Contacts of the helix formed by residues 235 - 256 (chain D) in PDB entry 6XAV
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 PRO 235 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ASN* 4.8 14.4 - - - +
295C HIS* 3.4 31.6 - - + +
234D GLU* 1.3 97.3 - - + +
236D ALA* 1.3 66.4 + - - +
237D SER* 3.1 11.0 - - - +
238D ARG* 3.2 27.6 + - + +
239D HIS* 3.5 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ALA 5.8 1.3 + - - +
292C ASN* 5.6 1.4 + - - +
235D PRO* 1.3 72.2 - - - +
237D SER* 1.3 64.8 + - - +
238D ARG 3.2 0.2 - - - -
239D HIS* 3.2 15.1 + - + +
240D VAL* 3.1 26.9 + - - +
273D ALA* 3.8 21.1 - - - +
276D THR* 4.2 16.4 - - + -
277D VAL* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D PRO* 3.1 10.9 - - - +
236D ALA* 1.3 79.3 - - - +
238D ARG* 1.3 62.1 + - - +
240D VAL* 3.4 6.1 + - - +
241D GLN* 3.1 23.7 + - - +
277D VAL* 4.0 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D SER 4.5 1.6 + - - -
71D SER* 3.5 25.7 + - - -
72D TYR 5.2 1.2 + - - -
73D LEU* 3.3 35.1 - - + +
74D ALA* 5.6 0.9 - - - +
229D ALA 4.8 0.6 + - - -
230D SER* 4.0 11.4 + - - +
234D GLU* 2.4 55.1 + - + +
235D PRO* 3.2 22.5 + - + +
237D SER* 1.3 76.5 - - - +
239D HIS* 1.3 59.8 + - - +
241D GLN* 3.8 8.3 - - - +
242D VAL* 2.9 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D ILE* 3.5 27.9 - - + +
210D ASP* 3.4 26.8 + - + +
230D SER* 3.1 24.8 + - - -
231D THR 3.3 24.0 - - - -
234D GLU 3.6 19.9 + - - -
235D PRO 3.6 6.7 + - - -
236D ALA* 3.2 15.6 + - + +
238D ARG* 1.3 76.3 - - - +
240D VAL* 1.3 61.1 + - - +
242D VAL* 4.8 2.0 - - - -
243D ALA* 3.2 25.1 + - - +
269D ARG 5.4 2.0 - - - -
270D LEU* 3.8 5.8 - - + +
273D ALA* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D ALA 3.1 15.0 + - - +
237D SER* 3.7 7.9 - - - +
238D ARG 3.2 0.4 - - - -
239D HIS* 1.3 76.4 - - - +
241D GLN* 1.3 60.3 + - - +
243D ALA* 3.5 2.3 + - - +
244D GLU* 3.0 33.0 + - - +
273D ALA* 4.4 8.7 - - + +
274D TYR* 3.6 43.7 + - + +
277D VAL* 3.8 24.9 - - + -
296D ARG* 4.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLU* 2.8 45.2 + - - +
57D ILE 5.8 0.2 + - - -
58D LEU* 6.3 1.1 - - - -
72D TYR* 5.3 5.8 - - + +
93D THR* 5.8 0.4 - - - +
237D SER 3.1 16.4 + - - +
238D ARG* 3.9 10.8 - - - +
240D VAL* 1.3 76.7 - - - +
242D VAL* 1.3 62.6 + - + +
244D GLU* 3.2 24.9 + - - +
245D MET* 3.0 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D SER* 3.4 15.5 - - - +
72D TYR* 5.4 3.1 - - + +
207D LEU* 3.9 14.4 - - + -
209D ILE* 4.7 2.2 - - + -
228D VAL* 3.9 27.4 - - + -
229D ALA 5.0 0.4 - - - +
230D SER* 4.4 17.0 - - - -
238D ARG* 2.9 53.2 + - - +
