Contacts of the helix formed by residues 230 - 261 (chain J) in PDB entry 5KHU
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 ASN 230 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229J GLU* 3.8 30.5 - - - +
231J LEU* 3.7 29.6 - - - +
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Residues in contact with LEU 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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230J ASN* 3.7 29.8 - - - +
232J ASP* 3.7 25.8 - - - +
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Residues in contact with ASP 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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231J LEU* 3.7 29.8 - - - +
233J VAL* 3.8 27.1 - - - +
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Residues in contact with VAL 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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232J ASP* 3.8 26.0 - - - +
234J VAL* 3.7 30.1 - - - +
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Residues in contact with VAL 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233J VAL* 3.7 29.4 - - - +
235J VAL* 3.7 27.4 - - - +
237J LEU* 4.3 18.6 - - - +
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Residues in contact with VAL 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234J VAL* 3.7 23.6 - - - +
236J SER* 3.7 29.4 - - - +
238J ALA* 4.3 17.9 - - - +
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Residues in contact with SER 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235J VAL* 3.7 29.6 - - - +
237J LEU* 3.8 24.9 - - - +
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Residues in contact with LEU 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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234J VAL* 4.3 15.3 - - - +
236J SER* 3.8 25.4 - - - +
238J ALA* 3.7 29.6 - - - +
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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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235J VAL* 4.3 17.7 - - - +
237J LEU* 3.7 29.2 - - - +
239J GLU* 3.8 27.4 - - - +
241J HIS* 4.5 15.9 - - - +
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Residues in contact with GLU 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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238J ALA* 3.8 29.2 - - - +
240J ARG* 3.8 25.8 - - - +
242J TYR* 4.3 16.6 - - - +
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Residues in contact with ARG 240 (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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239J GLU* 3.8 25.6 - - - +
241J HIS* 3.7 29.6 - - - +
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Residues in contact with HIS 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238J ALA* 4.5 14.6 - - - +
240J ARG* 3.7 29.8 - - - +
242J TYR* 3.8 26.0 - - - +
244J ASN* 4.5 16.8 - - - +
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Residues in contact with TYR 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239J GLU* 4.3 19.7 - - - +
241J HIS* 3.8 27.8 - - - +
243J TYR* 3.8 29.8 - - - +
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Residues in contact with TYR 243 (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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242J TYR* 3.8 29.6 - - - +
244J ASN* 3.8 25.1 - - - +
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Residues in contact with ASN 244 (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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241J HIS* 4.5 19.1 - - - +
243J TYR* 3.8 29.4 - - - +
245J CYS* 3.8 23.8 - - - +
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Residues in contact with CYS 245 (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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244J ASN* 3.8 29.6 - - - +
246J ASP* 3.8 24.7 - - - +
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Residues in contact with ASP 246 (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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245J CYS* 3.8 24.7 - - - +
247J PHE* 3.7 30.1 - - - +
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Residues in contact with PHE 247 (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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246J ASP* 3.7 29.2 - - - +
248J LYS* 3.8 25.8 - - - +
250J CYS* 4.6 14.8 - - - +
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Residues in contact with LYS 248 (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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247J PHE* 3.8 29.6 - - - +
249J MET* 3.8 26.0 - - - +
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Residues in contact with MET 249 (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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248J LYS* 3.8 25.1 - - - +
250J CYS* 3.8 29.2 - - - +
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Residues in contact with CYS 250 (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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247J PHE* 4.6 16.4 - - - +
249J MET* 3.8 30.3 - - - +
251J TYR* 3.8 27.4 - - - +
253J LEU* 4.7 14.4 - - - +
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Residues in contact with TYR 251 (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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250J CYS* 3.8 29.2 - - - +
252J LYS* 3.8 25.8 - - - +
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Residues in contact with LYS 252 (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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251J TYR* 3.8 25.8 - - - +
253J LEU* 3.7 29.4 - - - +
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Residues in contact with LEU 253 (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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250J CYS* 4.7 13.2 - - - +
252J LYS* 3.7 29.4 - - - +
254J THR* 3.8 27.6 - - - +
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Residues in contact with THR 254 (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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253J LEU* 3.8 25.4 - - - +
255J SER* 3.8 29.2 - - - +
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Residues in contact with SER 255 (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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254J THR* 3.8 29.6 - - - +
256J VAL* 3.8 27.1 - - - +
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Residues in contact with VAL 256 (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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255J SER* 3.8 24.9 - - - +
257J VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 257 (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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256J VAL* 3.8 29.4 - - - +
258J MET* 3.8 26.9 - - - +
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Residues in contact with MET 258 (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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257J VAL* 3.8 24.5 - - - +
259J GLU* 3.7 29.6 - - - +
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Residues in contact with GLU 259 (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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258J MET* 3.7 30.3 - - - +
260J LYS* 3.8 26.9 - - - +
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Residues in contact with LYS 260 (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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259J GLU* 3.8 26.5 - - - +
261J ASP* 3.7 29.8 - - - +
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Residues in contact with ASP 261 (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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260J LYS* 3.7 30.1 - - - +
262J PRO* 3.7 28.7 - - - -
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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
------------------------------------------------------------
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