Contacts of the strand formed by residues 189 - 196 (chain D) in PDB entry 3U1K
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 GLY 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D ASN* 3.5 6.5 - - - -
188D VAL* 1.3 76.2 - - - +
190D ALA* 1.3 62.0 + - - -
219D ALA* 3.3 2.3 - - - -
220D GLY 2.7 33.8 + - - -
252D THR* 3.3 21.3 - - - +
255D ILE* 3.9 14.1 - - - -
256D ILE* 3.6 4.3 - - - +
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Residues in contact with ALA 190 (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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167D VAL* 3.4 5.4 - - + +
170D ILE* 3.6 43.3 - - + -
171D ASN* 2.8 30.7 + - - +
188D VAL* 5.0 0.2 - - + -
189D GLY* 1.3 74.6 - - - +
191D VAL* 1.3 70.3 + - - +
203D ASN* 5.3 0.3 + - - -
217D VAL* 5.0 0.7 - - + -
218D VAL 3.1 12.8 - - - +
219D ALA* 4.2 5.8 - - + -
252D THR* 3.9 1.1 - - - -
255D ILE* 3.2 5.7 - - - +
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Residues in contact with VAL 191 (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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51D LEU* 4.3 5.8 - - + -
167D VAL* 3.8 8.1 - - - -
190D ALA* 1.3 81.7 - - - +
192D ARG* 1.3 66.3 + - - +
193D ILE* 4.0 17.5 - - + -
202D VAL* 3.9 10.8 - - + -
203D ASN* 3.5 13.9 - - - +
216D LEU 3.8 0.2 - - - +
217D VAL* 3.4 2.6 - - - +
218D VAL* 2.9 33.0 + - + +
248D GLY* 3.9 22.9 - - - +
251D TYR* 3.9 22.4 - - + -
252D THR* 4.2 3.6 - - + +
255D ILE* 3.6 17.3 - - + -
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Residues in contact with ARG 192 (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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126D LYS* 5.7 0.2 - - - +
133D ILE* 5.8 3.2 - - - +
164D GLU* 3.7 22.6 + - - +
166D ASP* 2.9 42.8 + - - -
167D VAL* 3.9 15.3 - - + +
191D VAL* 1.3 73.8 - - - +
193D ILE* 1.3 72.5 + - - +
202D VAL* 3.9 0.9 - - - +
203D ASN* 2.7 38.6 + - - +
204D PRO* 3.8 22.6 + - + -
209D MET* 3.8 27.6 - - - +
215D ASN* 2.9 31.1 + - - +
216D LEU 3.2 11.0 - - - +
217D VAL* 3.8 20.2 - - + +
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Residues in contact with ILE 193 (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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191D VAL* 4.0 7.6 - - + -
192D ARG* 1.3 88.4 - - - +
194D GLY* 1.3 72.7 + - - +
200D TYR* 4.5 4.9 - - + -
201D VAL 3.3 6.1 - - - +
202D VAL* 3.7 28.3 - - + -
214D LEU* 3.7 4.2 - - + +
216D LEU* 2.8 45.1 + - + +
218D VAL* 5.1 1.6 - - + -
244D ALA* 3.8 32.5 - - + +
247D VAL* 4.3 11.0 - - + -
248D GLY* 3.7 28.3 - - - +
251D TYR* 4.4 5.8 - - + -
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Residues in contact with GLY 194 (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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193D ILE* 1.3 78.1 - - - +
195D ILE* 1.3 69.4 + - - +
196D ILE* 4.2 1.1 - - - -
200D TYR* 3.6 0.5 - - - -
201D VAL* 2.9 37.0 + - - -
204D PRO* 4.1 13.2 - - - +
212D SER* 3.4 6.5 - - - -
214D LEU* 3.4 15.9 - - - -
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Residues in contact with ILE 195 (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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194D GLY* 1.3 77.6 - - - +
196D ILE* 1.3 63.0 + - - +
197D ASP 4.3 0.5 + - - -
198D GLY* 3.8 31.6 - - - +
199D GLU 3.5 4.0 - - - +
200D TYR* 3.5 36.1 - - + +
211D SER 4.1 0.7 - - - +
212D SER* 2.8 11.7 + - - -
213D THR* 2.9 55.1 + - + -
214D LEU* 3.9 22.8 + - + -
236D ILE* 4.3 8.1 - - + -
240D ASP* 4.1 13.9 - - + +
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Residues in contact with ILE 196 (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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194D GLY 4.2 0.4 - - - -
195D ILE* 1.3 77.5 - - - +
197D ASP* 1.3 75.7 + - + +
198D GLY 3.0 0.4 - - - -
199D GLU* 2.9 30.1 + - + +
201D VAL* 4.4 20.0 - - + -
204D PRO* 5.4 1.1 - - + -
208D GLU* 3.1 55.6 - - + +
211D SER* 3.7 24.2 - - - +
212D SER* 4.1 4.7 - - - -
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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