Contacts of the helix formed by residues 223 - 239 (chain J) in PDB entry 5T0G
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 GLU 223 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221J ASN* 2.4 30.8 + - + +
222J PRO* 1.3 68.7 - - - +
224J GLU* 1.3 69.8 + - + +
225J ILE 3.3 0.7 - - - -
226J GLU* 3.4 6.5 + - - +
227J LYS* 3.4 17.7 + - - +
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Residues in contact with GLU 224 (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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220J LEU* 5.1 13.5 - - + -
221J ASN 3.6 4.4 + - - +
223J GLU* 1.3 82.1 - - + +
225J ILE* 1.3 60.5 + - - +
227J LYS* 3.2 12.6 + - - +
228J TYR* 2.9 61.4 + - + +
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Residues in contact with ILE 225 (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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192J ILE* 5.8 1.0 - - - +
203J GLY 5.8 4.3 - - - +
206J ILE* 5.5 11.0 - - + +
220J LEU* 3.8 24.0 - - + +
221J ASN 4.1 1.6 + - - -
222J PRO* 4.6 11.4 - - + -
223J GLU 3.3 1.6 - - - +
224J GLU* 1.3 78.6 - - - +
226J GLU* 1.3 57.1 + - - +
228J TYR* 3.7 12.5 - - + +
229J VAL* 2.9 27.7 + - - +
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Residues in contact with GLU 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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222J PRO* 4.1 15.1 - - + +
223J GLU* 3.4 10.6 + - - +
224J GLU 3.2 0.6 - - - -
225J ILE* 1.3 77.7 - - - +
227J LYS* 1.3 59.6 + - - +
229J VAL* 3.4 8.2 + - - +
230J ALA* 2.9 26.7 + - - +
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Residues in contact with LYS 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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223J GLU 3.4 9.1 + - - +
224J GLU* 3.2 19.4 + - - +
226J GLU* 1.3 78.3 - - - +
228J TYR* 1.3 64.1 + - + +
230J ALA* 3.3 9.8 + - - +
231J GLU* 2.9 28.1 + - - +
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Residues in contact with TYR 228 (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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185J ASP* 5.6 6.0 - - - -
188J ILE* 3.5 46.6 - - + +
189J LYS* 5.1 6.1 - - + +
192J ILE* 4.7 18.8 - - + +
220J LEU* 5.3 6.1 - - + -
224J GLU* 2.9 49.4 + - + +
225J ILE* 3.7 10.3 - - - +
226J GLU 3.3 0.2 - - - -
227J LYS* 1.3 78.1 - - + +
229J VAL* 1.3 59.9 + - - +
231J GLU* 3.0 32.1 - - - +
232J ILE* 3.0 26.2 + - - +
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Residues in contact with VAL 229 (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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192J ILE* 5.3 3.5 - - + +
203J GLY* 5.8 7.6 - - - -
225J ILE 2.9 17.8 + - - +
226J GLU* 3.6 8.5 - - - +
228J TYR* 1.3 72.8 - - - +
230J ALA* 1.3 66.2 + - - +
232J ILE* 3.0 17.6 + - - +
233J GLU* 3.0 15.2 + - - +
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Residues in contact with ALA 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 GLU 2.9 14.9 + - - +
227J LYS* 3.3 13.4 + - - +
229J VAL* 1.3 77.5 - - - +
231J GLU* 1.3 57.9 + - - +
233J GLU* 3.4 4.6 + - - +
234J LYS* 2.9 27.3 + - - +
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Residues in contact with GLU 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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185J ASP 5.3 1.0 - - - +
189J LYS* 3.5 24.2 - - + +
227J LYS 2.9 10.3 + - - +
228J TYR* 3.0 50.3 - - - +
230J ALA* 1.3 74.1 - - - +
232J ILE* 1.3 59.8 + - - +
234J LYS* 3.7 7.9 - - - +
235J GLU* 2.9 27.7 + - - +
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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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189J LYS 6.2 0.2 - - - +
192J ILE* 5.6 9.6 - - + +
193J LYS* 6.0 5.2 - - + +
196J LEU* 6.0 5.6 - - + -
228J TYR 3.0 14.7 + - - +
229J VAL* 3.0 13.2 + - - +
231J GLU* 1.3 75.4 - - - +
233J GLU* 1.3 64.1 + - - +
235J GLU* 3.1 7.8 + - - +
236J LYS* 3.0 21.8 + - - +
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Residues in contact with GLU 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 VAL 3.0 13.5 + - - +
230J ALA* 4.0 4.9 - - - +
232J ILE* 1.3 76.8 - - - +
234J LYS* 1.3 56.9 + - - +
236J LYS* 3.4 8.8 + - - +
237J GLU* 2.9 26.2 + - - +
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Residues in contact with LYS 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 ALA 2.9 19.3 + - - +
231J GLU* 3.9 9.9 - - + +
232J ILE 3.2 0.2 - - - -
233J GLU* 1.3 74.2 - - - +
235J GLU* 1.3 58.8 + - - +
237J GLU* 3.1 8.5 + - - +
238J GLU* 2.9 47.2 + - - +
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Residues in contact with GLU 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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231J GLU 2.9 19.1 + - - +
232J ILE* 3.1 7.2 + - - +
234J LYS* 1.3 74.8 - - - +
236J LYS* 1.3 60.0 + - - +
238J GLU* 3.4 12.3 + - - +
239J ASN* 3.0 29.6 + - - +
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Residues in contact with LYS 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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232J ILE 3.0 12.4 + - - +
233J GLU* 3.7 11.0 - - - +
235J GLU* 1.3 76.3 - - - +
237J GLU* 1.3 59.8 + - - +
239J ASN* 3.7 12.7 + - - +
240J GLU* 4.0 9.7 + - - +
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Residues in contact with GLU 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 GLU 2.9 14.3 + - - +
234J LYS* 3.1 14.1 + - + +
236J LYS* 1.3 75.6 - - - +
238J GLU* 1.3 64.9 + - + +
239J ASN 3.3 0.5 + - - -
240J GLU* 3.4 18.4 + - - +
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Residues in contact with GLU 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 LYS* 2.9 36.8 + - - +
235J GLU* 3.4 14.5 + - - +
237J GLU* 1.3 76.4 - - + +
239J ASN* 1.3 60.9 + - - +
240J GLU 3.2 6.6 + - - +
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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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235J GLU 3.0 17.8 + - - +
236J LYS* 4.0 10.1 - - - +
237J GLU 3.2 1.0 - - - -
238J GLU* 1.3 77.4 - - - +
240J GLU* 1.3 60.4 + - - +
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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