Contacts of the helix formed by residues 222 - 240 (chain A) in PDB entry 4B92
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 GLU 222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 1.3 72.6 - - - +
223A GLU* 1.3 64.1 + - - +
224A LEU 3.1 0.4 - - - -
225A GLU* 3.0 4.9 + - - +
226A ALA* 2.9 23.1 + - - +
250A SER* 3.5 24.4 + - - -
251A ILE* 3.7 9.8 + - - +
252A SER* 2.3 44.4 + - - +
301A ARG* 3.4 35.1 - - - +
303A ASP* 5.2 6.8 - - - +
306A THR* 5.0 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 6.4 0.2 - - - -
221A PRO* 2.8 26.8 + - + +
222A GLU* 1.3 80.4 - - + +
224A LEU* 1.3 66.8 + - + +
226A ALA* 3.6 7.4 - - - +
227A GLU* 2.9 32.5 + - - +
252A SER* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 4.5 4.9 - - - +
194A ASN* 3.2 28.3 + - + +
197A LEU* 3.2 45.5 - - + +
198A VAL* 3.6 40.6 - - + +
219A SER 4.0 2.7 - - - +
220A ARG* 3.9 18.8 - - - -
221A PRO* 2.9 21.0 + - + +
223A GLU* 1.3 87.8 - - + +
225A GLU* 1.3 59.9 + - - +
227A GLU* 4.4 3.1 - - + -
228A ALA 3.3 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA 3.4 21.3 - - - +
193A GLU* 4.4 6.8 - - + +
221A PRO 4.1 0.2 + - - -
222A GLU 3.0 9.7 + - - +
224A LEU* 1.3 77.2 - - - +
226A ALA* 1.3 65.7 + - - +
227A GLU 3.2 0.2 + - - -
228A ALA 3.3 0.5 + - - -
229A THR* 2.8 33.0 + - - +
246A VAL 5.5 0.2 - - - +
247A ASN 4.0 1.2 - - - +
248A VAL* 3.4 10.0 - - - +
249A SER* 2.4 51.6 + - - -
250A SER* 3.2 7.3 + - - -
253A ALA* 3.3 22.7 - - + +
298A PRO* 4.1 9.7 - - + +
301A ARG* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU 2.9 9.5 + - - +
223A GLU* 3.6 8.1 - - - +
225A GLU* 1.3 76.8 - - - +
227A GLU* 1.3 57.6 + - - +
229A THR* 3.6 2.0 - - - -
230A HIS* 3.0 30.3 + - - +
252A SER* 3.4 35.9 - - - +
253A ALA* 4.0 12.5 - - - +
256A VAL* 3.7 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN* 2.7 40.4 + - + +
197A LEU* 5.6 4.3 - - + -
223A GLU 2.9 18.8 + - - +
224A LEU* 3.8 7.4 - - + +
226A ALA* 1.3 72.7 - - - +
228A ALA* 1.3 69.0 + - - +
230A HIS* 3.0 8.2 + - - +
231A ARG* 2.9 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 3.5 23.3 - - + +
192A ALA* 3.5 16.2 - - - +
193A GLU* 3.3 35.4 - - - +
194A ASN 3.4 3.4 - - - +
224A LEU 3.3 1.6 + - - +
225A GLU 3.3 1.8 + - - -
227A GLU* 1.3 85.9 + - - +
229A THR* 1.3 57.8 + - - +
231A ARG* 3.1 5.0 + - - +
232A VAL* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ALA* 3.4 20.8 + - - +
225A GLU* 2.8 32.5 + - - +
226A ALA* 3.6 5.4 - - - -
228A ALA* 1.3 77.1 - - - +
230A HIS* 1.3 63.3 + - - +
232A VAL* 3.4 3.8 - - - +
233A ILE* 3.2 27.9 + - + +
245A LEU* 4.0 10.6 - - + +
248A VAL* 6.1 0.3 - - - +
253A ALA* 4.1 7.4 - - - +
256A VAL* 3.7 20.4 - - + -
257A ILE* 3.9 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 3.0 18.8 + - - +
227A GLU* 3.0 6.2 + - - +
229A THR* 1.3 77.4 - - - +
231A ARG* 1.3 60.8 + - - +
233A ILE* 3.5 6.8 + - + +
234A THR* 3.0 30.8 + - - -
