Contacts of the helix formed by residues 190 - 204 (chain D) in PDB entry 2UZ1
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 ASP 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A HIS* 3.2 44.0 + - + +
186A GLY 4.3 11.7 + - - +
187A ALA* 4.9 0.4 - - - +
188A ARG* 3.3 24.7 + - - +
324A GLY* 5.9 0.7 - - - -
327A GLU* 5.3 3.1 - - - +
188D ARG 3.6 1.4 + - - -
189D PRO* 1.3 74.3 - - - +
191D PRO* 1.4 75.7 - - - +
192D ALA* 2.8 36.6 + - - +
193D ASP* 3.0 20.2 + - - +
194D LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 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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188A ARG* 3.4 39.9 - - - +
331A GLN* 4.8 12.3 - - - +
189D PRO 3.5 2.0 - - - +
190D ASP* 1.4 89.7 - - - +
192D ALA* 1.3 55.6 + - - +
194D LEU* 3.3 8.4 + - + +
195D ASP* 2.8 42.1 + - - +
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Residues in contact with ALA 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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185A HIS* 4.2 17.3 - - + +
190D ASP* 2.8 15.5 + - - +
191D PRO* 1.3 80.2 - - - +
193D ASP* 1.3 59.6 + - - +
195D ASP* 3.7 7.5 - - - +
196D GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 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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183A SER* 2.5 37.9 + - - -
185A HIS* 3.4 24.2 - - - +
189D PRO* 4.4 4.3 - - + -
190D ASP* 3.0 13.5 + - - +
192D ALA* 1.3 75.8 - - - +
194D LEU* 1.3 59.9 + - - +
196D GLN* 3.3 8.3 + - - -
197D ALA* 2.9 29.1 + - - +
316D LEU* 3.6 19.3 - - - +
318D ILE* 3.9 26.8 - - + +
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Residues in contact with LEU 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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189D PRO* 3.8 29.3 - - + +
190D ASP 3.0 12.7 + - - +
191D PRO* 3.7 11.2 - - + +
193D ASP* 1.3 73.2 - - - +
195D ASP* 1.3 63.6 + - - +
197D ALA* 3.3 5.8 + - + +
198D LEU* 2.9 41.5 + - + +
318D ILE* 5.4 1.8 - - + -
325D THR* 4.5 2.2 - - + +
328D ALA* 3.5 38.1 - - + +
329D LEU* 3.7 25.6 - - + +
332D ALA* 3.8 19.1 - - + -
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Residues in contact with ASP 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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191D PRO* 2.8 27.9 + - - +
192D ALA* 3.7 7.7 - - - +
194D LEU* 1.3 77.2 - - - +
196D GLN* 1.3 58.5 + - - +
198D LEU* 3.4 10.6 + - - +
199D ALA* 2.9 30.5 + - - +
332D ALA* 6.0 1.0 - - - +
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Residues in contact with GLN 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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192D ALA 3.0 17.3 + - - +
193D ASP* 3.7 10.5 + - - +
195D ASP* 1.3 77.9 - - - +
197D ALA* 1.3 62.1 + - - +
199D ALA* 3.5 6.8 + - + +
200D LEU* 3.1 34.3 + - + +
315D ALA 4.7 8.5 - - - +
316D LEU* 3.7 30.2 - - + +
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Residues in contact with ALA 197 (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 ASP 2.9 16.7 + - - +
194D LEU* 3.3 7.4 + - + +
196D GLN* 1.3 74.4 - - - +
198D LEU* 1.3 60.4 + - + +
200D LEU* 3.3 4.6 + - - +
201D LEU* 2.9 28.2 + - - +
274D LEU* 5.2 5.4 - - + -
299D ILE* 3.6 30.9 - - + +
316D LEU* 3.6 14.3 - - + +
318D ILE* 4.7 4.3 - - + -
329D LEU* 5.2 8.5 - - + -
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Residues in contact with LEU 198 (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 LEU* 2.9 32.1 + - + +
195D ASP* 3.8 8.7 - - - +
197D ALA* 1.3 76.2 - - - +
199D ALA* 1.3 60.1 + - - +
201D LEU* 4.1 6.5 - - + -
202D ARG* 2.9 31.0 + - - +
227D PHE* 4.0 7.4 - - + -
329D LEU* 3.7 22.2 - - + -
332D ALA* 3.5 31.9 - - + -
333D THR* 3.8 24.5 - - + -
336D ASP* 5.5 1.8 - - - +
339D TRP* 3.4 21.2 - - + -
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Residues in contact with ALA 199 (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 ASP 2.9 17.2 + - - +
196D GLN* 3.7 7.9 - - + +
198D LEU* 1.3 77.0 - - - +
200D LEU* 1.3 62.5 + - + +
202D ARG* 3.3 8.8 + - - +
203D LYS* 3.1 24.8 + - - +
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Residues in contact with LEU 200 (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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196D GLN* 3.1 35.2 + - + +
197D ALA* 3.5 6.5 - - - +
199D ALA* 1.3 76.3 - - + +
201D LEU* 1.3 63.4 + - - +
203D LYS* 3.3 5.9 + - + +
204D ALA* 3.1 24.9 + - - +
272D LEU* 4.1 13.3 - - + +
297D GLN* 3.5 30.7 - - - +
299D ILE* 3.9 27.8 - - + -
315D ALA* 4.8 15.5 - - + -
316D LEU* 4.7 4.3 - - + -
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Residues in contact with LEU 201 (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 2.9 17.2 + - - +
198D LEU* 3.6 11.0 - - + +
200D LEU* 1.3 76.7 - - - +
202D ARG* 1.3 57.9 - - - +
204D ALA* 3.7 6.6 + - - +
207D PRO* 3.9 16.9 - - + +
208D VAL 5.4 0.7 - - - +
209D ILE* 5.1 0.9 - - + -
227D PHE* 3.6 35.4 - - + -
231D THR* 4.3 1.8 - - + -
233D VAL* 3.9 24.2 - - + -
272D LEU* 3.8 26.4 - - + +
274D LEU* 4.9 15.9 - - + -
299D ILE* 5.5 1.1 - - + -
339D TRP* 3.9 19.6 - - + -
342D ARG* 2.9 22.0 + - - -
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Residues in contact with ARG 202 (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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198D LEU 2.9 17.0 + - - +
199D ALA* 3.6 8.3 - - - +
200D LEU 3.2 0.2 - - - -
201D LEU* 1.3 77.4 - - - +
203D LYS* 1.3 57.7 + - - +
204D ALA 4.0 0.5 - - - +
336D ASP* 3.8 12.9 + - - +
338D ALA 2.9 29.9 + - - -
339D TRP* 3.3 42.2 - - + +
340D PRO* 3.4 29.2 - - + +
342D ARG* 3.0 18.7 + - - +
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Residues in contact with LYS 203 (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 ALA 3.1 16.8 + - - +
200D LEU* 3.3 7.2 + - + +
202D ARG* 1.3 74.3 - - - +
204D ALA* 1.3 64.9 + - - +
205D GLU* 3.7 5.9 + - - +
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Residues in contact with ALA 204 (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 LEU 3.1 12.7 + - - +
201D LEU 3.9 2.5 - - - +
202D ARG 3.4 1.3 - - - +
203D LYS* 1.3 80.4 - - - +
205D GLU* 1.3 55.8 + - - +
207D PRO* 3.8 16.8 - - + -
271D ASP* 3.6 12.6 - - - +
272D LEU* 3.6 31.0 - - + -
342D ARG* 2.8 30.3 + - - -
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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