239D HIS* 4.3 2.0 - - - +
241D GLN* 1.3 75.8 - - + +
243D ALA* 1.3 64.5 + - - +
245D MET* 3.2 7.5 + - - +
246D VAL* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LEU* 4.5 11.0 - - + -
209D ILE* 4.0 10.7 - - + +
239D HIS 3.2 18.6 + - - +
240D VAL 3.9 2.9 - - - +
242D VAL* 1.3 77.6 - - - +
244D GLU* 1.3 61.2 + - - +
246D VAL* 3.5 2.1 + - - +
247D ILE* 3.2 25.6 + - - +
270D LEU* 3.8 29.8 - - + -
274D TYR* 4.4 7.2 - - - +
300D PHE* 3.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 5.0 11.0 + - + +
240D VAL* 3.0 22.7 + - - +
241D GLN* 3.5 28.3 - - - +
242D VAL 3.2 0.2 - - - -
243D ALA* 1.3 75.9 - - - +
245D MET* 1.3 60.1 + - - +
247D ILE* 3.2 8.3 - - + +
248D GLU* 3.0 48.4 + - + +
274D TYR* 5.0 2.0 + - - +
296D ARG* 4.9 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 3.7 23.0 - - + +
55D LEU 3.4 22.9 - - - +
56D GLU* 3.6 32.1 - - + +
72D TYR* 3.9 45.4 + - + -
93D THR* 3.8 16.8 - - + -
94D GLY 4.9 0.4 - - - +
241D GLN* 3.0 34.6 + - + +
242D VAL 3.2 4.7 + - - +
244D GLU* 1.3 75.1 - - - +
246D VAL* 1.3 58.5 + - - +
248D GLU* 4.1 2.1 - - - +
249D LYS* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 5.1 5.8 - - + -
205D MET* 4.5 14.7 - - + +
207D LEU* 3.8 39.0 - - + -
228D VAL* 4.0 23.3 - - + -
242D VAL 3.0 17.7 + - - +
243D ALA 3.9 4.5 - - - +
244D GLU 3.2 0.2 - - - -
245D MET* 1.3 76.8 - - - +
247D ILE* 1.3 60.6 + - - +
249D LYS* 3.3 5.6 + - - +
250D ALA* 2.9 28.1 + - - +
262D ILE* 4.3 23.3 - - + -
300D PHE* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ALA 3.2 11.3 + - - +
244D GLU* 3.2 18.4 - - + +
246D VAL* 1.3 79.1 - - - +
248D GLU* 1.3 67.1 + - + +
250D ALA* 4.3 5.4 - - + -
251D LYS* 3.0 50.3 + - + +
262D ILE* 5.2 2.0 - - + -
300D PHE* 3.5 37.9 - - + +
303D ALA* 3.8 27.4 - - + -
313D LEU* 4.6 10.1 - - + -
315D ILE* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ARG* 5.6 0.2 - - - +
93D THR* 2.9 50.5 + - + +
94D GLY* 4.0 2.5 - - - -
244D GLU* 3.0 34.1 + - + +
245D MET 4.1 2.0 - - - +
247D ILE* 1.3 79.6 - - + +
249D LYS* 1.3 63.8 + - - +
251D LYS* 3.4 15.1 + - - +
252D ARG* 3.0 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 4.4 16.7 - - + +
68D ALA* 5.0 4.8 - - - +
72D TYR* 3.5 21.0 + - - +
94D GLY* 4.0 21.0 - - - +
96D THR* 4.9 7.6 - - - +
205D MET* 4.6 15.7 - - + -
226D GLU* 3.1 33.7 + - - +
245D MET 3.1 19.2 + - - +
246D VAL* 3.8 4.9 - - - +
248D GLU* 1.3 77.8 - - - +
250D ALA* 1.3 61.9 + - - +
252D ARG* 3.5 3.1 + - - +
253D LEU* 3.3 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D MET* 4.6 5.8 - - - +
246D VAL 2.9 18.5 + - - +
