Contacts of the strand formed by residues 208 - 219 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194M PHE* 3.5 1.2 - - - +
195M VAL* 3.2 6.5 - - - -
196M SER* 2.8 51.9 + - - +
199M PRO* 6.2 5.6 - - - -
206M LYS 4.3 7.5 + - - +
207M PRO* 1.3 74.0 - - - +
209M LEU* 1.3 59.6 + - - +
210M SER* 4.1 1.3 + - - -
245M GLU* 3.3 23.7 - - + +
247M HIS* 3.8 42.0 + - + +
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Residues in contact with LEU 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M ILE* 3.8 23.3 - - + -
193M PHE* 4.1 11.0 - - + -
194M PHE 3.5 12.6 - - - +
195M VAL* 4.0 11.2 - - + -
207M PRO 3.8 0.4 + - - -
208M LYS* 1.3 72.8 - - - +
210M SER* 1.3 69.7 + - - +
235M THR* 3.7 38.1 - - + +
238M ILE* 3.9 15.3 - - + -
239M ALA* 3.8 9.0 - - + +
244M THR* 3.7 25.1 - - + +
245M GLU 2.8 15.4 + - - +
246M PRO* 3.6 2.9 - - + +
247M HIS 2.7 28.6 + - - -
248M GLU 3.7 0.9 + - - -
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Residues in contact with SER 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M PHE* 3.2 10.7 - - - +
194M PHE* 2.8 37.5 + - - +
196M SER* 5.5 1.6 + - - -
208M LYS 5.1 1.0 + - - -
209M LEU* 1.3 74.6 - - - +
211M CYS* 1.3 62.3 + - - +
235M THR* 4.9 0.9 - - - -
247M HIS* 3.5 28.1 - - - +
248M GLU* 3.1 19.3 + - - +
250M ILE* 4.9 1.3 - - - -
49N PHE* 3.9 24.0 - - - -
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Residues in contact with CYS 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M CYS* 3.9 24.0 - - - -
192M GLN 3.4 5.2 - - - -
193M PHE* 3.8 24.5 - - + -
210M SER* 1.3 76.6 - - - +
212M LEU* 1.3 57.7 + - - +
231M TYR* 4.3 10.5 - - - -
235M THR* 3.3 24.5 - - - +
248M GLU 2.9 8.2 + - - +
249M PHE* 3.2 19.1 - - + -
250M ILE* 2.7 32.4 + - - +
49N PHE* 4.2 2.9 - - - -
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Residues in contact with LEU 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M PHE* 4.9 1.3 - - + -
191M CYS* 2.9 4.3 - - - -
192M GLN 2.7 36.6 + - - +
211M CYS* 1.3 74.3 - - - +
213M MET* 1.3 77.1 + - - +
214M TYR* 4.3 2.7 - - + +
250M ILE* 3.2 20.2 - - + +
252M GLN* 4.7 9.6 - - + -
49N PHE* 3.6 18.6 - - + -
50N ALA* 3.3 27.4 - - + -
214N TYR* 3.6 39.5 - - + +
252N GLN* 3.6 19.3 - - - +
253N MET 3.9 2.5 - - - +
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Residues in contact with MET 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M HIS* 3.5 21.3 - - + -
190M PHE 3.5 13.2 - - - +
191M CYS* 3.8 6.3 - - + -
211M CYS 4.1 0.2 - - - -
212M LEU* 1.3 78.3 - - - +
214M TYR* 1.3 79.7 + - - +
215M GLN* 3.5 19.7 - - - +
227M ASN* 4.1 9.9 - - + +
231M TYR* 3.7 38.8 - - + -
249M PHE* 3.8 19.1 - - + -
250M ILE 2.8 6.3 + - - -
251M LEU* 3.4 27.1 - - + +
252M GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M PHE* 4.5 0.2 - - - -
189M MET* 3.3 31.5 + - + +
190M PHE* 3.0 33.5 + - + +
212M LEU* 4.3 3.1 - - + +
213M MET* 1.3 78.4 - - - +
215M GLN* 1.3 59.5 + - - +
216M ARG* 3.9 12.6 - - - -
252M GLN* 3.4 34.1 - - + -
253M MET 4.3 2.2 - - - -
254M GLY* 3.4 13.9 - - - -
190N PHE* 3.2 33.7 - + - -
192N GLN* 2.6 36.1 + - - +
212N LEU* 3.5 34.6 - - + +
214N TYR* 5.2 5.6 - + + -
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Residues in contact with GLN 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M CYS 3.3 18.2 - - - +
188M HIS* 3.9 3.1 - - - +
213M MET* 3.5 14.3 - - - +
214M TYR* 1.3 73.9 - - - +
216M ARG* 1.3 57.2 + - - +
217M SER 3.0 14.5 + - - +
218M CYS* 3.4 25.0 - - - +
219M ASP 4.4 0.4 - - - +
224M VAL* 4.5 4.9 - - - +
227M ASN* 2.9 38.9 + - - +
251M LEU* 4.1 10.4 - - + +
252M GLN 2.9 12.3 + - - +
253M MET* 3.5 0.7 - - - -
254M GLY 2.8 31.4 + - - -
550M UMP 2.9 30.8 + - - -
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Residues in contact with ARG 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M TRP* 3.7 24.8 - - - -
185M PRO* 3.0 30.3 + - - +
186M PRO 2.6 19.1 + - - +
187M CYS* 3.0 23.1 + - - +
189M MET* 3.7 17.9 - - - +
214M TYR* 3.9 5.6 + - - -
215M GLN* 1.3 72.1 - - - +
217M SER* 1.3 67.2 + - - +
255M ASP* 2.7 28.5 + - - +
550M UMP 2.6 44.4 + - - -
167N ARG 3.0 24.1 + - - -
168N ARG* 3.8 9.3 - - - +
170N ILE* 4.4 2.2 - - + -
192N GLN* 3.1 35.2 + - - +
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Residues in contact with SER 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M CYS* 3.8 2.7 + - - +
215M GLN* 3.0 18.2 + - - +
216M ARG* 1.3 108.6 - - - +
218M CYS* 1.3 62.3 + - - +
255M ASP* 3.5 3.8 - - - -
257M HIS* 3.1 20.6 - - - -
550M UMP 3.1 35.3 + - - +
167N ARG* 3.4 10.0 + - - -
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Residues in contact with CYS 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215M GLN* 3.4 39.3 - - - +
217M SER* 1.3 76.7 - - - +
219M ASP* 1.3 59.5 + - - +
220M LEU* 3.2 2.4 + - + +
224M VAL* 3.8 14.4 - - + -
253M MET* 3.4 40.8 - - - -
254M GLY 4.3 0.4 - - - -
255M ASP 2.8 16.0 + - - +
256M ALA* 4.2 2.0 - - - -
257M HIS* 3.0 36.7 + - - +
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Residues in contact with ASP 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218M CYS* 1.3 68.3 - - - +
220M LEU* 1.3 59.9 + - - +
221M GLY 3.2 5.7 + - - -
222M LEU* 3.2 29.4 + - - +
223M GLY* 2.8 34.8 + - - +
224M VAL* 3.0 7.0 + - - +
257M HIS* 3.8 7.4 - - - +
259M TYR* 3.4 25.9 + - - -
262M HIS* 3.6 14.3 + - - -
315M MET* 5.1 6.8 - - - +
316M SER 5.5 0.9 + - - -
550M UMP 3.0 36.8 + - - +
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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