Contacts of the helix formed by residues 321 - 335 (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 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ALA* 3.5 16.6 - - + +
154D ARG* 3.0 31.0 + - - -
186D GLY* 3.4 23.7 + - - -
187D ALA* 3.0 22.8 + - + +
214D GLU* 4.3 0.3 - - - +
218D THR* 3.8 8.7 - - - +
301D VAL* 4.9 0.4 - - - -
303D PRO* 5.0 0.2 - - - -
320D ALA* 1.3 71.4 - - - +
322D VAL* 1.3 61.8 + - - +
323D GLY* 3.1 8.3 + - - -
324D GLY 2.8 22.6 + - - +
325D THR* 2.8 31.1 + - - -
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Residues in contact with VAL 322 (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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214D GLU* 3.7 21.9 - - + +
215D ALA* 3.7 27.6 - - + +
276D LEU* 3.8 26.2 - - + +
277D GLY* 3.5 31.2 - - - +
301D VAL* 4.0 12.3 - - + +
303D PRO* 4.4 10.4 - - + +
321D ASP* 1.3 77.3 + - - +
323D GLY* 1.3 58.5 + - - +
325D THR* 3.2 6.9 + - - -
326D ILE* 2.9 34.0 + - + +
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Residues in contact with GLY 323 (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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214D GLU 4.8 0.2 + - - -
218D THR* 3.2 26.6 + - - -
220D ARG* 3.7 19.0 - - - +
321D ASP* 3.1 8.4 + - - -
322D VAL* 1.3 75.8 - - - +
324D GLY* 1.3 64.8 + - - +
326D ILE* 3.2 7.7 + - - +
327D GLU* 3.0 27.6 + - - +
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Residues in contact with GLY 324 (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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190A ASP* 5.6 1.8 - - - -
185D HIS* 6.4 0.2 - - - -
186D GLY* 3.7 25.8 - - - +
187D ALA 4.0 3.1 - - - -
188D ARG* 3.8 13.1 + - - +
321D ASP* 2.8 18.2 + - - -
323D GLY* 1.3 71.6 - - - +
325D THR* 1.3 56.8 + - - +
327D GLU* 3.3 9.9 + - - +
328D ALA* 3.0 27.5 + - - +
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Residues in contact with THR 325 (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 ALA 4.4 0.2 + - - -
189D PRO* 3.4 38.6 - - + +
194D LEU* 4.6 2.0 - - + -
276D LEU* 4.3 4.9 - - + -
301D VAL* 3.4 33.8 - - + +
320D ALA* 3.6 2.8 - - - +
321D ASP 2.8 21.3 + - - -
322D VAL* 3.5 5.4 - - - -
323D GLY 3.2 0.2 - - - -
324D GLY* 1.3 73.3 - - - +
326D ILE* 1.3 59.7 + - - +
328D ALA* 3.2 1.7 + - - +
329D LEU* 2.8 47.7 + - + +
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Residues in contact with ILE 326 (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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211D LEU* 4.7 1.8 - - + -
215D ALA* 4.4 15.0 - - + +
218D THR* 5.7 0.2 - - - +
220D ARG* 3.8 16.2 - - + +
223D ALA* 3.9 3.8 - - + +
224D LEU* 3.5 51.1 - - + +
227D PHE* 4.9 3.6 - - + +
244D MET* 5.1 5.6 - - + -
276D LEU* 4.1 23.6 - - + -
322D VAL* 2.9 34.2 + - + +
323D GLY* 3.2 11.0 + - - +
325D THR* 1.3 74.5 - - - +
327D GLU* 1.3 58.1 + - - +
329D LEU* 3.3 8.9 + - + +
330D ALA* 3.0 27.5 + - - +
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Residues in contact with GLU 327 (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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190A ASP* 5.0 4.9 - - - +
188D ARG* 3.6 16.6 - - - +
220D ARG* 2.8 44.7 + - - -
223D ALA* 3.3 24.4 + - - +
323D GLY 3.0 18.5 + - - +
324D GLY* 3.5 10.3 - - - +
326D ILE* 1.3 75.2 - - - +
328D ALA* 1.3 57.2 + - - +
330D ALA* 3.3 3.3 + - - +
331D GLN* 2.9 30.0 + - - +
