Contacts of the helix formed by residues 220 - 234 (chain D) in PDB entry 3OLJ
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 220 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D GLU 4.2 7.2 - - - +
219D ALA* 1.3 77.2 - - - +
221D TYR* 1.3 65.4 + - - +
222D GLY* 3.5 5.4 + - - -
223D GLU* 3.0 32.8 + - - +
224D ARG* 2.9 22.2 + - - +
282D HIS 5.5 2.7 + - - -
284D PRO* 5.1 3.3 - - - +
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Residues in contact with TYR 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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72D LEU* 4.3 11.0 - - + -
73D LEU* 4.0 28.0 - - + +
149D PHE* 3.6 37.9 - + - -
152D GLU* 3.8 17.7 - - + +
153D VAL* 3.6 25.6 - - + +
162D TYR* 2.7 22.1 + - - -
220D THR* 1.3 73.4 - - - +
222D GLY* 1.3 54.3 + - - +
224D ARG* 3.3 15.5 - - - +
225D VAL* 2.8 44.8 + - + +
276D MET* 3.5 20.1 - - + +
280D LEU* 3.9 27.4 - - + -
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Residues in contact with GLY 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D THR* 3.1 7.1 + - - -
221D TYR* 1.3 80.4 - - - +
223D GLU* 1.3 59.0 + - - +
225D VAL* 3.5 4.5 - - - +
226D VAL* 3.4 25.5 + - - +
277D PHE* 3.8 2.4 - - - -
280D LEU* 3.4 28.6 - - - +
282D HIS 5.4 1.8 - - - -
284D PRO* 4.0 15.7 - - - -
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Residues in contact with GLU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TRP* 4.3 13.6 - - + -
218D GLU 4.9 0.2 - - - +
219D ALA* 3.6 9.5 - - + -
220D THR* 3.0 39.2 + - - +
222D GLY* 1.3 75.1 - - - +
224D ARG* 1.3 59.8 + - - +
226D VAL* 3.3 7.3 + - - +
227D ALA* 3.1 25.8 + - - +
284D PRO* 3.9 23.8 - - + -
288D ARG* 2.6 41.7 + - + +
292D ILE* 4.3 10.9 - - + +
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Residues in contact with ARG 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ASN* 4.8 1.2 + - - +
148D ARG* 3.2 53.6 - - - +
149D PHE* 3.5 22.9 - - + -
152D GLU* 2.3 47.1 + - - -
213D TRP* 3.8 23.5 + - + +
216D ASP 4.3 0.9 - - - -
219D ALA* 3.2 38.2 + - + -
220D THR* 2.9 9.7 + - - +
221D TYR* 3.3 25.1 - - - +
223D GLU* 1.3 73.3 - - - +
225D VAL* 1.3 60.8 + - - +
227D ALA* 3.3 6.5 + - - +
228D PHE* 3.0 30.7 + - + -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D PHE* 3.6 15.4 - - + -
162D TYR* 4.0 9.9 - - - +
221D TYR* 2.8 45.8 + - + +
222D GLY* 3.5 15.5 - - - +
224D ARG* 1.3 76.9 - - - +
226D VAL* 1.3 64.0 + - - +
228D PHE* 4.0 0.7 - - - +
229D ALA* 3.1 22.5 + - - +
273D ALA* 4.0 31.6 - - + +
276D MET* 4.5 2.0 - - + -
277D PHE* 4.1 22.2 - - + -
280D LEU* 5.0 0.2 - - + -
335D LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 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 GLY 3.4 13.4 + - - +
223D GLU* 3.3 10.4 + - - +
224D ARG 3.2 0.4 - - - -
225D VAL* 1.3 79.7 - - + +
227D ALA* 1.3 64.6 + - - +
229D ALA* 3.2 8.7 + - - +
230D ALA* 3.0 21.3 + - - +
277D PHE* 3.5 28.3 - - + -
284D PRO* 4.9 0.4 - - + -
289D VAL* 4.2 21.5 - - + -
292D ILE* 4.1 18.2 - - + -
293D ILE* 4.0 23.0 - - + +
335D LEU* 4.0 19.3 - - + -
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Residues in contact with ALA 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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209D TRP* 3.5 11.2 - - + -
213D TRP* 3.5 51.8 - - + +
223D GLU 3.1 11.6 + - - +
224D ARG 3.3 8.5 + - - +
226D VAL* 1.3 77.4 - - - +
228D PHE* 1.3 57.6 + - + +
230D ALA* 3.1 6.5 + - - +
231D VAL* 2.9 29.1 + - - +
292D ILE* 4.2 4.7 - - + -