247D ILE* 3.8 10.3 - - + +
248D GLU 3.2 0.2 - - - -
249D LYS* 1.3 77.5 - - - +
251D LYS* 1.3 61.9 + - - +
253D LEU* 3.2 5.3 + - - +
254D VAL* 3.0 28.7 + - - +
260D VAL* 4.1 15.4 - - + +
262D ILE* 3.8 26.0 - - + -
313D LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 4.5 31.8 - - + -
134D GLU* 5.3 7.6 + - - +
247D ILE* 3.0 47.0 + - + +
248D GLU* 3.9 15.6 + - - +
249D LYS 3.4 0.2 - - - -
250D ALA* 1.3 75.8 - - - +
252D ARG* 1.3 79.8 + - - +
254D VAL* 3.3 7.1 + - - +
255D GLU* 3.0 34.0 + - - +
299D ARG* 5.4 7.7 - - - +
303D ALA* 4.4 12.5 - - - +
313D LEU* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ARG* 3.3 41.2 - - - +
93D THR 3.3 9.9 + - - -
94D GLY 3.8 19.1 - - - +
95D ASP* 3.2 23.6 - - - +
120D ASN* 4.2 13.5 - - - +
130D LYS* 4.4 4.7 - - - +
133D PHE* 4.9 2.4 - - - +
134D GLU* 5.1 5.3 + - - -
248D GLU* 3.0 42.0 + - - +
249D LYS 3.9 4.7 - - - +
250D ALA 3.3 0.6 - - - -
251D LYS* 1.3 101.1 - - - +
253D LEU* 1.3 59.6 + - + +
255D GLU* 3.0 32.9 + - - +
256D HIS* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D THR* 6.1 0.9 - - - +
120D ASN* 5.3 14.8 - - + +
203D VAL* 4.1 14.6 - - + -
205D MET* 3.8 29.6 - - + -
249D LYS* 3.3 25.7 + - + +
250D ALA 3.2 7.0 + - - +
252D ARG* 1.3 77.0 - - + +
254D VAL* 1.3 60.3 + - - +
256D HIS* 2.9 20.6 + - + -
257D LYS 3.3 0.3 + - - -
258D LYS* 3.0 36.6 + - + +
260D VAL* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 3.7 18.6 - - + -
136D LEU* 4.4 2.4 - - + +
250D ALA 3.0 19.5 + - - +
251D LYS* 3.8 5.4 - - - +
253D LEU* 1.3 75.4 - - - +
255D GLU* 1.3 62.5 + - - +
257D LYS* 3.1 10.2 + - - -
258D LYS 3.8 8.3 - - - +
260D VAL* 4.2 7.0 - - + -
305D ARG 5.3 0.2 - - - +
307D VAL* 3.7 28.9 - - + -
310D GLY 3.4 12.6 - - - +
312D SER 3.8 29.8 - - - +
313D LEU* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ARG* 3.5 8.4 + - - -
130D LYS* 2.9 41.0 + - - +
131D ILE* 3.9 13.5 - - - +
132D LEU* 3.3 8.3 - - - +
133D PHE* 2.5 45.6 + - + +
134D GLU* 4.6 0.5 - - - +
136D LEU* 4.4 9.1 - - + +
251D LYS 3.0 16.7 + - - +
252D ARG* 3.0 33.1 + - - +
253D LEU 3.2 0.2 - - - -
254D VAL* 1.3 76.8 - - - +
256D HIS* 1.3 58.6 + - - +
257D LYS* 3.2 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN* 3.2 42.2 - - + +
122D ASP* 4.0 27.1 + - + +
126D ASN 4.9 3.0 + - - -
127D ALA* 4.0 23.2 - - + +
130D LYS* 3.1 35.6 + - - -
252D ARG 3.1 14.0 + - - +
253D LEU* 2.9 16.1 + - + +
255D GLU* 1.3 75.7 + - - +
257D LYS* 1.3 72.1 + - - +
258D LYS* 3.7 16.9 - - + +
----------------------------------------------------------
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