Contacts of the strand formed by residues 208 - 219 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H PHE* 3.5 1.7 - - - +
195H VAL* 3.3 7.1 - - - -
196H SER* 2.8 50.5 + - - +
199H PRO* 6.3 4.3 - - - -
206H LYS 4.3 7.1 + - - +
207H PRO* 1.3 75.1 - - - +
209H LEU* 1.3 59.7 + - - +
210H SER* 5.1 1.1 + - - -
244H THR* 5.0 0.2 - - - -
245H GLU* 3.3 23.5 - - + +
246H PRO 5.9 0.2 + - - -
247H HIS* 3.7 42.0 + - + +
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Residues in contact with LEU 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H ILE* 3.9 23.3 - - + -
193H PHE* 4.1 11.2 - - + -
194H PHE 3.5 11.7 - - - +
195H VAL* 4.1 9.9 - - + -
207H PRO 3.9 0.2 + - - -
208H LYS* 1.3 72.9 - - - +
210H SER* 1.3 69.0 + - - +
235H THR* 3.7 39.0 - - + +
238H ILE* 3.9 15.5 - - + -
239H ALA* 3.8 10.1 - - + +
244H THR* 3.7 26.5 - - + +
245H GLU 2.8 15.6 + - - +
246H PRO* 3.7 2.3 - - + +
247H HIS* 2.7 28.1 + - - +
248H GLU 3.6 0.5 + - - -
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Residues in contact with SER 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PHE* 3.9 24.7 - - - -
193H PHE* 3.2 11.5 - - - +
194H PHE* 2.9 36.7 + - - -
196H SER* 5.7 1.0 + - - -
208H LYS 5.1 0.7 + - - -
209H LEU* 1.3 74.5 - - - +
211H CYS* 1.3 63.4 + - - +
235H THR* 4.8 1.1 - - - -
247H HIS* 3.5 27.7 - - - +
248H GLU* 3.2 19.1 + - - +
250H ILE* 4.8 1.6 - - - -
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Residues in contact with CYS 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PHE* 4.3 1.3 - - - -
191H CYS* 4.0 22.7 - - - -
192H GLN 3.4 5.4 - - - -
193H PHE* 3.8 22.9 - - + -
210H SER* 1.3 77.5 - - - +
212H LEU* 1.3 57.5 + - - +
231H TYR* 4.2 12.1 - - - -
235H THR* 3.3 24.5 - - + +
248H GLU 2.9 7.7 + - - +
249H PHE* 3.3 18.7 - - + -
250H ILE* 2.7 35.4 + - - +
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Residues in contact with LEU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PHE* 3.7 18.3 - - + -
50G ALA* 3.5 26.0 - - + -
214G TYR* 3.5 44.6 - - + +
252G GLN* 3.6 16.4 - - + +
253G MET 4.0 2.2 - - - +
190H PHE* 4.9 1.3 - - + -
191H CYS* 3.0 3.5 - - - -
192H GLN 2.7 36.7 + - - +
211H CYS* 1.3 73.0 - - - +
213H MET* 1.3 76.9 + - - +
214H TYR* 4.2 2.5 - - + +
250H ILE* 3.3 21.1 - - + +
252H GLN* 4.7 8.7 - - + -
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Residues in contact with MET 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H HIS* 3.6 21.5 - - + -
190H PHE 3.5 12.3 - - - +
191H CYS* 3.9 5.8 - - + -
211H CYS* 4.8 0.2 - - - -
212H LEU* 1.3 80.2 - - - +
214H TYR* 1.3 80.8 + - - +
215H GLN* 3.5 19.5 - - - +
227H ASN* 4.0 9.4 - - + -
231H TYR* 3.7 38.6 - - + -
249H PHE* 3.8 20.2 - - + -
250H ILE 2.9 6.7 + - - -
251H LEU* 3.5 27.0 - - + +
252H GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G PHE* 3.1 33.9 - + - -
192G GLN* 2.5 38.3 + - - +
212G LEU* 3.5 35.1 - - + +
214G TYR* 5.1 6.1 - + + -
189H MET* 3.3 28.4 + - + +
190H PHE* 3.0 33.2 + - + +
212H LEU* 4.2 2.6 - - + +
213H MET* 1.3 79.5 - - - +
215H GLN* 1.3 59.6 + - - +
216H ARG* 3.8 14.4 - - + -
252H GLN* 3.4 33.2 - - + -
253H MET 4.3 1.6 - - - -
254H GLY* 3.4 14.2 - - - -
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Residues in contact with GLN 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H CYS 3.3 17.9 - - - +
188H HIS* 4.0 1.8 - - - +
213H MET* 3.5 15.1 - - - +
214H TYR* 1.3 74.6 - - - +
216H ARG* 1.3 61.8 + - - +
217H SER 3.0 24.7 + - - +
218H CYS* 3.4 24.3 - - - +
224H VAL* 4.4 5.5 - - - +
227H ASN* 2.9 45.7 + - - +
251H LEU* 4.0 13.2 - - + +
252H GLN 2.9 8.6 + - - +
253H MET* 3.4 0.7 - - - -
254H GLY 2.8 24.9 + - - -
700H UMP 3.1 15.0 + - - -
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Residues in contact with ARG 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ARG 3.0 28.0 + - - +
168G ARG* 3.7 10.5 - - - +
170G ILE* 4.3 2.2 - - + -
192G GLN* 2.9 37.7 + - - +
174H TRP* 3.8 24.4 - - - -
185H PRO* 3.0 30.9 + - - +
186H PRO 2.6 19.0 + - - -
187H CYS* 3.0 24.1 + - - +
189H MET* 3.7 18.4 - - - +
214H TYR* 3.8 5.5 + - - -
215H GLN* 1.3 72.2 - - - +
217H SER* 1.3 70.0 + - - +
255H ASP* 2.8 26.4 + - - +
700H UMP 3.0 40.6 + - - -
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Residues in contact with SER 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ARG* 3.2 8.7 - - - -
187H CYS* 3.8 5.1 - - - +
215H GLN* 3.0 18.6 + - - +
216H ARG* 1.3 108.9 - - - +
218H CYS* 1.3 61.6 + - - +
255H ASP* 3.5 5.2 - - - -
257H HIS* 3.1 20.8 - - - -
700H UMP 2.8 33.3 + - - +
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Residues in contact with CYS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215H GLN* 3.4 43.3 - - - +
217H SER* 1.3 79.8 - - - +
219H ASP* 1.3 59.9 + - - +
220H LEU* 3.1 3.4 + - + +
224H VAL* 3.7 14.6 - - + -
253H MET* 3.5 36.1 - - - -
255H ASP 2.8 15.6 + - - +
256H ALA* 4.3 1.8 - - - -
257H HIS* 3.0 36.0 + - - +
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Residues in contact with ASP 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H CYS* 1.3 70.6 - - - +
220H LEU* 1.3 58.6 + - - +
221H GLY 3.2 5.2 + - - -
222H LEU* 3.1 25.7 + - - +
223H GLY 2.8 26.2 + - - -
224H VAL* 3.0 7.6 + - - -
257H HIS* 3.7 9.8 + - - +
259H TYR* 3.4 21.3 + - + -
262H HIS* 3.7 13.6 + - - -
316H SER 5.5 0.3 + - - -
700H UMP 3.1 23.5 + - - +
2701H CB3 2.8 39.6 + - - +
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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