Contacts of the strand formed by residues 208 - 219 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194I PHE* 3.4 1.6 - - - +
195I VAL* 3.2 7.2 - - - -
196I SER* 2.8 51.6 + - - +
199I PRO* 6.2 5.4 - - - -
206I LYS 4.3 7.5 + - - +
207I PRO* 1.3 74.4 - - - +
209I LEU* 1.3 59.9 + - - +
210I SER* 5.1 1.0 + - - -
245I GLU* 3.3 22.7 - - + +
247I HIS* 3.8 41.1 + - + +
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Residues in contact with LEU 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I ILE* 3.8 23.1 - - + -
193I PHE* 4.0 11.9 - - + -
194I PHE 3.4 12.3 - - - +
195I VAL* 4.0 10.3 - - + +
207I PRO 3.9 0.4 + - - -
208I LYS* 1.3 72.8 - - - +
210I SER* 1.3 69.0 + - - +
235I THR* 3.7 38.4 - - + +
238I ILE* 3.9 15.7 - - + -
239I ALA* 3.8 9.2 - - + +
244I THR* 3.7 25.4 - - + +
245I GLU 2.8 15.6 + - - +
246I PRO* 3.6 2.5 - - + +
247I HIS* 2.7 28.8 + - - +
248I GLU 3.7 0.5 + - - -
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Residues in contact with SER 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I PHE* 3.2 10.9 - - - +
194I PHE* 2.8 38.2 + - - -
196I SER* 5.6 1.2 + - - -
208I LYS 5.1 0.7 + - - -
209I LEU* 1.3 74.0 - - - +
211I CYS* 1.3 63.8 + - - +
235I THR* 4.9 1.3 - - - -
247I HIS* 3.5 27.2 - - - -
248I GLU* 3.1 19.0 + - - +
250I ILE* 4.8 1.1 - - - -
49J PHE* 3.9 24.2 - - - -
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Residues in contact with CYS 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I CYS* 3.9 22.9 - - - -
192I GLN 3.4 5.4 - - - -
193I PHE* 3.8 24.5 - - + -
210I SER* 1.3 76.8 - - - +
212I LEU* 1.3 57.2 + - - +
231I TYR* 4.2 11.4 - - - -
235I THR* 3.3 24.9 - - + +
248I GLU 2.9 8.0 + - - +
249I PHE* 3.3 18.9 - - + -
250I ILE* 2.7 36.4 + - - +
49J PHE* 4.3 0.7 - - - -
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Residues in contact with LEU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I PHE* 4.9 1.1 - - + -
191I CYS* 2.9 4.1 - - - -
192I GLN 2.7 35.3 + - - +
211I CYS* 1.3 73.6 - - - +
213I MET* 1.3 76.9 + - - +
214I TYR* 4.3 2.9 - - + +
250I ILE* 3.2 20.0 - - + +
252I GLN* 4.7 10.3 - - + -
49J PHE* 3.7 18.1 - - + -
50J ALA* 3.4 26.7 - - + -
214J TYR* 3.5 44.0 - - + +
252J GLN* 3.6 15.0 - - - +
253J MET 3.9 3.1 - - - +
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Residues in contact with MET 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I HIS* 3.5 20.6 - - + -
190I PHE 3.5 12.1 - - - +
191I CYS* 3.8 6.1 - - + -
211I CYS 4.1 0.4 - - - -
212I LEU* 1.3 77.5 - - - +
214I TYR* 1.3 80.0 + - - +
215I GLN* 3.4 18.4 - - - +
227I ASN* 4.0 10.8 - - + +
231I TYR* 3.7 38.8 - - + -
249I PHE* 3.8 19.1 - - + -
250I ILE 2.8 7.3 + - - -
251I LEU* 3.4 29.4 - - + +
252I GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I PHE* 4.5 0.2 - - - -
189I MET* 3.3 31.9 + - + +
190I PHE* 3.0 32.7 + - + +
212I LEU* 4.3 3.3 - - + +
213I MET* 1.3 78.5 - - - +
215I GLN* 1.3 60.8 + - - +
216I ARG* 3.9 12.3 - - - -
252I GLN* 3.4 33.7 - - + -
253I MET 4.3 1.8 - - - -
254I GLY* 3.4 13.5 - - - -
190J PHE* 3.2 33.7 - + - -
192J GLN* 2.5 37.3 + - - +
212J LEU* 3.5 34.2 - - + +
214J TYR* 5.2 6.3 - + + -
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Residues in contact with GLN 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I CYS 3.3 18.8 - - - +
188I HIS* 3.9 3.1 - - - +
213I MET* 3.4 13.4 - - - +
214I TYR* 1.3 74.5 - - - +
216I ARG* 1.3 61.7 + - - +
217I SER 3.0 24.7 + - - +
218I CYS* 3.4 27.0 - - - +
219I ASP 4.5 0.4 - - - +
224I VAL* 4.5 4.3 - - - +
227I ASN* 2.9 44.1 + - - +
251I LEU* 4.1 11.0 - - + +
252I GLN 2.9 12.0 + - - +
253I MET* 3.5 0.7 - - - -
254I GLY 2.8 25.5 + - - -
350I UMP 3.1 13.5 + - - -
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Residues in contact with ARG 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I TRP* 3.8 23.5 - - - -
185I PRO* 3.0 32.3 + - - +
186I PRO 2.7 19.1 + - - +
187I CYS* 3.0 24.3 + - - +
189I MET* 3.7 17.7 - - - +
214I TYR* 3.9 5.3 + - - -
215I GLN* 1.3 71.9 - - - +
217I SER* 1.3 73.1 + - - +
255I ASP* 2.7 30.0 + - - +
350I UMP 2.6 33.9 + - - -
167J ARG 2.9 26.4 + - - +
168J ARG* 3.8 10.9 - - - +
170J ILE* 4.4 2.5 - - + -
192J GLN* 3.2 33.8 + - - +
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Residues in contact with SER 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I CYS* 3.8 4.3 - - - +
215I GLN* 3.0 18.0 + - - +
216I ARG* 1.3 107.9 - - - +
218I CYS* 1.3 62.3 + - - +
255I ASP 3.5 4.3 - - - -
257I HIS* 3.1 21.0 - - - -
350I UMP 3.3 27.6 - - - +
167J ARG* 3.3 16.9 + - - -
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Residues in contact with CYS 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I GLN* 3.4 39.9 - - - +
217I SER* 1.3 78.6 - - - +
219I ASP* 1.3 59.5 + - - +
220I LEU* 3.1 2.8 + - + +
224I VAL* 3.8 14.8 - - + -
253I MET* 3.4 39.9 - - - -
254I GLY 4.3 0.2 - - - -
255I ASP 2.8 16.2 + - - +
256I ALA* 4.3 2.0 - - - -
257I HIS* 3.0 35.9 + - - +
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Residues in contact with ASP 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I CYS* 1.3 68.6 - - - +
220I LEU* 1.3 59.9 + - - +
221I GLY 3.2 5.5 + - - -
222I LEU* 3.1 31.1 + - - +
223I GLY* 2.7 32.6 + - - +
224I VAL* 3.0 7.6 + - - +
257I HIS* 3.9 7.2 - - - +
259I TYR* 3.5 24.1 + - + -
262I HIS* 3.6 14.4 + - - -
315I MET* 5.1 6.6 - - - +
316I SER 5.6 0.7 + - - -
350I UMP 3.1 38.4 + - - +
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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