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Residues in contact with ALA 328 (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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188D ARG* 3.9 37.0 - - + +
189D PRO* 4.3 1.3 - - + +
194D LEU* 3.5 24.3 - - + +
324D GLY 3.0 13.7 + - - +
325D THR* 3.5 9.0 - - - +
327D GLU* 1.3 75.5 - - - +
329D LEU* 1.3 58.3 + - - +
331D GLN* 3.3 3.5 + - - +
332D ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 329 (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* 3.7 24.2 - - + +
197D ALA* 5.2 7.6 - - + -
198D LEU* 3.7 28.5 - - + -
201D LEU* 5.9 0.2 - - + -
227D PHE* 3.8 34.3 - - + -
274D LEU* 4.3 17.5 - - + -
276D LEU* 4.6 9.2 - - + -
325D THR* 2.8 35.9 + - + +
326D ILE* 3.7 9.0 - - - +
328D ALA* 1.3 77.2 - - - +
330D ALA* 1.3 55.6 + - - +
332D ALA* 3.5 2.3 + - - +
333D THR* 2.9 35.0 + - - +
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Residues in contact with ALA 330 (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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223D ALA* 3.2 37.7 - - + +
226D ALA* 4.3 9.1 - - + +
227D PHE* 4.1 10.0 - - + +
326D ILE 3.0 14.8 + - - +
327D GLU* 3.7 4.5 - - - +
329D LEU* 1.3 75.4 - - - +
331D GLN* 1.3 64.7 + - - +
333D THR* 3.4 6.8 + - - -
334D ALA* 3.1 25.3 + - - +
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Residues in contact with GLN 331 (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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191A PRO* 6.4 0.9 - - + -
188D ARG* 4.7 11.7 - - - +
327D GLU 2.9 18.7 + - - +
328D ALA* 3.6 8.3 - - - +
330D ALA* 1.3 78.5 - - - +
332D ALA* 1.3 63.3 + - - +
334D ALA* 3.4 12.3 + - - +
335D GLN* 3.5 19.2 - - + +
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Residues in contact with ALA 332 (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* 3.8 9.2 - - + -
195D ASP* 6.0 1.6 - - - +
198D LEU* 3.5 29.8 - - + -
328D ALA 2.9 17.5 + - - +
329D LEU 3.8 2.0 - - - +
331D GLN* 1.3 79.5 - - - +
333D THR* 1.3 56.5 + - - +
335D GLN* 3.2 25.1 + - - +
336D ASP* 3.6 12.4 - - - +
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Residues in contact with THR 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 3.8 11.0 - - + -
226D ALA 4.7 0.3 + - - -
227D PHE* 3.7 17.1 - - + -
230D ALA* 3.9 29.1 - - - +
231D THR* 3.8 12.8 - - + -
329D LEU 2.9 20.7 + - - +
330D ALA* 3.4 8.8 + - - -
332D ALA* 1.3 73.7 - - - +
334D ALA* 1.3 62.0 + - - +
335D GLN 3.2 0.2 - - - -
336D ASP* 3.4 25.7 + - - +
339D TRP* 3.7 30.6 - - + -
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Residues in contact with ALA 334 (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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226D ALA* 6.4 0.9 - - + -
230D ALA* 5.8 0.7 - - - -
330D ALA 3.1 19.3 + - - +
331D GLN* 3.6 9.0 - - - +
332D ALA 3.2 0.2 - - - -
333D THR* 1.3 76.5 + - - +
335D GLN* 1.3 63.4 + - + +
336D ASP 3.2 6.7 + - - +
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Residues in contact with GLN 335 (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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331D GLN* 3.5 20.6 - - + +
332D ALA* 3.2 10.8 + - - +
334D ALA* 1.3 80.3 - - - +
336D ASP* 1.3 63.1 + - - +
337D ALA 3.8 1.2 + - - -
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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