Contacts of the strand formed by residues 208 - 219 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194F PHE* 3.5 1.9 - - - +
195F VAL* 3.2 7.6 - - - -
196F SER* 2.8 50.2 + - - +
199F PRO* 6.3 3.8 - - - -
206F LYS 4.3 6.6 + - - +
207F PRO* 1.3 76.9 - - - +
209F LEU* 1.3 58.6 + - - +
210F SER* 4.1 0.9 + - - -
245F GLU* 3.3 23.3 - - + +
246F PRO 5.9 0.2 + - - -
247F HIS* 3.8 42.0 + - + +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F ILE* 3.8 23.8 - - + -
193F PHE* 4.1 10.3 - - + -
194F PHE 3.5 12.8 - - - +
195F VAL* 4.0 11.0 - - + -
207F PRO 3.9 0.2 + - - -
208F LYS* 1.3 73.1 - - - +
210F SER* 1.3 68.5 + - - +
235F THR* 3.7 37.7 - - + +
238F ILE* 3.8 15.0 - - + -
239F ALA* 3.8 10.3 - - + +
244F THR* 3.7 26.0 - - + +
245F GLU 2.8 15.6 + - - +
246F PRO* 3.6 2.1 - - + +
247F HIS* 2.7 28.8 + - - +
248F GLU 3.6 0.5 + - - -
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Residues in contact with SER 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E PHE* 3.9 24.7 - - - -
193F PHE* 3.2 11.3 - - - +
194F PHE* 2.9 37.6 + - - -
196F SER* 5.6 0.9 + - - -
208F LYS 5.1 0.5 + - - -
209F LEU* 1.3 74.2 - - - +
211F CYS* 1.3 62.7 + - - +
235F THR* 4.9 1.1 - - - -
247F HIS* 3.5 27.9 - - - +
248F GLU* 3.2 19.0 + - - +
250F ILE* 4.8 1.6 - - - -
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Residues in contact with CYS 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE* 4.3 1.1 - - - -
191F CYS* 3.9 22.9 - - - -
192F GLN 3.4 5.4 - - - -
193F PHE* 3.8 19.7 - - + -
210F SER* 1.3 77.2 - - - +
212F LEU* 1.3 57.5 + - - +
231F TYR* 4.2 13.2 - - - -
235F THR* 3.3 27.4 - - + +
248F GLU 2.9 7.7 + - - +
249F PHE* 3.3 18.7 - - + -
250F ILE* 2.7 34.9 + - - +
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E PHE* 3.7 18.8 - - + -
50E ALA* 3.4 27.1 - - + -
214E TYR* 3.6 44.4 - - + +
252E GLN* 3.7 15.9 - - + +
253E MET 4.0 2.2 - - - +
190F PHE* 4.8 1.3 - - + -
191F CYS* 3.0 3.8 - - - -
192F GLN* 2.7 37.4 + - - +
211F CYS* 1.3 73.2 - - - +
213F MET* 1.3 76.3 + - - +
214F TYR* 4.3 2.5 - - + +
250F ILE* 3.2 21.1 - - + +
252F GLN* 4.8 8.1 - - + -
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Residues in contact with MET 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F HIS* 3.6 18.8 - - + -
190F PHE 3.5 12.3 - - - +
191F CYS* 3.9 6.1 - - + -
211F CYS* 4.1 0.6 - - - -
212F LEU* 1.3 80.0 - - - +
214F TYR* 1.3 80.0 + - - +
215F GLN* 3.5 18.6 - - - +
227F ASN* 4.0 11.0 - - + +
231F TYR* 3.7 42.8 - - + -
249F PHE* 3.8 18.8 - - + -
250F ILE 2.9 6.5 + - - -
251F LEU* 3.4 27.6 - - + +
252F GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E PHE* 3.1 34.5 - + - -
192E GLN* 2.6 37.8 + - - +
212E LEU* 3.6 33.9 - - + +
214E TYR* 5.1 6.1 - + + -
189F MET* 3.2 28.8 + - + +
190F PHE* 3.0 32.6 + - + +
212F LEU* 4.3 2.6 - - + +
213F MET* 1.3 79.6 - - - +
215F GLN* 1.3 59.8 + - - +
216F ARG* 3.9 13.9 - - + -
252F GLN* 3.4 33.9 - - + -
253F MET 4.3 1.8 - - - -
254F GLY* 3.4 13.3 - - - -
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Residues in contact with GLN 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F CYS 3.3 20.0 - - - +
188F HIS* 3.9 3.1 - - - +
213F MET* 3.5 14.3 - - - +
214F TYR* 1.3 75.1 - - - +
216F ARG* 1.3 56.3 + - - +
217F SER 3.0 21.9 + - - +
218F CYS* 3.4 24.0 - - - +
224F VAL* 4.4 4.9 - - - +
227F ASN* 2.9 45.2 + - - +
251F LEU* 4.0 10.9 - - + +
252F GLN 2.9 9.7 + - - +
253F MET* 3.4 2.4 - - - -
254F GLY 2.8 30.3 + - - -
600F UMP 3.0 14.7 + - - -
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Residues in contact with ARG 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG 3.0 27.5 + - - +
168E ARG* 3.7 9.5 - - - +
170E ILE* 4.3 2.0 - - + -
192E GLN* 2.9 36.1 + - - +
174F TRP* 3.8 24.2 - - - -
185F PRO* 3.0 30.1 + - - +
186F PRO 2.6 19.7 + - - +
187F CYS* 3.0 24.3 + - - +
189F MET* 3.7 17.9 - - - +
214F TYR* 3.9 5.4 + - - -
215F GLN* 1.3 71.7 - - - +
217F SER* 1.3 65.7 + - - +
255F ASP* 2.8 27.8 + - - +
600F UMP 3.0 42.8 + - - -
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Residues in contact with SER 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 3.1 9.0 - - - -
187F CYS* 3.8 3.9 - - - +
215F GLN* 3.0 18.4 + - - +
216F ARG* 1.3 97.7 - - - +
218F CYS* 1.3 62.3 + - - +
255F ASP* 3.5 5.4 - - - -
257F HIS* 3.1 19.9 - - - -
600F UMP 2.8 46.2 + - - +
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Residues in contact with CYS 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F GLN* 3.4 39.7 - - - +
217F SER* 1.3 79.1 - - - +
219F ASP* 1.3 60.1 + - - +
220F LEU* 3.1 3.0 + - + +
224F VAL* 3.7 14.6 - - + -
253F MET* 3.4 39.7 - - - -
254F GLY 4.4 0.2 - - - -
255F ASP 2.8 15.8 + - - +
256F ALA* 4.3 1.8 - - - -
257F HIS* 3.0 36.4 + - - +
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Residues in contact with ASP 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F CYS* 1.3 70.2 - - - +
220F LEU* 1.3 58.9 + - - +
221F GLY 3.3 5.4 + - - -
222F LEU* 3.1 25.2 + - - +
223F GLY 2.8 26.2 + - - -
224F VAL* 2.9 7.4 + - - -
257F HIS* 3.8 9.6 + - - +
259F TYR* 3.4 21.0 + - - -
262F HIS* 3.6 13.9 + - - -
315F MET* 5.5 0.2 - - - -
316F SER 5.5 0.2 + - - -
600F UMP 3.0 18.0 + - - +
2601F CB3 2.6 45.5 + - - +
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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