Contacts of the strand formed by residues 209 - 216 (chain D) in PDB entry 3O9Z
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 VAL 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D LEU* 3.7 0.9 - - - +
204D ALA* 4.3 15.5 - - + -
205D ARG* 3.5 1.9 + - - -
206D THR* 2.8 39.5 + - + +
208D THR* 1.3 92.1 - - - +
210D ASN* 1.3 75.3 + - - +
224D PHE* 3.7 24.7 - - + -
225D LEU 3.3 8.1 - - - +
226D SER* 3.7 4.0 - - - +
231D PHE* 3.6 34.1 - - + -
309D LEU* 4.9 2.2 - - + -
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Residues in contact with ASN 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LEU* 3.9 15.3 + - + +
179D ALA* 3.0 37.0 + - + +
202D VAL* 5.8 1.3 - - + -
204D ALA 3.1 5.8 - - - +
205D ARG* 3.5 32.4 - - - +
206D THR 3.7 8.1 + - - -
209D VAL* 1.3 88.9 + - - +
211D ALA* 1.3 61.2 + - - +
223D TRP* 3.4 18.8 - - + -
225D LEU* 2.8 38.2 + - + +
292D LEU 5.1 1.2 - - - +
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Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D VAL* 3.7 3.8 - - - +
203D HIS* 2.8 22.1 + - - -
204D ALA* 3.0 16.0 + - + +
209D VAL* 4.6 0.2 - - + -
210D ASN* 1.3 76.1 - - - +
212D GLY* 1.3 60.3 + - - +
223D TRP* 3.3 22.1 - - - +
224D PHE* 3.9 20.6 - - + -
306D HIS* 5.1 0.4 - - + -
309D LEU* 3.9 27.4 - - + -
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Residues in contact with GLY 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLU 3.3 12.6 - - - -
203D HIS* 3.6 19.3 + - - -
211D ALA* 1.3 76.0 - - - +
213D TYR* 1.3 62.0 + - - +
222D ARG* 3.7 3.3 - - - +
223D TRP* 3.0 42.9 + - - +
304D ASN 4.4 1.6 - - - +
306D HIS* 4.8 2.6 - - - +
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Residues in contact with TYR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D HIS* 4.3 7.4 - + - -
200D VAL* 3.7 2.1 - - - -
201D GLU* 2.8 45.8 + - - +
203D HIS* 3.6 20.2 - - + +
212D GLY* 1.3 75.8 - - - +
214D LEU* 1.3 70.7 + - - +
215D GLU* 2.6 46.2 + - + +
220D ARG* 2.9 45.6 + - + +
221D VAL 3.3 16.2 - - - -
222D ARG* 3.8 16.2 - - + -
223D TRP* 3.2 1.6 - - - +
304D ASN* 3.2 36.9 + - + +
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D PHE* 4.1 21.8 - - + -
190D LEU* 4.2 15.3 - - + -
197D ALA* 4.9 0.4 - - + -
199D HIS 3.4 3.6 - - - +
200D VAL* 3.9 33.0 - - + -
213D TYR* 1.3 84.1 - - - +
215D GLU* 1.3 64.3 + - - +
216D LEU* 3.5 27.4 - - + -
220D ARG* 3.5 2.3 - - - -
221D VAL* 2.8 37.6 + - + +
223D TRP* 3.6 26.5 - - + +
288D VAL* 4.3 13.9 - - + -
292D LEU* 4.5 2.7 - - + -
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Residues in contact with GLU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA* 3.6 1.9 - - - -
198D LEU* 2.8 35.4 + - + +
199D HIS* 2.9 37.4 + - + +
213D TYR* 2.6 44.2 + - + +
214D LEU* 1.3 72.1 - - - +
216D LEU* 1.3 58.6 + - - +
219D ALA 3.8 4.3 - - - +
220D ARG* 4.3 7.3 - - + +
304D ASN* 5.0 1.2 + - - +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D LEU* 3.6 37.0 - - + +
191D ALA* 4.2 1.8 - - + +
194D PHE* 3.5 17.9 - - + +
195D GLY 3.3 20.6 - - - +
196D ARG 3.2 6.3 - - - +
197D ALA* 3.6 21.5 - - + +
198D LEU* 4.7 4.0 - - - +
214D LEU* 3.5 33.0 - - + -
215D GLU* 1.3 78.8 - - - +
217D GLU* 1.3 69.2 + - - +
218D GLY 3.0 0.9 + - - -
219D ALA 2.8 23.2 + - - +
221D VAL* 4.5 7.6 - - + -
288D VAL* 6.0 0.2 - - + -
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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