 53.5 + - - +
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Residues in contact with SER 209 (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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172D LEU* 4.1 20.3 + - - -
176D PRO* 3.9 31.8 - - - +
180D LEU* 6.2 1.3 - - - -
206D TYR* 3.4 15.9 + - - +
208D GLU* 1.3 76.3 + - - +
210D LEU* 1.3 61.0 + - - +
212D LYS* 3.6 8.5 - - - +
213D VAL* 2.8 37.1 + - - +
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Residues in contact with LEU 210 (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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172D LEU* 3.5 15.0 - - + +
195D LEU* 3.7 26.2 - - + -
196D ASN 5.5 0.4 - - - +
197D LEU* 4.2 11.9 - - + -
202D ILE* 4.5 10.3 - - + +
203D SER* 4.0 21.1 - - - +
206D TYR 3.0 17.6 + - - +
207D LYS* 3.5 9.6 - - + +
209D SER* 1.3 78.0 - - - +
211D MET* 1.3 52.6 + - + +
213D VAL* 3.6 2.1 - - - +
214D MET* 2.7 52.3 + - + +
230D PHE* 3.6 32.1 - - + -
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Residues in contact with MET 211 (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 LYS* 2.7 26.7 + - + +
208D GLU* 4.0 2.7 - - - +
210D LEU* 1.3 74.4 - - + +
212D LYS* 1.3 60.7 + - - +
213D VAL 3.2 1.6 - - - -
214D MET* 3.8 15.4 - - + +
215D PRO* 3.1 23.0 - - - +
230D PHE* 3.9 26.7 - - + -
234D GLN* 3.5 39.7 - - + +
251D LEU* 4.7 21.1 - - + -
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Residues in contact with LYS 212 (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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180D LEU* 3.9 32.2 - - + +
208D GLU* 2.9 47.2 + - - +
209D SER* 3.6 9.3 - - - +
211D MET* 1.3 76.9 - - - +
213D VAL* 1.3 61.6 + - - +
215D PRO* 3.5 9.8 - - - +
216D TYR* 4.1 8.0 - - - -
254D MET* 5.8 0.3 - - - +
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Residues in contact with VAL 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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172D LEU* 4.1 9.2 - - + -
176D PRO* 5.0 1.1 - - + +
179D VAL* 3.5 27.1 - - + -
180D LEU* 3.5 28.5 - - + -
183D ALA* 5.1 3.1 - - + -
193D PHE* 4.4 5.8 - - + -
195D LEU* 4.0 29.8 - - + -
209D SER* 2.8 19.0 + - - +
210D LEU 3.7 4.3 - - - +
212D LYS* 1.3 76.4 - - - +
214D MET* 1.3 65.4 + - - +
215D PRO* 3.3 3.8 - - - -
216D TYR* 2.9 22.1 + - - +
217D VAL* 3.8 11.8 + - + -
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Residues in contact with MET 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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195D LEU* 5.2 1.1 - - + -
210D LEU* 2.7 45.6 + - + +
211D MET* 4.0 16.4 - - + +
213D VAL* 1.3 72.5 - - - +
215D PRO* 1.3 64.0 - - + +
216D TYR 2.8 6.4 + - - -
217D VAL* 3.0 29.5 + - - +
220D LEU* 4.0 34.5 - - + -
230D PHE* 4.0 17.9 - - + -
248D THR* 4.8 0.2 - - - -
251D LEU* 4.1 26.0 - - + -
252D PRO 5.4 0.4 - - - +
260D ARG* 3.3 28.4 + - - +
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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