Contacts of the strand formed by residues 208 - 219 (chain D) in PDB entry 2AAZ
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 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D PHE 3.5 1.4 - - - +
195D VAL* 3.2 7.5 - - - -
196D SER* 2.8 51.4 + - - +
199D PRO* 6.3 5.2 - - - -
206D LYS 3.5 7.5 + - - +
207D PRO* 1.3 72.7 - - - +
209D LEU* 1.3 60.4 + - - +
210D SER* 5.1 0.9 + - - -
245D GLU* 3.3 22.3 - - + +
246D PRO 5.8 0.4 + - - -
247D HIS* 3.8 41.1 + - + +
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Residues in contact with LEU 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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160D ILE* 3.8 23.6 - - + -
193D PHE* 4.1 11.0 - - + -
194D PHE 3.5 12.1 - - - +
195D VAL* 4.0 11.7 - - + +
207D PRO 3.9 0.4 + - - -
208D LYS* 1.3 71.9 - - - +
210D SER* 1.3 67.7 + - - +
235D THR* 3.7 37.9 - - + +
238D ILE* 3.9 15.7 - - + -
239D ALA* 3.8 9.0 - - + +
244D THR* 3.7 26.5 - - - +
245D GLU 2.8 16.2 + - - +
246D PRO* 3.6 2.0 - - + +
247D HIS* 2.7 28.5 + - - +
248D GLU 3.7 0.9 + - - -
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Residues in contact with SER 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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49C PHE* 3.9 25.8 - - - -
193D PHE* 3.2 10.0 - - - +
194D PHE* 2.8 38.3 + - - -
196D SER* 5.6 1.2 + - - -
208D LYS 4.0 1.2 + - - -
209D LEU* 1.3 72.1 - - - +
211D CYS* 1.3 62.3 + - - +
235D THR* 4.9 0.7 - - - -
247D HIS* 3.5 27.9 - - - -
248D GLU* 3.1 20.0 + - - +
250D ILE* 4.8 0.7 - - - -
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Residues in contact with CYS 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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49C PHE* 4.2 0.4 - - - -
191D CYS* 3.9 24.7 - - - -
192D GLN 3.4 4.3 - - - -
193D PHE* 3.8 23.3 - - + -
210D SER* 1.3 77.4 - - - +
212D LEU* 1.3 58.7 + - - +
231D TYR* 4.2 11.0 - - - -
235D THR* 3.3 25.8 - - + +
248D GLU 2.9 7.2 + - - +
249D PHE* 3.3 19.2 - - + -
250D ILE* 2.7 35.6 + - - +
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Residues in contact with LEU 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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49C PHE* 3.7 17.7 - - + -
50C ALA* 3.4 27.6 - - + -
214C TYR* 3.5 43.3 - - + +
252C GLN* 3.7 15.5 - - - +
253C MET 4.0 2.5 - - - +
190D PHE* 4.9 1.3 - - + -
191D CYS* 3.0 4.3 - - - +
192D GLN 2.7 38.5 + - - +
211D CYS* 1.3 73.9 - - - +
213D MET* 1.3 77.1 + - - +
214D TYR* 4.3 2.2 - - + +
250D ILE* 3.3 19.5 - - + +
252D GLN* 4.7 10.1 - - + -
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Residues in contact with MET 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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188D HIS* 3.5 23.1 - - + -
190D PHE 3.5 11.9 - - - +
191D CYS* 3.9 5.8 - - + -
211D CYS 4.1 0.2 - - - -
212D LEU* 1.3 80.5 - - - +
214D TYR* 1.3 79.3 + - - +
215D GLN* 3.4 19.1 - - - +
227D ASN* 4.0 11.7 - - + +
231D TYR* 3.6 38.8 - - + -
249D PHE* 3.8 19.5 - - + -
250D ILE 2.8 6.7 + - - -
251D LEU* 3.4 26.9 - - + +
252D GLN 2.9 25.1 + - - -
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Residues in contact with TYR 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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190C PHE* 3.1 35.7 - + - -
192C GLN* 2.5 36.7 + - - +
212C LEU* 3.6 33.2 - - + +
214C TYR* 5.0 5.6 - + - -
189D MET* 3.3 28.8 + - + +
190D PHE* 2.9 33.4 + - + +
212D LEU* 4.3 3.3 - - + +
213D MET* 1.3 78.9 - - - +
215D GLN* 1.3 59.8 + - - +
216D ARG* 3.9 15.3 - - + -
252D GLN* 3.4 33.2 - - + -
253D MET 4.3 2.0 - - - -
254D GLY* 3.4 14.1 - - - -
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Residues in contact with GLN 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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187D CYS 3.3 17.5 - - - +
188D HIS* 4.0 2.2 - - - +
213D MET* 3.4 14.8 - - - +
214D TYR* 1.3 76.0 - - - +
216D ARG* 1.3 63.2 + - - +
217D SER 3.1 24.7 + - - +
218D CYS* 3.4 25.2 - - - +
224D VAL* 4.4 4.9 - - - +
227D ASN* 2.9 44.0 + - - +
251D LEU* 4.0 10.8 - - + +
252D GLN 2.9 9.6 + - - +
253D MET* 3.5 0.5 - - - -
254D GLY 2.9 24.8 + - - -
500D UMP 3.1 15.3 + - - -
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Residues in contact with ARG 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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167C ARG* 3.1 26.6 + - - +
168C ARG* 3.8 10.2 - - - +
170C ILE* 4.3 2.5 - - + -
192C GLN* 3.0 35.1 + - - +
174D TRP* 3.7 24.7 - - - -
185D PRO* 3.0 30.7 + - - +
186D PRO 2.7 19.4 + - - -
187D CYS* 3.1 21.9 + - - +
189D MET* 3.6 19.0 - - - +
214D TYR* 3.9 4.9 - - - -
215D GLN* 1.3 71.9 - - - +
217D SER* 1.3 68.1 + - - +
255D ASP* 2.7 28.8 + - - +
500D UMP 2.7 43.4 + - - -
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Residues in contact with SER 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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167C ARG* 3.2 10.0 - - - -
187D CYS* 3.8 4.5 - - - +
215D GLN* 3.1 18.5 + - - +
216D ARG* 1.3 97.9 - - - +
218D CYS* 1.3 60.2 + - - +
255D ASP* 3.5 5.2 - - - -
257D HIS* 3.1 19.2 - - - -
500D UMP 2.7 45.0 + - - +
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Residues in contact with CYS 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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215D GLN* 3.4 44.4 - - - +
217D SER* 1.3 78.8 - - - +
219D ASP* 1.3 60.9 + - - +
220D LEU* 3.1 2.9 + - + +
224D VAL* 3.8 14.8 - - + -
253D MET* 3.5 35.4 - - - -
254D GLY 4.2 0.4 - - - -
255D ASP 2.8 15.6 + - - +
256D ALA* 4.2 2.0 - - - -
257D HIS* 3.0 36.0 + - - +
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Residues in contact with ASP 219 (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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218D CYS* 1.3 67.8 - - - +
220D LEU* 1.3 60.1 + - - +
221D GLY 3.2 5.4 + - - -
222D LEU* 3.1 26.3 + - - +
223D GLY 2.9 20.1 + - - -
224D VAL* 3.0 8.4 + - - -
257D HIS* 3.8 10.7 + - - +
259D TYR* 3.5 21.4 + - - -
262D HIS* 3.6 14.6 + - - -
315D MET* 5.5 0.3 - - - -
316D SER 5.5 0.2 + - - -
500D UMP 3.1 19.1 + - - +
2501D CB3 2.6 44.6 + - - +
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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