Contacts of the helix formed by residues 230 - 245 (chain K) in PDB entry 5A31
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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ASP* 3.8 12.7 + - - +
28J LYS* 3.3 50.3 - - - +
31J SER* 3.4 26.5 + - - +
227K LEU* 2.5 25.5 + - - +
229K LYS* 1.3 74.0 - - - +
231K LEU* 1.3 82.6 + - - +
232K ASP* 2.7 23.7 + - - +
233K VAL* 3.2 23.4 + - + +
234K VAL* 3.3 4.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
27J ASP* 5.3 4.0 + - - +
63J ARG* 6.4 0.2 - - - +
229K LYS 3.8 13.2 - - - +
230K ASN* 1.3 77.4 + - - +
232K ASP* 1.3 64.8 + - - +
234K VAL* 3.2 12.9 + - + +
235K VAL* 2.9 28.1 + - - +
257K VAL* 4.1 17.9 - - + +
260K LYS* 4.1 28.3 - - + -
261K ASP* 3.6 32.3 - - + +
264K HIS* 4.0 19.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
24J PHE* 4.3 10.2 - - - -
27J ASP* 3.9 11.3 - - - +
28J LYS* 3.1 36.7 + - - +
164K PHE* 5.7 1.9 - - - -
207K ASN* 5.0 0.6 + - - -
208K LYS* 3.8 21.1 + - - +
230K ASN* 2.7 12.8 + - - +
231K LEU* 1.3 72.4 - - - +
233K VAL* 1.3 59.6 + - - +
235K VAL* 3.6 4.9 + - - +
236K SER* 3.1 22.2 + - - -
264K HIS* 3.8 21.3 + - - -
266K SER* 4.2 13.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
28J LYS* 4.9 0.7 - - - +
203K PHE* 3.9 29.4 - - + -
204K LEU* 4.9 7.9 - - + -
207K ASN* 4.0 15.9 + - - +
222K GLU* 4.9 4.7 - - + +
227K LEU* 3.2 26.7 - - + +
228K GLU* 3.0 34.5 - - - +
230K ASN* 3.2 15.0 + - + +
232K ASP* 1.3 77.1 - - + +
234K VAL* 1.3 62.8 + - + +
236K SER* 3.3 4.7 + - - -
237K LEU* 3.1 20.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
228K GLU 3.6 22.0 - - - +
229K LYS* 4.4 6.1 - - - +
230K ASN 3.3 4.2 + - - +
231K LEU* 3.2 24.5 + - + +
233K VAL* 1.3 74.7 - - + +
235K VAL* 1.3 63.7 + - - +
237K LEU* 3.3 11.8 + - + +
238K ALA* 3.0 24.8 + - - +
253K LEU* 4.2 21.5 - - + +
257K VAL* 3.5 25.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
231K LEU 2.9 21.8 + - - +
232K ASP 4.0 2.2 - - - +
234K VAL* 1.3 75.2 - - - +
236K SER* 1.3 59.9 + - - +
238K ALA* 3.2 7.7 + - + +
239K GLU* 2.8 30.5 + - + +
254K THR* 5.3 0.9 - - - +
257K VAL* 3.8 21.5 - - + -
264K HIS* 4.6 1.8 - - + -
266K SER* 3.7 22.4 - - - +
267K CYS* 3.3 45.5 - - + +
270K VAL* 4.3 11.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
207K ASN* 3.3 46.3 + - - +
208K LYS* 5.8 2.9 - - - -
211K LYS* 5.9 0.3 - - - -
232K ASP 3.1 15.1 + - - -
233K VAL 3.5 9.9 - - - -
234K VAL 3.3 0.2 - - - -
235K VAL* 1.3 75.3 - - - +
237K LEU* 1.3 62.7 + - - +
239K GLU* 3.2 18.4 + - - +
240K ARG* 3.0 34.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
215K PRO* 3.9 26.7 - - + -
233K VAL 3.1 13.1 + - - +
234K VAL* 3.4 13.5 - - + +
235K VAL 3.2 0.2 - - - -
236K SER* 1.3 76.7 - - - +
238K ALA* 1.3 63.0 + - - +
240K ARG* 3.0 14.3 + - + +
241K HIS* 3.0 50.6 + - + +
253K LEU* 4.1 22.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
234K VAL 3.0 13.5 + - - +
235K VAL* 3.2 11.6 + - + +
237K LEU* 1.3 73.8 - - - +
239K GLU* 1.3 65.6 + - - +
240K ARG 3.1 0.2 + - - -
241K HIS* 3.2 5.3 + - - +
242K TYR* 2.9 23.0 + - - +
