Contacts of the helix formed by residues 230 - 250 (chain A) in PDB entry 4CZ8
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 230 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 1.3 117.0 - - + +
231A GLU* 1.3 63.7 + - + +
232A ILE 3.3 0.2 - - - -
233A GLU* 2.9 21.2 - - - +
234A ALA* 3.5 16.8 + - + +
21B MSE 4.4 17.7 - - + -
25B ARG* 4.6 13.7 - - - +
296B THR* 4.8 5.9 - - + +
299B ALA* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY 4.4 1.7 - - - +
226A ILE* 3.7 21.4 - - + -
227A PHE 4.6 0.7 + - - -
228A ASP* 3.2 15.5 + - - +
230A PRO* 1.3 79.6 - - - +
232A ILE* 1.3 57.3 + - - +
234A ALA* 3.5 1.9 + - - +
235A PHE* 2.9 31.9 + - - +
18B VAL* 5.1 1.6 - - - +
21B MSE 4.1 15.0 - - - -
22B LEU* 3.5 25.1 - - + +
25B ARG* 2.7 41.6 + - - +
26B ARG* 2.8 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 4.4 23.6 - - + -
226A ILE* 3.5 24.2 - - + +
227A PHE 4.1 19.1 - - - +
228A ASP 4.0 5.4 + - - +
229A PHE* 4.9 0.4 - - - -
231A GLU* 1.3 76.7 - - - +
233A GLU* 1.3 78.8 + - - +
235A PHE* 3.9 3.0 - - + +
236A SER* 2.9 32.0 + - - -
286A ALA* 3.6 36.3 - - + +
287A ILE* 4.8 10.3 - - + -
289A LYS* 5.2 2.0 - - + -
290A GLU* 3.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 3.9 7.5 - - - -
230A PRO* 2.9 29.6 - - - +
232A ILE* 1.3 86.7 - - - +
234A ALA* 1.3 62.1 + - - +
236A SER* 2.3 26.8 + - - -
237A LEU* 2.9 11.5 + - - +
289A LYS* 3.6 11.1 - - - +
290A GLU* 3.9 14.4 - - - -
293A PHE* 3.8 31.9 - - + -
294A ASN* 4.5 1.6 - - - +
292B HIS* 2.9 25.4 + - - +
296B THR* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 3.5 10.1 + - + +
231A GLU* 3.5 8.4 + - - +
232A ILE 3.4 0.4 - - - -
233A GLU* 1.3 77.5 - - - +
235A PHE* 1.3 54.4 + - - +
237A LEU* 3.4 5.3 + - - +
238A SER* 2.6 37.6 + - - -
14B LEU* 4.8 0.9 - - - +
18B VAL* 3.7 19.3 - - + -
21B MSE 5.1 4.9 - - + -
296B THR* 5.1 1.3 - - + +
300B LEU* 3.7 29.8 - - + +
303B ILE* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 6.3 1.1 - - + -
217A GLY* 4.3 11.7 - - - -
220A PHE* 4.2 31.4 - + + -
221A ILE* 3.5 38.6 - - + -
226A ILE* 4.2 16.2 - - + -
231A GLU* 2.9 19.8 + - + +
232A ILE* 3.9 5.6 - - + +
234A ALA* 1.3 76.2 - - - +
236A SER* 1.3 60.3 + - - +
238A SER* 3.5 6.2 - - - -
239A LEU* 2.9 48.1 + - + +
15B PHE* 5.2 12.3 - + - -
18B VAL* 4.0 24.4 - - + +
19B ILE* 5.4 4.3 - - + -
22B LEU* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.1 10.5 - - - -
232A ILE* 2.9 17.0 + - - -
233A GLU 2.3 28.6 + - - -
235A PHE* 1.3 77.0 - - - +
237A LEU* 1.3 66.3 + - - +
239A LEU* 3.0 10.5 + - - +
240A ALA* 2.9 23.9 + - - +
265A LEU* 5.2 5.4 - - - -
290A GLU* 3.3 23.5 - - - +
294A ASN* 3.2 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 5.2 2.5 - - + -
68A ILE* 3.9 22.7 - - + -
71A PHE* 5.2 0.7 - - - -
233A GLU 2.9 11.6 + - - +
234A ALA* 3.6 4.5 - - - +
236A SER* 1.3 81.8 + - - +
238A SER* 1.3 64.9 + - - +
240A ALA* 3.3 3.6 + - + +
241A PHE* 3.0 60.9 + - + -
293A PHE* 4.2 9.4 - - + -
294A ASN* 4.1 10.5 - - - +
297A LEU* 4.5 11.7 - - + -
1424A PTY 4.9 12.6 - - + -
14B LEU* 4.0 17.9 - - + -
300B LEU* 4.1 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA 2.6 21.7 + - - -
235A PHE* 3.5 9.9 - - - -
237A LEU* 1.3 75.0 - - - +
239A LEU* 1.3 56.9 + - - +
242A LEU* 2.9 27.3 + - - +
11B PHE* 3.1 16.5 - - - -
14B LEU* 3.5 16.5 - - - +
15B PHE* 4.0 26.6 - - - -
18B VAL* 3.2 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 5.9 0.2 - - + -
213A LEU* 3.7 35.8 - - + +
216A LEU* 6.2 2.5 - - + -
217A GLY* 4.2 16.6 - - - -
221A ILE* 5.6 0.4 - - + -
235A PHE* 2.9 33.3 + - + +
236A SER* 3.0 9.4 + - - +
238A SER* 1.3 74.3 - - - +
