Contacts of the strand formed by residues 208 - 219 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B PHE 3.5 1.4 - - - +
195B VAL* 3.2 8.0 - - - -
196B SER* 2.8 51.0 + - - +
199B PRO* 6.3 4.7 - - - -
206B LYS 4.3 7.2 + - - +
207B PRO* 1.3 74.6 - - - +
209B LEU* 1.3 60.4 + - - +
210B SER* 5.2 0.7 + - - -
245B GLU* 3.3 22.0 - - + +
246B PRO 5.8 0.4 + - - -
247B HIS* 3.7 41.3 + - + +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 3.9 23.1 - - + -
193B PHE* 4.1 11.0 - - + -
194B PHE 3.5 12.1 - - - +
195B VAL* 4.0 11.9 - - + +
207B PRO 3.9 0.4 + - - -
208B LYS* 1.3 72.3 - - - +
210B SER* 1.3 67.4 + - - +
235B THR* 3.7 38.1 - - + +
238B ILE* 3.8 21.8 - - + -
239B ALA* 3.8 2.7 - - + +
244B THR* 3.7 26.2 - - - +
245B GLU 2.8 16.0 + - - +
246B PRO* 3.6 2.0 - - + +
247B HIS* 2.7 28.5 + - - +
248B GLU 3.7 1.0 + - - -
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.9 26.0 - - - -
193B PHE* 3.2 10.8 - - - +
194B PHE* 2.8 38.2 + - - +
196B SER* 5.7 1.0 + - - -
208B LYS 4.1 1.1 + - - -
209B LEU* 1.3 73.2 - - - +
211B CYS* 1.3 61.9 + - - +
235B THR* 4.8 0.7 - - - -
247B HIS* 3.5 27.7 - - - -
248B GLU* 3.2 20.3 + - - +
250B ILE* 4.8 0.7 - - - -
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Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.2 0.9 - - - -
191B CYS* 3.9 24.7 - - - -
192B GLN 3.4 4.5 - - - -
193B PHE* 3.8 22.9 - - + -
210B SER* 1.3 76.4 - - - +
212B LEU* 1.3 58.7 + - - +
231B TYR* 4.1 10.8 - - - -
235B THR* 3.3 25.6 - - + +
248B GLU 2.9 8.0 + - - +
249B PHE* 3.3 19.5 - - + -
250B ILE* 2.7 35.6 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.7 18.1 - - + -
50A ALA* 3.5 27.1 - - + -
214A TYR* 3.5 43.5 - - + +
252A GLN* 3.7 15.7 - - - +
253A MET 3.9 2.5 - - - +
190B PHE* 4.9 1.3 - - + -
191B CYS* 3.0 4.9 - - - +
192B GLN 2.7 37.2 + - - +
211B CYS* 1.3 74.8 - - - +
213B MET* 1.3 76.9 + - - +
214B TYR* 4.3 2.2 - - + +
250B ILE* 3.2 19.7 - - + +
252B GLN* 4.7 9.9 - - + -
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Residues in contact with MET 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B HIS* 3.5 22.2 - - + -
190B PHE 3.5 12.3 - - - +
191B CYS* 3.8 6.3 - - + -
211B CYS 4.2 0.2 - - - -
212B LEU* 1.3 79.7 - - - +
214B TYR* 1.3 79.1 + - - +
215B GLN* 3.5 19.7 - - - +
227B ASN* 4.0 11.9 - - + +
231B TYR* 3.7 39.3 - - + -
249B PHE* 3.8 19.3 - - + -
250B ILE 2.8 6.5 + - - -
251B LEU* 3.4 26.6 - - + +
252B GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PHE* 3.1 33.9 - + - -
192A GLN* 2.5 37.0 + - - +
212A LEU* 3.6 33.6 - - + +
214A TYR* 5.1 5.6 - + - -
189B MET* 3.3 28.6 + - + +
190B PHE* 3.0 34.0 + - + +
212B LEU* 4.3 3.3 - - + +
213B MET* 1.3 79.2 - - - +
215B GLN* 1.3 59.2 - - - +
216B ARG* 3.9 15.3 - - + -
252B GLN* 3.4 33.2 - - + -
253B MET 4.3 2.0 - - - -
254B GLY* 3.4 14.5 - - - -
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B CYS 3.3 17.7 - - - +
188B HIS* 4.0 2.2 - - - +
213B MET* 3.5 14.2 - - - +
214B TYR* 1.3 75.9 - - - +
216B ARG* 1.3 62.6 + - - +
217B SER 3.1 24.2 + - - +
218B CYS* 3.4 24.6 - - - +
224B VAL* 4.4 5.1 - - - +
227B ASN* 2.9 44.4 + - - +
251B LEU* 4.0 11.3 - - + +
252B GLN 2.9 10.1 + - - +
253B MET* 3.5 0.9 - - - -
254B GLY 2.8 24.6 + - - -
400B UMP 3.1 15.5 + - - -
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.1 26.8 + - - +
168A ARG* 3.8 10.4 - - - +
170A ILE* 4.3 2.7 - - + -
192A GLN* 3.0 35.1 + - - +
174B TRP* 3.8 24.3 - - - -
185B PRO* 3.0 30.9 + - - +
186B PRO 2.6 18.3 + - - -
187B CYS* 3.1 23.8 + - - +
189B MET* 3.7 18.6 - - - +
214B TYR* 3.9 4.9 - - - -
215B GLN* 1.3 71.2 - - - +
217B SER* 1.3 68.3 + - - +
255B ASP* 2.8 28.1 + - - +
400B UMP 2.8 42.8 + - - -
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Residues in contact with SER 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.2 9.4 - - - -
187B CYS* 3.9 5.0 - - - +
215B GLN* 3.1 18.9 + - - +
216B ARG* 1.3 97.4 - - - +
218B CYS* 1.3 61.2 + - - +
255B ASP* 3.5 5.2 - - - -
257B HIS* 3.1 19.6 - - - -
400B UMP 2.8 43.5 + - - +
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Residues in contact with CYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLN* 3.4 44.0 - - - +
217B SER* 1.3 79.8 - - - +
219B ASP* 1.3 60.4 + - - +
220B LEU* 3.1 6.2 + - + +
224B VAL* 3.8 14.6 - - + -
253B MET* 3.5 36.3 - - - -
254B GLY 4.3 0.7 - - - -
255B ASP 2.9 15.4 + - - +
256B ALA* 4.2 2.0 - - - -
257B HIS* 3.1 32.4 + - - +
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B CYS* 1.3 70.0 - - - +
220B LEU* 1.3 58.7 + - - +
221B GLY 3.2 5.2 + - - -
222B LEU* 3.1 26.1 + - - +
223B GLY 2.9 20.4 + - - -
224B VAL* 3.0 7.8 + - - -
257B HIS* 3.8 10.2 + - - +
259B TYR* 3.4 21.4 + - - -
262B HIS* 3.6 14.6 + - - -
315B MET* 5.5 0.3 - - - -
400B UMP 3.0 18.9 + - - +
2401B CB3 2.7 44.0 + - - +
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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