Contacts of the helix formed by residues 218 - 261 (chain K) 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 THR 218 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217K GLU* 3.8 27.1 - - - +
219K VAL* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K THR* 3.8 29.4 - - - +
220K ILE* 3.8 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K VAL* 3.8 28.9 - - - +
221K PRO* 3.8 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 221 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220K ILE* 3.8 26.9 - - - -
222K GLU* 3.8 28.9 - - - -
224K VAL* 4.4 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221K PRO* 3.8 25.1 - - - -
223K SER* 3.8 29.8 - - - +
225K ASP* 4.4 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222K GLU* 3.8 28.9 - - - +
224K VAL* 3.8 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221K PRO* 4.4 16.2 - - - -
223K SER* 3.8 24.5 - - - +
225K ASP* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222K GLU* 4.4 15.7 - - - +
224K VAL* 3.8 29.2 - - - +
226K GLY* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K ASP* 3.8 25.6 - - - +
227K LEU* 3.8 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226K GLY* 3.8 28.0 - - - +
228K GLN* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K LEU* 3.8 26.5 - - - +
229K GLU* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K GLN* 3.8 28.7 - - - +
230K ASN* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229K GLU* 3.8 29.4 - - - +
231K LEU* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230K ASN* 3.8 29.8 - - - +
232K ASP* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K LEU* 3.8 28.0 - - - +
233K VAL* 3.8 30.5 - - - +
235K VAL* 4.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K ASP* 3.8 28.9 - - - +
234K VAL* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233K VAL* 3.8 28.9 - - - +
235K VAL* 3.8 26.5 - - - +
237K LEU* 4.2 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K ASP* 4.5 16.4 - - - +
234K VAL* 3.8 24.5 - - - +
236K SER* 3.8 29.2 - - - +
238K ALA* 4.6 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K VAL* 3.8 28.7 - - - +
237K LEU* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234K VAL* 4.2 16.8 - - - +
236K SER* 3.8 24.9 - - - +
238K ALA* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K VAL* 4.6 16.8 - - - +
237K LEU* 3.8 28.9 - - - +
239K GLU* 3.8 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238K ALA* 3.8 25.4 - - - +
240K ARG* 3.8 29.2 - - - +
242K TYR* 4.5 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K GLU* 3.8 24.7 - - - +
241K HIS* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K ARG* 3.8 28.9 - - - +
242K TYR* 3.8 26.7 - - - +
244K ASN* 4.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 242 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K GLU* 4.5 16.4 - - - +
241K HIS* 3.8 26.9 - - - +
243K TYR* 3.8 28.9 - - - +
245K CYS* 4.4 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K TYR* 3.8 28.7 - - - +
244K ASN* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 244 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241K HIS* 4.6 13.9 - - - +
243K TYR* 3.8 28.7 - - - +
245K CYS* 3.8 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 245 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K TYR* 4.4 18.6 - - - +
244K ASN* 3.8 27.6 - - - +
246K ASP* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245K CYS* 3.8 27.4 - - - +
247K PHE* 3.7 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246K ASP* 3.7 30.1 - - - +
248K LYS* 3.8 29.2 - - - +
250K CYS* 4.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K PHE* 3.8 29.6 - - - +
249K MET* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248K LYS* 3.8 26.7 - - - +
250K CYS* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K PHE* 4.6 12.8 - - - +
249K MET* 3.8 26.2 - - - +
251K TYR* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K CYS* 3.8 29.4 - - - +
252K LYS* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K TYR* 3.8 24.0 - - - +
253K LEU* 3.8 29.2 - - - +
255K SER* 4.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K LYS* 3.8 29.2 - - - +
254K THR* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253K LEU* 3.8 25.1 - - - +
255K SER* 3.8 28.9 - - - +
257K VAL* 4.2 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K LYS* 4.4 18.8 - - - +
254K THR* 3.8 29.4 - - - +
256K VAL* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 256 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K SER* 3.8 29.2 - - - +
257K VAL* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K THR* 4.2 17.0 - - - +
256K VAL* 3.8 27.8 - - - +
258K MET* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257K VAL* 3.8 26.0 - - - +
259K GLU* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K MET* 3.8 29.4 - - - +
260K LYS* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259K GLU* 3.8 26.9 - - - +
261K ASP* 3.6 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K LYS* 3.6 30.5 - - - +
262K PRO* 3.8 27.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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