240A ALA* 1.3 66.1 + - - +
242A LEU* 3.3 18.3 + - + +
243A GLY* 2.9 21.0 + - - -
261A THR* 4.0 16.6 - - + +
265A LEU* 4.0 29.4 - - + -
15B PHE* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 5.0 3.8 - - + -
68A ILE* 5.6 1.1 - - + -
71A PHE* 3.5 50.2 - - + -
236A SER 2.9 10.2 + - - +
237A LEU* 3.6 8.3 - - - +
239A LEU* 1.3 77.2 - - - +
241A PHE* 1.3 63.3 + - + +
243A GLY* 3.3 2.1 + - - -
244A PHE* 2.9 25.3 + - - +
258A ALA* 4.2 12.4 - - + +
261A THR* 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 5.5 1.3 - - + -
64A PHE* 3.3 45.3 - + - -
67A VAL* 3.6 33.7 - - + -
68A ILE* 4.6 7.0 - - + -
237A LEU* 3.0 54.6 + - + +
240A ALA* 1.3 74.7 - - + +
242A LEU* 1.3 61.0 + - - +
244A PHE* 3.1 9.3 + + - +
245A PHE* 2.9 52.1 + + + -
1424A PTY 4.1 26.5 - - + -
11B PHE* 3.8 18.2 - - + -
14B LEU* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 4.8 11.2 - - + -
238A SER 2.9 20.9 + - - +
239A LEU* 3.4 17.7 - - + +
241A PHE* 1.3 75.4 - - - +
243A GLY* 1.3 62.8 - - - +
245A PHE* 3.3 2.3 + - + +
246A ILE* 2.9 56.8 + - + +
11B PHE* 3.4 29.3 - - + -
15B PHE* 4.2 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 5.0 0.2 - - - +
213A LEU* 3.6 24.4 - - - +
239A LEU 2.9 14.0 + - - -
240A ALA 3.6 4.3 - - - -
242A LEU* 1.3 75.9 - - - +
244A PHE* 1.3 61.0 + - - +
246A ILE* 4.1 0.4 - - - +
247A GLY 2.9 18.9 + - - -
257A VAL* 3.3 26.7 - - - +
258A ALA 5.1 0.2 - - - -
261A THR* 5.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 4.1 25.4 - - + -
67A VAL* 3.6 30.5 - - + -
240A ALA 2.9 13.1 + - - +
241A PHE* 3.3 13.5 - + - +
243A GLY* 1.3 77.3 - - - +
245A PHE* 1.3 94.7 + + - +
248A GLU* 2.9 47.3 + - + +
254A GLY* 3.4 35.7 + - - +
255A TYR* 3.7 28.3 - + - -
258A ALA* 5.0 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 2.9 48.7 + + + +
242A LEU* 4.0 2.9 - - + +
244A PHE* 1.3 97.8 - + - +
246A ILE* 1.3 66.3 + - + +
248A GLU* 3.1 5.4 + - + +
249A ARG* 2.9 31.9 + - + +
1424A PTY 4.4 7.9 - - + -
7B ALA* 3.5 42.2 - - + -
8B GLU* 3.9 24.0 - - + +
11B PHE* 3.3 40.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.7 24.9 - - + -
213A LEU* 4.4 14.1 - - + -
242A LEU* 2.9 48.4 + - + +
243A GLY* 4.1 3.1 - - - +
245A PHE* 1.3 76.0 - - + +
247A GLY* 1.3 62.6 + - - +
249A ARG* 3.2 18.7 + - - +
250A LEU* 3.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 6.2 0.2 - - - -
209A LEU* 4.2 9.8 - - - +
243A GLY 2.9 19.2 + - - -
244A PHE 3.7 0.9 - - - -
246A ILE* 1.3 76.8 - - - +
248A GLU* 1.3 55.0 + - - +
250A LEU* 3.4 8.7 + - - +
252A ALA* 2.8 37.9 + - - +
254A GLY* 4.4 0.7 - - - -
257A VAL* 4.0 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 5.1 13.5 - - - +
177A TYR* 5.7 3.6 - - - -
244A PHE* 2.9 36.3 + - + +
245A PHE* 3.1 7.8 + - + +
247A GLY* 1.3 72.3 - - - +
249A ARG* 1.3 65.1 + - + +
250A LEU 3.1 2.5 - - - -
251A ASP* 3.2 12.8 + - - -
252A ALA 3.1 9.2 + - - +
253A SER* 3.8 3.0 - - - -
254A GLY* 2.9 25.8 + - - -
255A TYR* 4.7 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 2.9 22.9 + - - +
246A ILE* 3.2 10.9 + - - +
248A GLU* 1.3 76.9 - - + +
250A LEU* 1.3 65.7 + - + +
251A ASP 3.2 3.4 + - - -
2B ILE* 3.5 50.9 + - - +
3B GLU 5.0 2.0 + - - -
4B LEU* 5.6 4.0 - - - +
8B GLU* 3.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 5.2 0.9 - - - +
201A TYR* 3.4 23.4 + - - +
205A VAL* 4.7 15.0 - - + -
209A LEU* 4.4 19.1 - - + -
246A ILE* 3.4 20.2 - - + +
247A GLY* 3.4 7.5 + - - +
248A GLU 3.1 1.0 - - - -
249A ARG* 1.3 86.2 - - + +
251A ASP* 1.3 69.8 + - - +
252A ALA* 3.2 6.4 + - + +
----------------------------------------------------------
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