Contacts of the helix formed by residues 220 - 234 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B GLU 4.3 5.4 - - - +
219B ALA* 1.3 76.3 - - - +
221B TYR* 1.3 64.5 + - - +
222B GLY* 3.3 7.1 + - - -
223B GLU* 3.1 33.9 + - - +
224B ARG* 3.0 23.6 + - - +
282B HIS 5.7 2.3 + - - -
284B PRO* 4.9 2.8 - - - +
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 4.5 5.8 - - + -
73B LEU* 4.0 26.9 - - + +
149B PHE* 3.7 25.1 - + - -
152B GLU* 3.9 27.8 - - + +
153B VAL* 3.6 27.3 - - + +
162B TYR* 2.7 22.4 + - - -
220B THR* 1.3 72.9 - - - +
222B GLY* 1.3 52.7 + - - +
224B ARG* 3.4 11.2 - - - +
225B VAL* 2.5 63.2 + - + +
276B MET* 3.4 26.6 - - + +
280B LEU* 3.9 27.8 - - + -
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Residues in contact with GLY 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B THR* 3.1 9.0 + - - -
221B TYR* 1.3 81.6 - - - +
223B GLU* 1.3 59.5 + - - +
225B VAL* 4.0 1.1 - - - +
226B VAL* 3.3 25.1 + - - +
277B PHE* 3.7 5.1 - - - -
280B LEU* 3.5 28.0 - - - +
282B HIS 5.3 2.5 - - - -
284B PRO* 3.9 15.3 - - - -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TRP* 4.2 14.5 - - + -
219B ALA* 3.4 11.1 - - + +
220B THR* 3.1 37.8 + - - +
222B GLY* 1.3 72.5 - - - +
224B ARG* 1.3 60.7 + - - +
226B VAL* 3.3 5.8 + - - +
227B ALA* 2.9 26.5 + - - +
284B PRO* 3.9 21.8 - - + -
288B ARG* 2.8 40.7 + - + +
292B ILE* 4.1 11.4 - - + +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 5.3 0.8 + - - +
148B ARG* 3.4 47.4 - - - +
149B PHE* 3.6 30.1 - - + -
152B GLU* 2.3 47.8 + - - -
213B TRP* 3.8 23.5 + - + +
216B ASP 4.3 0.9 - - - -
219B ALA* 3.2 39.6 + - + -
220B THR 3.0 10.5 + - - +
221B TYR* 3.4 21.2 - - - +
223B GLU* 1.3 72.7 - - - +
225B VAL* 1.3 59.9 + - - +
227B ALA* 3.2 8.2 + - - +
228B PHE* 2.9 31.0 + - + -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.7 13.9 - - + -
162B TYR* 4.6 2.0 - - - +
221B TYR* 2.5 72.0 - - + +
222B GLY* 4.0 6.1 - - - +
224B ARG* 1.3 72.1 - - - +
226B VAL* 1.3 62.1 + - + +
228B PHE* 3.9 0.9 - - - +
229B ALA* 3.0 27.0 + - - +
273B ALA* 3.6 37.9 - - + +
276B MET* 4.5 2.9 - - + -
277B PHE* 5.0 5.6 - - + +
280B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B GLY 3.3 15.8 + - - +
223B GLU* 3.3 9.2 + - - +
224B ARG 3.3 0.2 - - - -
225B VAL* 1.3 75.3 - - - +
227B ALA* 1.3 60.5 + - - +
229B ALA* 3.2 8.3 + - - +
230B ALA* 2.8 28.1 + - - +
277B PHE* 3.5 27.8 - - + -
289B VAL* 4.2 19.5 - - + -
292B ILE* 4.0 18.4 - - + -
293B ILE* 3.7 24.7 - - + +
335B LEU* 4.1 17.5 - - + -
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TRP* 3.6 11.3 - - - -
213B TRP* 3.4 51.8 - - + +
223B GLU 2.9 12.9 + - - +
224B ARG 3.2 8.9 + - - +
226B VAL* 1.3 76.0 - - - +
228B PHE* 1.3 58.9 + - + +
