Contacts of the helix formed by residues 214 - 228 (chain B) in PDB entry 2OZL
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 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B TRP* 4.1 2.6 + - - -
172B ASN* 3.8 34.8 - - - +
174B LEU* 3.6 36.2 + - - +
175B MET* 3.9 26.4 - - + +
213B SER* 1.3 79.8 + - - +
215B PRO* 1.3 69.2 - - + +
217B GLY* 2.9 17.5 + - - -
218B HIS* 3.4 37.3 + - + +
313B ILE* 5.2 14.3 - - - +
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Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 3.3 18.2 - - - +
212B HIS 3.2 14.1 - - - +
213B SER* 3.3 3.1 - - - -
214B ARG* 1.3 93.3 - - + +
216B VAL* 1.3 60.1 + - - -
217B GLY 3.0 0.4 - - - -
218B HIS* 2.9 28.8 + - + +
219B CYS* 2.9 16.3 + - - -
262B VAL* 3.9 17.7 - - + +
263B GLU 4.4 1.8 - - - -
264B GLY* 4.0 26.7 - - - +
313B ILE* 6.2 1.6 - - + -
314B PRO* 4.9 7.9 - - + -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.6 33.2 - - + -
201B GLU* 4.4 6.7 - - + -
211B SER* 3.6 15.2 + - - +
212B HIS* 3.8 26.9 - - - +
213B SER 3.0 19.6 + - - +
214B ARG 2.9 0.6 + - - -
215B PRO* 1.3 77.1 - - - +
217B GLY* 1.3 61.9 + - - +
219B CYS* 3.2 5.3 + - - +
220B LEU* 3.1 24.3 + - + +
235B VAL* 4.7 8.3 - - + -
236B ILE 5.1 0.2 - - - +
237B ASN* 4.0 26.2 - - + +
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Residues in contact with GLY 217 (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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148B TRP* 3.6 25.6 - - - +
214B ARG 2.9 10.6 + - - -
216B VAL* 1.3 80.1 - - - +
218B HIS* 1.3 60.3 + - - +
220B LEU* 3.3 6.1 + - - +
221B GLU* 3.1 30.3 + - - +
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Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 3.4 47.5 + - + +
215B PRO* 2.9 23.1 + - + +
217B GLY* 1.3 74.5 - - - +
219B CYS* 1.3 60.2 + - - +
221B GLU* 3.1 24.6 + - - +
222B ALA* 2.9 27.4 + - - +
313B ILE* 5.9 2.2 - - + -
314B PRO* 4.0 20.0 + - - +
315B GLN* 5.7 1.1 - - - -
316B VAL* 3.8 18.3 - - + +
319B ILE* 3.7 18.2 - - + +
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Residues in contact with CYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.7 18.0 - - + +
211B SER* 3.8 13.0 - - - -
215B PRO 2.9 16.6 + - - -
216B VAL 3.2 7.8 + - - +
218B HIS* 1.3 73.6 - - - +
220B LEU* 1.3 61.5 + - - +
222B ALA* 3.3 5.0 + - - +
223B ALA* 2.8 29.8 + - - +
235B VAL* 4.0 19.3 - - + +
262B VAL* 3.6 38.1 - - - -
319B ILE* 4.1 8.5 - - - -
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.4 39.7 - - + -
201B GLU* 4.1 16.2 - - + +
202B ARG* 4.0 22.2 - - + -
216B VAL* 3.1 14.3 + - + +
217B GLY* 3.6 7.6 - - - +
218B HIS 3.3 0.2 - - - -
219B CYS* 1.3 76.5 - - - +
221B GLU* 1.3 57.2 + - - +
223B ALA* 3.4 4.0 + - - +
224B ALA* 3.0 27.5 + - - +
235B VAL* 3.9 26.7 - - + -
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Residues in contact with GLU 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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217B GLY 3.1 14.3 + - - +
218B HIS* 3.1 39.2 - - - +
219B CYS 3.2 0.2 - - - -
220B LEU* 1.3 74.3 - - - +
222B ALA* 1.3 64.8 + - - +
224B ALA* 3.3 7.7 + - - +
225B VAL* 3.2 27.9 + - + +
316B VAL* 3.7 16.1 - - + +
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Residues in contact with ALA 222 (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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218B HIS 2.9 18.2 + - - +
219B CYS 3.3 4.7 + - - +
221B GLU* 1.3 77.2 - - - +
223B ALA* 1.3 56.2 + - - +
225B VAL* 3.3 2.8 + - - +
226B LEU* 3.0 34.9 + - - +
316B VAL* 3.9 14.5 - - + +
319B ILE* 3.8 27.1 - - + -
320B ILE* 3.8 18.8 - - + +
323B ILE* 4.8 4.7 - - + -
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Residues in contact with ALA 223 (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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202B ARG* 3.6 33.3 + - - +
219B CYS 2.8 17.7 + - - +
220B LEU 3.7 4.5 - - - +
221B GLU 3.2 0.4 - - - -
222B ALA* 1.3 77.1 - - - +
224B ALA* 1.3 56.3 + - - +
226B LEU* 3.9 0.9 - - - +
227B SER* 2.8 30.7 + - - -
231B VAL 4.4 1.6 - - - +
233B CYS* 3.9 29.7 - - + -
235B VAL* 4.0 4.5 - - + -
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Residues in contact with ALA 224 (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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202B ARG* 4.9 3.1 - - - +
220B LEU 3.0 14.5 + - - +
221B GLU* 3.6 10.3 - - - +
222B ALA 3.3 0.2 - - - -
223B ALA* 1.3 74.6 - - - +
225B VAL* 1.3 68.7 + - + +
227B SER* 3.4 17.3 + - - -
228B LYS* 3.5 19.5 + - - +
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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
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221B GLU 3.2 14.7 + - - +
222B ALA* 3.6 6.3 - - - +
223B ALA 3.3 0.2 - - - -
224B ALA* 1.3 78.7 - - + +
226B LEU* 1.3 63.8 + - + +
228B LYS* 3.2 25.7 + - + +
229B GLU* 3.8 19.6 + - - +
316B VAL* 5.2 4.7 - - + -
320B ILE* 4.0 25.1 - - + -
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Residues in contact with LEU 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 ALA 3.0 20.7 + - - +
223B ALA 3.9 3.6 - - - +
225B VAL* 1.3 73.8 - - + +
227B SER* 1.3 59.4 + - - +
229B GLU* 2.8 29.4 + - - +
230B GLY 3.3 0.2 + - - -
231B VAL* 3.1 41.5 + - + +
233B CYS* 3.7 11.4 - - - -
320B ILE* 3.9 29.4 - - + -
323B ILE* 3.4 46.2 - - + -
324B LYS* 3.9 22.2 - - + -
329B ILE* 5.6 0.2 - - + -
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 3.3 20.1 + - - -
223B ALA 2.8 19.1 + - - -
224B ALA* 3.5 10.1 - - - -
225B VAL 3.2 0.4 - - - -
226B LEU* 1.3 76.4 - - - +
228B LYS* 1.3 60.7 + - - +
229B GLU 3.1 0.2 - - - -
230B GLY* 3.2 13.3 + - - -
231B VAL 3.2 12.3 + - - -
232B GLU* 3.1 18.6 + - - +
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Residues in contact with LYS 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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224B ALA* 3.5 18.6 + - - +
225B VAL* 3.2 14.7 + - + +
226B LEU 3.1 0.8 - - - -
227B SER* 1.3 77.3 - - - +
229B GLU* 1.3 61.1 + - + +
230B GLY 3.4 0.6 + - - -
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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