Contacts of the strand formed by residues 208 - 219 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194O PHE* 3.5 1.4 - - - +
195O VAL* 3.3 6.5 - - - -
196O SER* 2.8 51.1 + - - +
199O PRO* 6.3 4.9 - - - -
206O LYS 4.3 7.7 + - - +
207O PRO* 1.3 74.6 - - - +
209O LEU* 1.3 59.7 + - - +
210O SER* 4.1 0.9 + - - -
245O GLU* 3.3 24.0 - - + +
246O PRO 5.8 0.4 + - - -
247O HIS* 3.8 40.0 + - + +
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Residues in contact with LEU 209 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O ILE* 3.9 23.3 - - + -
193O PHE* 4.1 11.2 - - + -
194O PHE 3.7 12.6 - - - +
195O VAL* 4.0 10.5 - - + -
207O PRO 3.8 0.4 + - - -
208O LYS* 1.3 72.8 - - - +
210O SER* 1.3 69.0 + - - +
235O THR* 3.7 38.3 - - + +
238O ILE* 3.9 15.7 - - + -
239O ALA* 3.9 9.4 - - + +
244O THR* 3.7 26.0 - - + +
245O GLU 2.8 15.1 + - - +
246O PRO* 3.6 3.1 - - + +
247O HIS 2.7 28.5 + - - -
248O GLU 3.7 0.9 + - - -
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Residues in contact with SER 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193O PHE* 3.3 10.2 - - - +
194O PHE* 2.9 35.9 + - - -
196O SER* 5.6 1.2 + - - -
208O LYS 5.1 1.0 + - - -
209O LEU* 1.3 75.1 - - - +
211O CYS* 1.3 62.0 + - - +
235O THR* 4.9 0.9 - - - -
247O HIS* 3.5 28.2 - - - +
248O GLU* 3.1 19.5 + - - +
250O ILE* 4.8 1.3 - - - -
49P PHE* 3.9 25.1 - - - -
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Residues in contact with CYS 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O CYS* 4.0 23.8 - - - -
192O GLN 3.5 5.4 - - - -
193O PHE* 3.8 24.5 - - + -
210O SER* 1.3 77.2 - - - +
212O LEU* 1.3 58.1 + - - +
231O TYR* 4.3 11.2 - - - -
235O THR* 3.3 24.2 - - - +
248O GLU 2.9 8.1 + - - +
249O PHE* 3.3 18.7 - - + -
250O ILE* 2.7 34.5 + - - +
49P PHE* 4.3 0.7 - - - -
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Residues in contact with LEU 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O PHE* 4.9 1.3 - - + -
191O CYS* 3.0 4.7 - - - -
192O GLN 2.8 35.9 + - - +
211O CYS* 1.3 74.5 - - - +
213O MET* 1.3 77.1 + - - +
214O TYR* 4.3 2.7 - - + +
250O ILE* 3.3 20.0 - - + -
252O GLN* 4.7 9.9 - - + -
49P PHE* 3.8 17.9 - - + -
50P ALA* 3.4 27.1 - - + -
214P TYR* 3.6 39.9 - - + +
252P GLN* 3.6 20.0 - - - +
253P MET 3.9 2.0 - - - +
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Residues in contact with MET 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O HIS* 3.5 20.9 - - + -
190O PHE 3.5 13.2 - - - +
191O CYS* 3.8 6.3 - - + -
212O LEU* 1.3 78.0 - - - +
214O TYR* 1.3 79.2 + - - +
215O GLN* 3.4 17.7 - - - +
227O ASN* 4.0 10.8 - - + +
231O TYR* 3.7 39.3 - - + -
249O PHE* 3.8 19.1 - - + -
250O ILE 2.9 6.5 + - - -
251O LEU* 3.4 29.2 - - + +
252O GLN 2.9 24.9 + - - -
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Residues in contact with TYR 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O PHE* 4.6 0.2 - - - -
189O MET* 3.4 28.0 + - + +
190O PHE* 3.1 33.7 + - + +
212O LEU* 4.3 3.7 - - + +
213O MET* 1.3 79.0 - - - +
215O GLN* 1.3 58.0 + - - +
216O ARG* 3.9 13.9 - - + -
252O GLN* 3.4 28.0 - - + -
253O MET 4.3 2.2 - - - -
254O GLY* 3.3 14.6 - - - -
190P PHE* 3.2 32.3 - + - -
192P GLN* 2.5 36.8 + - - +
212P LEU* 3.5 41.5 - - + +
214P TYR* 5.3 5.6 - + + -
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Residues in contact with GLN 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187O CYS 3.4 18.6 - - - +
188O HIS* 4.0 3.1 - - - +
213O MET* 3.4 13.9 - - - +
214O TYR* 1.3 75.0 - - - +
216O ARG* 1.3 56.8 + - - +
217O SER 3.0 25.3 + - - +
218O CYS* 3.4 24.4 - - - +
219O ASP 4.5 0.4 - - - +
224O VAL* 4.5 4.1 - - - +
227O ASN* 2.9 45.0 + - - +
251O LEU* 4.1 10.2 - - + +
252O GLN 2.9 12.1 + - - +
253O MET* 3.5 0.7 - - - -
254O GLY 2.8 31.2 + - - -
650O UMP 3.0 14.9 + - - -
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Residues in contact with ARG 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O TRP* 3.8 23.5 - - - -
185O PRO* 3.0 30.5 + - - +
186O PRO 2.7 18.6 + - - -
187O CYS* 3.1 22.4 + - - +
189O MET* 3.7 17.0 - - - +
214O TYR* 3.9 4.9 - - - -
215O GLN* 1.3 71.5 - - - +
217O SER* 1.3 66.3 + - - +
255O ASP* 2.7 28.5 + - - +
650O UMP 2.7 44.6 + - - -
167P ARG 2.8 33.0 + - - -
168P ARG* 3.7 10.7 - - - +
170P ILE* 4.4 2.2 - - + -
192P GLN* 3.1 36.8 + - - +
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Residues in contact with SER 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187O CYS* 3.8 4.9 + - - +
215O GLN* 3.0 18.2 + - - +
216O ARG* 1.3 96.1 - - - +
218O CYS* 1.3 62.3 + - - +
255O ASP* 3.5 4.0 - - - -
257O HIS* 3.1 20.6 - - - -
650O UMP 2.8 46.2 + - - +
167P ARG* 3.3 9.7 + - - -
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Residues in contact with CYS 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215O GLN* 3.4 43.3 - - - +
217O SER* 1.3 77.6 - - - +
219O ASP* 1.3 59.8 + - - +
220O LEU* 3.2 2.4 + - + +
224O VAL* 3.8 14.4 - - + -
253O MET* 3.4 37.2 - - - -
254O GLY 4.3 0.4 - - - -
255O ASP 2.8 16.2 + - - +
256O ALA* 4.3 2.2 - - - -
257O HIS* 3.0 36.5 + - - +
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Residues in contact with ASP 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O CYS* 1.3 68.1 - - - +
220O LEU* 1.3 58.7 + - - +
221O GLY 3.2 5.9 + - - -
222O LEU* 3.2 29.8 + - - +
223O GLY 2.8 32.3 + - - +
224O VAL* 3.0 7.7 + - - +
257O HIS* 3.9 7.4 - - - +
259O TYR* 3.4 26.1 + - - -
262O HIS* 3.7 14.3 + - - -
315O MET* 5.2 6.6 - - - +
316O SER 5.5 0.9 + - - -
650O UMP 3.0 40.0 + - - +
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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