Contacts of the helix formed by residues 220 - 232 (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 ARG 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D ALA 4.3 0.8 + - - -
218D THR* 3.6 19.1 + - - +
219D ALA* 1.3 79.0 + - - +
221D LYS* 1.3 56.8 + - - +
222D THR* 3.4 4.9 - - - -
223D ALA 3.5 2.8 + - - +
224D LEU* 2.9 27.9 + - - +
244D MET* 3.8 8.3 - - - +
323D GLY* 3.7 30.7 - - - +
326D ILE* 3.8 18.0 - - + +
327D GLU* 2.8 49.1 + - - +
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Residues in contact with LYS 221 (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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219D ALA* 3.1 18.1 + - + +
220D ARG* 1.3 72.6 - - - +
222D THR* 1.3 62.3 + - - +
224D LEU* 3.6 6.9 - - - +
225D SER* 2.8 33.4 + - - -
243D SER* 4.0 22.5 + - - +
244D MET* 3.7 39.5 - - + +
246D SER* 6.0 1.4 - - - -
247D GLY* 5.8 7.6 - - - +
248D LEU* 5.4 0.5 - - - +
410D GLY* 4.6 11.9 + - - -
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Residues in contact with THR 222 (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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220D ARG* 3.4 2.2 - - - -
221D LYS* 1.3 79.2 - - - +
223D ALA* 1.3 61.2 + - - +
225D SER* 3.5 5.6 + - - -
226D ALA* 3.2 22.2 + - + +
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Residues in contact with ALA 223 (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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220D ARG* 3.5 4.7 + - - +
221D LYS 3.3 0.2 - - - -
222D THR* 1.3 76.2 - - - +
224D LEU* 1.3 64.9 + - - +
226D ALA* 3.2 3.1 + - - -
227D PHE* 3.0 20.4 + - - +
326D ILE* 3.9 14.8 - - + -
327D GLU* 3.3 39.9 + - - +
330D ALA* 3.2 24.1 - - + +
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Residues in contact with LEU 224 (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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209D ILE* 5.5 2.0 - - + -
211D LEU* 3.7 31.6 - - + -
220D ARG 2.9 19.6 + - - +
221D LYS* 3.6 6.7 - - - +
223D ALA* 1.3 75.4 - - - +
225D SER* 1.3 58.0 + - - +
227D PHE* 3.3 12.1 + - + +
228D VAL* 2.8 50.2 + - + +
235D VAL* 5.0 3.4 - - + -
244D MET* 3.5 35.9 - - + +
248D LEU* 4.2 14.8 - - + -
276D LEU* 5.3 3.1 - - + -
326D ILE* 3.5 27.1 - - + +
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Residues in contact with SER 225 (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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221D LYS 2.8 21.7 + - - -
222D THR* 3.7 6.5 - - - -
224D LEU* 1.3 73.7 - - - +
226D ALA* 1.3 57.4 + - - +
228D VAL* 3.8 0.7 - - - +
229D ALA* 2.8 33.5 + - - +
247D GLY* 3.5 22.7 + - - -
248D LEU* 3.6 18.1 - - - +
249D PRO* 5.0 4.7 - - - +
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Residues in contact with ALA 226 (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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222D THR 3.2 13.8 + - - +
223D ALA* 3.2 8.5 + - - +
225D SER* 1.3 75.3 - - - +
227D PHE* 1.3 59.2 + - - +
229D ALA* 3.4 5.3 + - - +
230D ALA* 2.9 31.1 + - - +
330D ALA* 4.3 13.7 - - + +
333D THR* 5.0 1.1 - - - -
334D ALA* 6.4 0.9 - - + -
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Residues in contact with PHE 227 (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* 4.0 3.8 - - + -
201D LEU* 3.6 26.5 - - + -
209D ILE* 3.6 28.3 - - + -
223D ALA 3.0 16.0 + - - +
224D LEU* 3.5 14.6 - - + +
226D ALA* 1.3 77.4 - - - +
228D VAL* 1.3 65.8 + - + +
230D ALA* 3.3 1.2 + - - +
231D THR* 3.0 48.0 + - + +
274D LEU* 4.3 6.7 - - + -
276D LEU* 5.3 3.4 - - + -
326D ILE* 4.9 3.6 - - + +
329D LEU* 3.8 44.6 - - + -
330D ALA* 4.1 10.0 - - - +
333D THR* 3.7 28.0 - - + -
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Residues in contact with VAL 228 (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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209D ILE* 4.6 2.9 - - + -
224D LEU* 2.8 39.4 + - + +
225D SER 4.0 2.5 - - - +
227D PHE* 1.3 80.1 - - + +
229D ALA* 1.3 58.7 + - - +
231D THR* 4.0 4.9 - - - -
232D GLY* 2.8 28.9 + - - -
233D VAL 3.9 6.5 - - - +
235D VAL* 3.4 26.2 - - + -
248D LEU* 4.1 15.0 - - + -
249D PRO* 4.7 2.9 - - + -
252D MET* 3.4 39.1 - - + +
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Residues in contact with ALA 229 (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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225D SER 2.8 19.5 + - - +
226D ALA* 3.8 6.1 - - - +
228D VAL* 1.3 79.4 - - - +
230D ALA* 1.3 60.8 + - - +
232D GLY* 4.1 4.0 + - - -
249D PRO* 5.3 8.2 - - + +
252D MET* 4.4 12.7 - - + +
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Residues in contact with ALA 230 (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 2.9 18.3 + - - +
227D PHE 3.8 3.8 - - - +
228D VAL 3.3 0.2 - - - -
229D ALA* 1.3 79.0 - - - +
231D THR* 1.3 60.5 + - - +
333D THR* 3.9 34.5 - - - +
334D ALA* 5.8 0.9 - - - -
339D TRP* 3.2 24.0 + - + +
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Residues in contact with THR 231 (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 LEU* 4.3 0.9 - - + -
209D ILE* 5.2 0.2 - - - +
227D PHE* 3.0 45.1 + - + +
228D VAL* 3.8 3.5 + - - -
230D ALA* 1.3 79.4 - - - +
232D GLY* 1.3 64.4 + - - +
233D VAL* 3.2 30.8 + - - +
333D THR* 3.8 12.1 - - + -
339D TRP* 3.7 37.3 - - + +
340D PRO 3.9 10.4 - - - +
342D ARG* 3.9 11.4 + - - -
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Residues in contact with GLY 232 (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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228D VAL 2.8 15.3 + - - -
229D ALA 4.1 2.8 + - - -
230D ALA 3.6 1.6 + - - -
231D THR* 1.3 76.3 - - - +
233D VAL* 1.3 58.7 + - - +
234D PRO* 3.6 0.2 - - - +
252D MET* 3.8 17.5 - - - -
340D PRO 5.6 0.2 - - - -
342D ARG* 3.5 16.5 - - - +
346D CYS* 3.2 26.5 - - - -
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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