Contacts of the strand formed by residues 211 - 220 (chain D) in PDB entry 4UI2
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 THR 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C GLY* 5.5 2.8 - - - +
169D PRO* 2.8 47.9 - - - +
180D THR* 6.4 0.2 - - - +
181D CYS 3.3 1.9 + - - -
182D LYS* 2.6 39.8 + - + +
184D GLU* 4.5 8.1 - - + -
201D ASN* 4.2 1.3 - - - -
202D VAL 3.3 27.4 - - - +
203D PRO* 4.0 6.1 - - + -
204D VAL* 4.0 5.1 - - - +
209D SER 3.5 12.5 + - - +
210D ALA* 1.3 78.6 - - - +
212D ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 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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167C GLY* 5.5 10.5 - - - +
169D PRO* 4.3 6.7 - - - -
201D ASN* 3.1 6.1 - - - -
202D VAL* 2.8 35.6 + - - +
204D VAL* 4.6 7.8 - - + +
211D THR* 1.3 75.4 - - - +
213D THR* 1.3 64.5 + - - +
288D TYR* 3.3 40.6 - - + -
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Residues in contact with THR 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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165C LEU* 3.5 18.9 + - + +
166C PHE 6.0 0.3 - - - -
169D PRO* 3.8 7.3 - - - +
199D VAL* 3.7 14.1 - - + -
200D THR 3.6 5.6 - - - +
201D ASN* 2.9 22.8 + - - +
212D ALA* 1.3 76.2 - - - +
214D ASN* 1.3 59.5 + - - +
215D LYS 3.6 16.6 - - - +
216D ILE* 3.8 15.7 - - + -
288D TYR* 3.2 7.4 - - - +
289D LEU* 2.7 48.1 + - - +
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Residues in contact with ASN 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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200D THR* 2.9 28.1 + - - +
202D VAL* 3.9 26.2 - - + +
212D ALA 3.8 1.2 + - - -
213D THR* 1.3 73.2 - - - +
215D LYS* 1.3 68.8 + - - +
235D VAL* 3.3 7.3 - - - +
236D THR* 3.2 39.0 + - - +
288D TYR* 4.5 9.9 - - + -
289D LEU* 3.8 7.4 - - - -
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Residues in contact with LYS 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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990A LYS* 3.4 32.9 - - - +
991A ASP* 3.1 27.4 + - - +
1009A GLN* 3.5 29.6 - - + +
1010A PRO 5.0 1.4 + - - -
1012A SER* 6.2 1.0 - - - -
199D VAL* 3.3 3.8 - - - -
200D THR* 3.1 28.3 + - - -
213D THR* 3.6 3.2 - - - +
214D ASN* 1.3 90.0 + - - +
216D ILE* 1.3 72.0 + - - +
217D THR* 4.1 5.6 - - - +
233D GLN* 4.0 16.9 + - + +
234D ALA 3.3 7.4 - - - +
235D VAL* 3.9 20.9 - - + -
289D LEU* 3.8 1.7 - - - +
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Residues in contact with ILE 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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197D VAL* 4.9 1.6 - - + -
198D GLN 3.5 5.2 - - - +
199D VAL* 4.0 7.2 - - + -
213D THR* 3.8 15.5 - - + -
215D LYS* 1.3 81.4 - - - +
217D THR* 1.3 70.1 + - - +
218D ILE* 4.6 4.9 - - + -
232D TYR* 4.0 2.6 - - + +
233D GLN* 3.3 3.1 - - - -
234D ALA* 3.0 33.5 + - + +
282D VAL* 4.0 22.2 - - + -
289D LEU* 3.5 31.2 - - + -
290D THR 3.8 17.7 - - - +
291D LEU* 3.9 33.0 - - + -
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Residues in contact with THR 217 (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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1009A GLN* 2.7 27.5 + - - +
1010A PRO* 4.0 23.6 - - + -
1046A LEU* 4.1 9.2 - - + -
196D SER 4.5 0.4 - - - -
197D VAL* 3.3 5.2 - - - +
198D GLN* 2.8 35.3 + - - -
215D LYS* 4.1 0.5 - - - +
216D ILE* 1.3 75.4 - - - +
218D ILE* 1.3 71.3 + - - +
219D ILE* 4.6 3.1 - - + -
231D VAL* 4.2 12.3 - - + -
232D TYR 3.3 10.1 - - - +
233D GLN* 3.3 20.6 + - + +
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Residues in contact with ILE 218 (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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195D LEU* 3.9 13.7 - - + -
196D SER 3.3 9.4 - - - +
197D VAL* 4.2 17.5 - - + -
216D ILE* 4.6 5.2 - - + -
217D THR* 1.3 78.8 - - - +
219D ILE* 1.3 66.4 + - - +
220D PHE* 3.4 31.0 - - + -
231D VAL* 3.3 8.0 - - - +
232D TYR* 2.8 47.0 + - + +
271D MET* 3.6 33.4 - - + -
280D VAL* 3.8 19.7 - - + -
282D VAL* 4.3 7.9 - - + -
291D LEU* 5.0 0.2 - - + -
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Residues in contact with ILE 219 (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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1010A PRO* 5.6 2.5 - - + -
1021A TYR* 6.1 0.4 - - - +
1043A GLY 4.8 3.4 - - - +
1044A ASN* 4.1 29.6 - - + +
1046A LEU* 3.8 28.7 - - + -
195D LEU* 3.5 5.5 - - - +
196D SER* 2.9 44.9 + - - +
217D THR* 4.6 7.4 - - + -
218D ILE* 1.3 79.0 - - - +
220D PHE* 1.3 64.1 + - - +
221D LYS* 3.4 20.9 + - + +
229D GLN* 4.2 17.7 - - - +
230D LYS 3.6 9.0 - - - +
231D VAL* 4.2 12.6 - - + -
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Residues in contact with PHE 220 (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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195D LEU* 3.6 20.9 - - + -
218D ILE* 3.4 25.6 - - + -
219D ILE* 1.3 70.1 - - - +
221D LYS* 1.3 66.0 + - - +
227D THR* 5.4 0.7 - - + -
228D ASP 4.3 0.9 - - - +
229D GLN* 3.4 4.7 - - - +
230D LYS 3.0 35.4 + - - +
232D TYR* 4.9 1.1 - - + -
243D PHE* 4.1 13.7 - + - -
258D LEU* 3.8 40.8 - - + -
271D MET* 3.7 39.9 - - + -
273D ALA* 3.9 16.2 - - + -
275D TYR* 3.5 17.3 - - - +
276D ILE* 4.6 1.1 - - + -
278D THR* 5.7 0.7 - - + -
280D VAL* 4.4 12.3 - - + -
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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