250K CYS* 4.0 13.8 - - - +
253K LEU* 4.1 26.2 - - + +
254K THR* 4.4 8.3 - - - +
257K VAL* 6.0 0.4 - - + -
270K VAL* 4.2 15.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
174K HIS* 4.7 2.4 + - - -
207K ASN 5.0 4.3 - - - +
208K LYS* 5.0 11.8 - - - +
211K LYS* 3.5 32.6 - - - +
235K VAL* 2.8 20.1 + - + +
236K SER* 3.3 19.4 + - - +
238K ALA* 1.3 71.8 - - - +
240K ARG* 1.3 65.0 + - + +
242K TYR* 3.2 6.5 + - - +
243K TYR* 3.1 37.9 + - + -
266K SER 5.9 0.2 - - - +
270K VAL* 3.5 30.4 - - + +
1W MET* 5.0 8.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
207K ASN* 3.6 28.1 + - - +
210K LYS* 3.5 38.3 - - - +
211K LYS* 3.1 32.7 - - - +
212K TYR 4.9 1.4 - - - +
213K ASN* 3.1 27.6 + - - +
214K LYS 5.4 0.2 + - - -
215K PRO* 4.7 15.4 - - + +
217K GLU* 3.9 15.2 + - - +
218K THR* 3.8 21.8 + - - +
236K SER* 3.0 25.6 + - - +
237K LEU* 3.0 15.4 + - - +
239K GLU* 1.3 77.5 - - - +
241K HIS* 1.3 66.0 + - - +
243K TYR* 3.1 13.2 + - - +
244K ASN* 3.1 18.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
215K PRO* 4.0 23.2 - - + +
237K LEU* 3.0 45.1 + - + -
238K ALA 3.5 6.7 - - - +
240K ARG* 1.3 75.9 - - - +
242K TYR* 1.3 62.7 + - - +
244K ASN* 3.1 13.5 + - - +
246K ASP* 3.0 47.0 + - - +
249K MET* 3.8 42.7 - - + +
250K CYS* 4.0 17.0 - - + +
253K LEU* 3.7 9.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
238K ALA 2.9 14.3 + - - +
239K GLU* 3.5 11.0 - - - +
240K ARG 3.2 0.2 - - - -
241K HIS* 1.3 77.1 - - - +
243K TYR* 1.3 67.9 + + - +
245K CYS 3.3 7.9 + - - +
247K PHE* 3.6 32.4 - + - -
250K CYS* 3.7 19.3 - - - -
270K VAL* 4.4 4.9 - - + -
273K GLY* 3.7 25.4 - - - -
274K THR* 3.8 9.9 - - + -
277K GLU* 3.5 12.9 + - + -
369K LEU* 5.8 0.4 - - + -
1W MET* 3.0 60.2 + - + -
2W LEU 3.7 1.2 + - - -
3W ARG* 2.9 48.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
174K HIS* 2.7 43.1 + + - -
211K LYS* 4.2 17.0 - - + +
212K TYR* 3.8 43.1 - + + +
239K GLU* 3.1 31.6 + - - -
240K ARG 3.1 5.6 + - - +
242K TYR* 1.3 80.8 - + - +
244K ASN* 1.3 63.4 + - - +
245K CYS 3.2 1.9 + - - -
367K CYS* 4.3 7.6 - - - -
368K HIS* 4.2 3.8 - + - -
369K LEU* 3.9 18.4 - - + -
401K ASP* 3.6 16.3 - - - +
1W MET* 3.6 35.7 - - + +
3W ARG* 3.4 18.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
212K TYR 4.0 11.4 - - - +
214K LYS* 3.3 36.3 - - - +
215K PRO* 4.1 8.9 - - - +
240K ARG 3.1 14.3 + - - +
241K HIS* 3.1 8.7 + - - +
243K TYR* 1.3 76.5 - - - +
245K CYS* 1.3 65.7 + - - +
246K ASP* 3.3 30.4 + - - +
400K GLU* 4.9 13.1 - - - +
401K ASP* 4.3 3.3 - - - +
402K PRO* 4.9 3.8 - - - +
435K ILE* 4.1 18.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
241K HIS 3.2 2.0 + - - -
242K TYR 3.3 8.0 + - - -
243K TYR 3.2 4.9 - - - -
244K ASN* 1.3 76.5 - - - +
246K ASP* 1.3 62.4 + - - +
247K PHE* 3.1 27.3 + - + -
401K ASP* 3.2 26.7 - - - -
402K PRO* 4.5 9.9 - - + -
403K PHE* 3.5 33.4 - - + -
436K GLY* 5.1 7.1 - - - -
438K GLU* 4.4 9.2 - - - +
444K TRP* 6.2 0.2 - - + -
3W ARG* 4.0 14.8 - - - -
----------------------------------------------------------
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