Contacts of the strand formed by residues 208 - 219 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C PHE* 3.5 1.4 - - - +
195C VAL* 3.2 7.2 - - - -
196C SER* 2.8 50.7 + - - +
199C PRO* 6.3 4.5 - - - -
206C LYS 4.3 7.2 + - - +
207C PRO* 1.3 75.7 - - - +
209C LEU* 1.3 59.5 + - - +
210C SER* 4.1 1.1 + - - -
245C GLU* 3.3 22.4 - - + +
246C PRO 5.8 0.4 + - - -
247C HIS* 3.8 40.7 + - + +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ILE* 3.8 25.1 - - + -
193C PHE* 4.1 10.8 - - + -
194C PHE 3.5 11.0 - - - +
195C VAL* 4.0 11.7 - - + +
207C PRO 3.9 0.4 + - - -
208C LYS* 1.3 73.0 - - - +
210C SER* 1.3 68.4 + - - +
235C THR* 3.6 38.4 - - + +
238C ILE* 3.8 22.4 - - + -
239C ALA* 3.8 3.1 - - + +
244C THR* 3.6 24.0 - - + +
245C GLU 2.8 16.5 + - - +
246C PRO* 3.7 1.9 - - + +
247C HIS 2.8 27.8 + - - -
248C GLU 3.7 0.5 + - - -
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C PHE* 3.2 11.2 - - - +
194C PHE* 2.8 37.9 + - - -
196C SER* 5.7 0.5 + - - -
208C LYS 5.1 0.5 + - - -
209C LEU* 1.3 74.0 - - - +
211C CYS* 1.3 63.7 + - - +
235C THR* 4.9 0.7 - - - -
247C HIS* 3.5 27.4 - - - -
248C GLU* 3.2 18.0 + - - +
250C ILE* 4.8 1.1 - - - -
49D PHE* 3.9 24.0 - - - -
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Residues in contact with CYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C CYS* 4.0 24.0 - - - -
192C GLN 3.4 4.9 - - - -
193C PHE* 3.7 23.3 - - + -
210C SER* 1.3 76.6 - - - +
212C LEU* 1.3 58.1 + - - +
231C TYR* 4.2 11.2 - - - -
234C LEU* 6.1 0.2 - - - -
235C THR* 3.3 24.7 - - - +
248C GLU 2.9 7.6 + - - +
249C PHE* 3.3 19.0 - - + -
250C ILE* 2.7 32.6 + - - +
49D PHE* 4.2 3.6 - - - -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PHE* 5.2 0.9 - - + -
191C CYS* 3.0 4.1 - - - -
192C GLN* 2.7 36.2 + - - +
211C CYS* 1.3 74.3 - - - +
213C MET* 1.3 77.9 + - - +
214C TYR* 4.3 2.7 - - + +
250C ILE* 3.3 19.3 - - + +
252C GLN* 4.6 9.4 - - + -
49D PHE* 3.7 18.8 - - + -
50D ALA* 3.4 27.1 - - + -
214D TYR* 3.6 38.8 - - + +
252D GLN* 3.6 19.3 - - - +
253D MET 3.9 2.0 - - - +
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Residues in contact with MET 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C HIS* 3.5 22.7 - - + -
190C PHE 3.5 11.9 - - - +
191C CYS* 3.8 5.6 - - + -
211C CYS 4.1 0.4 - - - -
212C LEU* 1.3 79.2 - - - +
214C TYR* 1.3 90.0 + - - +
215C GLN* 3.4 20.2 - - - +
227C ASN* 4.0 10.8 - - + +
231C TYR* 3.7 39.5 - - + -
249C PHE* 3.8 18.8 - - + -
250C ILE 2.8 7.3 + - - -
251C LEU* 3.4 26.7 - - + +
252C GLN 2.9 25.1 + - - -
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Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C PHE* 4.6 0.2 - - - -
189C MET* 3.2 29.0 + - + +
190C PHE* 3.0 33.2 + - + +
212C LEU* 4.3 3.3 - - + +
213C MET* 1.3 79.2 - - - +
215C GLN* 1.3 60.8 + - - +
216C ARG* 3.8 14.6 - - + -
252C GLN* 3.3 32.1 - - + -
253C MET 4.3 1.6 - - - -
254C GLY* 3.3 14.1 - - - -
190D PHE* 3.2 33.9 - + - -
192D GLN* 2.5 37.7 + - - +
212D LEU* 3.5 35.0 - - + +
214D TYR* 5.0 6.3 - + + -
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Residues in contact with GLN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C CYS 3.2 18.4 - - - +
188C HIS* 3.9 3.6 - - - +
213C MET* 3.4 13.7 - - - +
214C TYR* 1.3 74.3 - - - +
216C ARG* 1.3 61.5 + - - +
217C SER 3.1 25.2 + - - +
218C CYS* 3.4 24.1 - - - +
224C VAL* 4.4 5.3 - - - +
227C ASN* 2.8 44.8 + - - +
251C LEU* 4.1 11.2 - - + +
252C GLN 2.9 11.9 + - - +
253C MET* 3.5 0.5 - - - -
254C GLY 2.8 25.1 + - - -
450C UMP 3.1 14.5 + - - -
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Residues in contact with ARG 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TRP* 3.8 22.8 - - - -
185C PRO* 2.9 29.7 + - - +
186C PRO 2.6 18.8 + - - +
187C CYS* 2.9 25.4 + - - +
189C MET* 3.7 17.9 - - - +
214C TYR* 3.8 5.3 + - - -
215C GLN* 1.3 71.9 - - - +
217C SER* 1.3 69.2 + - - +
255C ASP* 2.8 29.0 + - - +
450C UMP 2.7 43.8 + - - -
167D ARG* 3.0 27.8 + - - +
168D ARG* 3.8 10.6 - - - +
170D ILE* 4.3 2.7 - - + -
192D GLN* 3.1 34.6 + - - +
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C CYS* 3.7 5.4 - - - +
215C GLN* 3.1 18.4 + - - +
216C ARG* 1.3 97.2 - - - +
218C CYS* 1.3 61.5 + - - +
255C ASP* 3.5 5.2 - - - -
257C HIS* 3.1 3.8 - - - -
450C UMP 2.7 57.2 + - - +
167D ARG* 3.1 16.0 - - - -
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Residues in contact with CYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C GLN* 3.4 43.5 - - - +
217C SER* 1.3 78.6 - - - +
219C ASP* 1.3 60.4 + - - +
220C LEU* 3.1 3.0 + - + +
224C VAL* 3.8 14.8 - - + -
253C MET* 3.5 37.0 - - - -
254C GLY 4.3 0.2 - - - -
255C ASP 2.8 15.9 + - - +
256C ALA* 4.3 1.6 - - - -
257C HIS* 3.0 35.6 + - - +
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Residues in contact with ASP 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C CYS* 1.3 68.0 - - - +
220C LEU* 1.3 59.7 + - - +
221C GLY 3.3 5.4 + - - -
222C LEU* 3.1 21.1 + - - +
223C GLY 2.8 25.8 + - - -
224C VAL* 3.0 7.3 + - - -
257C HIS* 3.8 10.1 + - - +
259C TYR* 3.3 21.8 + - - -
262C HIS* 3.6 17.2 + - - -
316C SER 5.5 0.5 + - - -
450C UMP 3.0 18.0 + - - +
2451C CB3 2.6 46.5 + - - +
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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