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Residues in contact with PHE 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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140D ILE* 4.2 3.4 - - + -
141D VAL* 4.2 28.0 - - + -
144D ASN* 3.3 49.4 - - + -
149D PHE* 4.1 14.6 - + + -
210D ALA* 3.6 26.0 - - + -
213D TRP* 3.9 22.9 - + + -
214D ILE* 3.7 9.0 - - + -
224D ARG* 3.0 21.6 + - + +
225D VAL 4.4 0.7 - - - +
227D ALA* 1.3 74.7 - - - +
229D ALA* 1.3 60.8 + - - +
230D ALA 3.2 1.1 - - - -
231D VAL* 3.3 21.3 + - + +
232D GLU* 2.9 40.6 + - - +
273D ALA* 5.6 0.7 - - - -
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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 VAL 3.1 15.4 + - - +
226D VAL* 3.2 11.6 + - - +
228D PHE* 1.3 77.2 - - - +
230D ALA* 1.3 53.2 + - - +
232D GLU* 5.0 0.9 - - - -
233D GLY* 2.7 32.9 + - - -
270D CYS* 3.5 13.5 - - - +
273D ALA* 3.8 21.4 - - + +
274D CYS* 5.3 1.6 - - - -
331D LEU* 4.0 26.3 - - + +
335D LEU* 5.6 3.8 - - + -
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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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209D TRP* 4.2 7.6 - - + -
226D VAL 3.0 13.4 + - - +
227D ALA* 3.1 11.9 + - - +
229D ALA* 1.3 75.4 - - - +
231D VAL* 1.3 59.0 + - - +
234D ILE* 2.7 36.1 + - + +
235D PHE* 2.9 12.1 + - - +
293D ILE* 3.9 19.7 - - + -
296D ALA* 4.0 21.1 - - + -
331D LEU* 4.2 3.1 - - - +
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Residues in contact with VAL 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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137D SER* 5.3 4.5 - - - +
140D ILE* 6.3 0.4 - - + -
141D VAL* 3.9 24.5 - - + -
209D TRP* 4.0 9.4 - - + -
210D ALA* 3.8 30.3 - - + -
227D ALA* 2.9 19.7 + - + +
228D PHE* 3.6 20.2 - - + +
230D ALA* 1.3 76.7 - - - +
232D GLU* 1.3 63.2 + - - +
233D GLY 3.3 0.2 + - - -
235D PHE* 3.1 44.4 + - + +
236D PHE* 3.4 19.3 + - + -
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Residues in contact with GLU 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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141D VAL* 3.8 28.0 - - + +
145D LEU* 5.8 0.3 - - - +
165D GLN* 3.0 33.1 + - - -
169D GLU* 3.2 7.8 - - - +
228D PHE* 2.9 25.1 + - - +
229D ALA* 5.6 0.3 - - - -
231D VAL* 1.3 74.1 - - - +
233D GLY* 1.3 57.3 + - - +
236D PHE* 3.6 26.1 - - + +
240D PHE* 4.4 2.6 - - - -
266D GLU* 2.4 37.6 - - - +
269D HIS* 3.2 16.1 + - - +
270D CYS* 3.5 17.3 - - - -
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Residues in contact with GLY 233 (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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229D ALA 2.7 17.9 + - - -
232D GLU* 1.3 79.2 - - - +
234D ILE* 1.3 62.6 + - - +
237D SER* 3.4 12.7 + - - -
270D CYS* 3.3 11.9 - - - -
327D VAL* 3.2 22.9 - - - +
331D LEU* 5.5 3.1 - - - -
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Residues in contact with ILE 234 (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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230D ALA* 2.7 23.6 + - + +
233D GLY* 1.3 76.3 - - - +
235D PHE* 1.3 64.2 + - - +
236D PHE 3.1 1.8 - - - -
237D SER* 2.7 22.3 + - - -
293D ILE* 3.8 45.1 - - + +
296D ALA* 4.0 9.9 - - + +
297D VAL* 4.0 21.3 - - + +
300D GLU* 3.4 9.6 - - + +
324D ILE* 3.8 24.2 - - + -
327D VAL* 4.4 4.9 - - + -
328D ALA* 3.9 21.1 - - + -
331D LEU* 4.2 9.6 - - + -
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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