230B ALA* 3.1 6.2 + - - +
231B VAL* 2.9 28.3 + - - +
292B ILE* 4.2 4.3 - - + -
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE* 4.2 3.4 - - + -
141B VAL* 4.1 28.7 - - + -
144B ASN* 3.4 48.5 - - + -
149B PHE* 4.2 15.5 - + + -
210B ALA* 3.6 26.2 - - + -
213B TRP* 3.9 24.2 - + + -
214B ILE* 3.6 8.7 - - + -
224B ARG* 2.9 22.6 + - + +
225B VAL 4.3 0.7 - - - +
227B ALA* 1.3 75.0 - - - +
229B ALA* 1.3 61.3 + - - +
231B VAL* 3.6 22.0 - - + +
232B GLU* 2.9 38.2 + - + +
273B ALA* 5.6 0.2 - - - -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL 3.0 19.7 + - - +
226B VAL* 3.2 8.5 + - - +
228B PHE* 1.3 75.7 - - - +
230B ALA* 1.3 53.8 + - - +
232B GLU* 4.9 1.1 - - - -
233B GLY* 2.7 34.7 + - - -
270B CYS* 3.6 13.3 - - - +
273B ALA* 3.8 21.4 - - + +
274B CYS* 5.4 1.6 - - - -
331B LEU* 4.1 27.3 - - + +
335B LEU* 5.7 3.4 - - + -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TRP* 4.2 7.0 - - + -
226B VAL 2.8 12.6 + - - +
227B ALA* 3.1 10.5 + - - +
229B ALA* 1.3 75.6 - - - +
231B VAL* 1.3 59.0 + - - +
234B ILE* 2.7 35.4 + - + +
235B PHE* 2.9 12.4 + - - +
293B ILE* 3.9 17.5 - - + -
296B ALA* 3.9 24.7 - - + -
331B LEU* 4.2 2.0 - - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B SER* 5.4 4.0 - - - +
140B ILE* 6.3 0.7 - - + -
141B VAL* 4.0 25.1 - - + -
209B TRP* 4.0 13.9 - - + -
210B ALA* 3.7 30.5 - - + -
213B TRP* 5.8 0.2 - - + -
227B ALA 2.9 19.0 + - - +
228B PHE* 3.3 20.6 + - + +
230B ALA* 1.3 76.9 - - - +
232B GLU* 1.3 61.5 + - - +
235B PHE* 3.2 39.3 + - + +
236B PHE* 3.5 17.7 + - + -
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 3.8 28.9 - - + +
145B LEU* 5.8 0.2 - - - +
165B GLN* 3.1 21.9 + - - -
169B GLU* 3.1 17.7 - - - +
228B PHE* 2.9 24.5 + - + +
229B ALA* 4.9 0.4 - - - -
231B VAL* 1.3 76.3 - - - +
233B GLY* 1.3 57.9 + - - +
236B PHE* 3.6 25.9 - - + +
240B PHE* 4.4 2.3 - - - -
266B GLU* 2.5 37.0 - - - +
269B HIS* 3.1 18.1 + - - +
270B CYS* 3.4 17.1 - - - -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ALA 2.7 20.0 + - - -
232B GLU* 1.3 77.1 - - - +
234B ILE* 1.3 62.9 + - - +
237B SER* 3.4 11.0 - - - -
270B CYS* 3.3 12.1 - - - -
327B VAL* 3.1 23.2 - - - +
331B LEU* 5.6 3.6 - - - -
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ALA* 2.7 36.0 + - + +
233B GLY* 1.3 76.5 - - - +
235B PHE* 1.3 61.8 + - + +
236B PHE 3.1 1.8 - - - -
237B SER* 2.8 23.2 + - - -
293B ILE* 3.7 34.8 - - + +
296B ALA* 3.9 28.7 - - + +
297B VAL* 4.0 3.1 - - + +
300B GLU* 3.3 10.5 - - + -
324B ILE* 4.0 18.6 - - + -
327B VAL* 4.3 5.6 - - + +
328B ALA* 4.0 22.4 - - + +
331B LEU* 4.1 12.8 - - + -
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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