Contacts of the helix formed by residues 225 - 239 (chain J) in PDB entry 4ZZ7
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 SER 225 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222J PHE* 3.9 3.3 - - - -
224J GLY* 1.3 73.6 - - - -
226J THR* 1.3 59.4 + - - +
227J PRO* 3.5 14.4 - - - +
228J ILE* 3.2 24.8 - - - +
229J ALA* 2.9 28.9 + - - +
247J GLY* 3.9 1.3 - - - -
248J GLY* 4.3 5.2 - - - +
382J GLU* 5.3 6.5 - - - -
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Residues in contact with THR 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J SER* 1.3 70.7 - - - +
227J PRO* 1.3 67.5 - - - +
229J ALA* 3.1 2.2 + - - +
230J GLU* 2.8 30.7 + - - +
247J GLY* 4.0 6.3 - - - -
248J GLY* 2.7 26.9 + - - +
407J GLU* 4.6 0.2 - - - +
408J TYR* 3.1 26.2 + - + -
454J ARG* 3.3 56.3 + - - +
457J PHE* 4.0 8.1 - - + -
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Residues in contact with PRO 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J SER* 3.5 14.8 - - - +
226J THR* 1.3 93.8 - - + +
228J ILE* 1.3 64.4 + - + +
230J GLU* 3.7 11.5 + - + +
231J TYR* 3.3 18.5 + - - +
408J TYR* 5.1 4.7 - - - +
454J ARG* 5.6 4.0 - - - +
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Residues in contact with ILE 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205J LYS* 6.4 0.2 - - - +
222J PHE* 3.6 27.8 - - + -
225J SER* 3.2 19.6 + - - +
226J THR 3.2 0.6 - - - -
227J PRO* 1.3 80.9 - - + +
229J ALA* 1.3 56.0 + - - +
230J GLU 3.1 1.6 - - - -
231J TYR* 2.9 13.0 + - + +
232J ILE* 2.7 44.5 + - + +
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Residues in contact with ALA 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222J PHE* 3.6 23.4 - - + -
225J SER 2.9 22.3 + - - +
226J THR* 3.3 7.9 - - - +
228J ILE* 1.3 70.8 - - - +
230J GLU* 1.3 59.1 + - - +
232J ILE* 3.1 2.9 + - - +
233J TYR* 2.8 30.8 + - - +
245J ALA* 3.7 10.2 - - + +
246J LEU 3.9 13.9 - - - +
457J PHE* 3.8 19.5 - - + -
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Residues in contact with GLU 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J THR 2.8 19.7 + - - +
227J PRO* 3.8 9.2 - - - +
229J ALA* 1.3 73.4 - - - +
231J TYR* 1.3 61.6 + - - +
233J TYR* 3.9 2.8 - - + +
234J ARG* 3.0 58.9 + - + +
454J ARG* 3.2 32.3 + - - +
457J PHE* 3.8 26.8 - - + -
237K SER 5.9 2.5 - - - +
238K ALA 4.1 9.4 - - - +
239K ASN 5.9 0.3 - - - -
240K GLY* 5.7 1.2 + - - -
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Residues in contact with TYR 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G LYS* 5.2 2.1 - - - -
205J LYS* 3.6 27.3 - - + -
208J VAL* 5.3 1.1 - - + -
209J ASP* 2.6 36.0 + - - -
212J LEU* 4.3 10.1 - - + -
213J HIS* 4.7 2.4 - - - -
227J PRO 3.3 12.1 + - - +
228J ILE* 2.9 17.1 + - + +
230J GLU* 1.3 78.5 - - - +
232J ILE* 1.3 69.1 + - + +
234J ARG* 3.9 16.2 - - + +
235J THR* 2.6 64.0 + - + +
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Residues in contact with ILE 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ILE* 4.4 4.5 - - + -
208J VAL* 3.4 33.0 - - + -
212J LEU* 3.7 15.7 - - + +
220J VAL* 3.9 27.4 - - + -
222J PHE* 3.8 35.2 - - + -
228J ILE* 2.7 29.5 + - + +
229J ALA 3.6 6.3 - - - +
231J TYR* 1.3 81.7 - - + +
233J TYR* 1.3 58.3 + - - +
235J THR* 3.4 1.2 + - - -
236J ALA* 2.8 29.8 + - - +
243J CYS* 4.2 5.6 - - - -
245J ALA* 5.0 0.4 - - + -
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Residues in contact with TYR 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229J ALA 2.8 20.5 + - - +
230J GLU* 3.9 3.6 - - + +
232J ILE* 1.3 74.6 - - - +
234J ARG* 1.3 53.2 + - - +
236J ALA* 3.9 0.9 - - - +
237J SER* 2.6 43.6 + - - -
243J CYS* 3.5 40.6 - - + -
245J ALA* 4.2 3.8 - - + -
457J PHE* 3.4 48.0 - + + -
458J GLY* 3.6 19.3 + - - -
233K TYR* 4.7 10.5 + - - -
237K SER* 3.7 43.3 + - - -
240K GLY 4.7 6.7 - - - -
241K LYS 4.6 1.6 + - - -
242K ARG* 4.5 12.5 - - - -
243K CYS 4.9 2.8 + - - -
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Residues in contact with ARG 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230J GLU* 3.0 61.4 + - + +
231J TYR* 3.9 18.0 - - - +
233J TYR* 1.3 79.8 - - - +
235J THR* 1.3 60.4 + - - +
237J SER* 3.5 4.5 + - - -
238J ALA* 3.0 29.1 + - + +
234K ARG* 5.5 5.8 - - + +
237K SER* 5.0 4.0 - - - +
238K ALA* 3.7 39.8 + - + +
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Residues in contact with THR 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J LEU* 3.7 27.4 - - + -
213J HIS* 3.8 27.4 - - + +
231J TYR* 2.6 49.9 + - - +
232J ILE 3.7 3.1 - - - -
234J ARG* 1.3 80.4 - - - +
236J ALA* 1.3 61.0 + - - +
238J ALA* 3.4 4.2 + - - +
239J ASN* 2.8 34.1 + - - +
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Residues in contact with ALA 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J LEU* 4.4 8.7 - - + +
220J VAL* 4.4 10.3 - - + -
232J ILE 2.8 21.6 + - - +
233J TYR 4.1 0.2 - - - +
235J THR* 1.3 73.3 - - - +
237J SER* 1.3 63.3 + - - +
239J ASN* 3.3 4.3 + - - -
240J GLY 3.2 16.1 + - - -
241J LYS* 3.2 33.4 + - + +
243J CYS* 3.8 27.4 - - + -
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Residues in contact with SER 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233J TYR* 2.6 34.7 + - - -
234J ARG 3.8 3.1 - - - -
235J THR 3.3 0.2 - - - -
236J ALA* 1.3 78.2 - - - +
238J ALA* 1.3 62.2 + - - +
240J GLY* 3.0 14.6 + - - -
241J LYS 4.1 3.1 + - - -
243J CYS* 5.1 1.2 - - - +
230K GLU* 6.0 1.7 - - - +
233K TYR* 3.7 31.2 + - - -
234K ARG* 5.0 5.1 - - - +
237K SER* 3.2 36.7 + - - -
457K PHE* 5.4 0.9 - - - -
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Residues in contact with ALA 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234J ARG* 3.0 19.8 + - + +
235J THR* 3.6 7.4 - - - +
237J SER* 1.3 75.5 - - - +
239J ASN* 1.3 64.3 + - - +
240J GLY 3.3 0.9 + - - -
230K GLU* 4.0 9.0 - - - +
234K ARG* 3.8 45.2 + - + +
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Residues in contact with ASN 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J LEU 3.6 23.7 + - - +
213J HIS* 3.7 36.5 + - - +
215J ASP* 5.2 7.6 - - - +
235J THR* 2.8 29.3 + - - +
236J ALA 3.9 4.3 - - - +
237J SER 3.2 1.0 - - - -
238J ALA* 1.3 81.2 - - - +
240J GLY* 1.3 54.3 + - - +
241J LYS* 3.3 20.2 + - - -
230K GLU* 5.7 0.9 - - - -
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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