256A VAL* 3.5 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 3.3 32.7 + - + +
168A MET* 6.0 6.1 - - - +
169A LEU 5.6 1.8 + - - -
171A ASP* 2.4 49.8 + - - +
174A LEU* 5.0 0.6 - - - +
194A ASN* 3.8 18.7 - - - +
195A GLY 5.1 1.0 - - - +
227A GLU* 2.9 43.1 + - - +
228A ALA* 3.4 12.0 - - - +
230A HIS* 1.3 78.2 - - - +
232A VAL* 1.3 58.0 + - - +
234A THR* 3.1 9.3 + - - -
235A ILE* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 3.7 20.1 - - + +
174A LEU* 4.5 11.7 - - + -
178A LEU* 4.5 8.5 - - + -
190A VAL* 3.8 20.2 - - + -
192A ALA* 4.4 1.3 - - + -
228A ALA 2.9 13.7 + - - +
229A THR* 3.4 17.0 - - - +
231A ARG* 1.3 71.8 - - - +
233A ILE* 1.3 63.9 + - + +
235A ILE* 4.2 8.1 - - + -
236A ALA* 2.9 31.9 + - - +
243A ILE* 3.8 26.5 - - + -
245A LEU* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 3.2 33.5 + - + +
230A HIS* 3.6 8.7 - - + +
232A VAL* 1.3 79.6 - - + +
234A THR* 1.3 59.2 + - - +
236A ALA* 3.6 5.0 - - - +
237A ASN* 2.8 28.2 + - - +
243A ILE* 4.2 9.3 - - + +
245A LEU* 4.1 14.4 - - + -
256A VAL* 4.0 10.8 - - + -
257A ILE* 4.4 4.3 - - - -
260A ALA* 3.8 33.4 - - + -
265A LYS* 4.0 16.2 - - + +
267A VAL* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A HIS* 3.0 27.6 + - - -
231A ARG* 3.1 10.8 + - - -
233A ILE* 1.3 78.2 - - - +
235A ILE* 1.3 67.9 + - - +
237A ASN* 3.2 6.8 + - + +
238A ARG* 2.8 40.4 + - + +
265A LYS* 5.6 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 3.9 33.0 - - + +
174A LEU* 4.0 22.7 - - + -
175A TYR* 3.8 37.5 - - + +
178A LEU* 3.8 13.5 - - + -
231A ARG* 3.0 23.8 + - + +
232A VAL* 3.7 12.1 - - - +
234A THR* 1.3 77.1 - - - +
236A ALA* 1.3 52.0 - - - +
238A ARG* 3.0 11.4 + - - +
239A THR* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 3.6 12.6 - - + -
232A VAL 2.9 19.4 + - - +
233A ILE 3.6 4.0 - - - +
235A ILE* 1.3 75.4 - - - +
237A ASN* 1.3 53.3 + - - +
239A THR* 3.0 10.0 + - - -
240A HIS 2.7 31.9 + - - -
241A CYS 3.0 27.4 + - - +
243A ILE* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE 2.8 21.5 + - - +
234A THR* 3.6 6.3 - - - +
236A ALA* 1.3 74.2 - - - +
238A ARG* 1.3 70.1 + - + +
240A HIS* 3.6 17.4 + - - +
241A CYS 5.2 0.4 - - - -
265A LYS* 3.4 51.1 - - + +
266A VAL 4.8 1.7 + - - -
478A ARG* 4.7 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 4.3 19.9 + - + +
234A THR* 2.8 32.4 + - + +
235A ILE* 3.0 10.3 + - - +
237A ASN* 1.3 87.1 + - - +
239A THR* 1.3 60.5 + - - +
240A HIS* 3.2 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.3 63.9 - - + +
178A LEU* 3.4 13.0 - - + +
179A HIS* 4.1 20.2 + - + +
182A LYS* 3.1 20.3 - - - +
235A ILE 2.8 16.8 + - - +
236A ALA* 3.0 16.6 + - - -
238A ARG* 1.3 70.3 - - - +
240A HIS* 1.3 70.3 + - - +
241A CYS* 3.2 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LYS* 3.8 18.0 - - - +
236A ALA 2.7 11.9 + - - -
237A ASN* 3.6 12.3 + - - +
238A ARG 3.2 23.1 + - - -
239A THR* 1.3 75.8 - - - +
241A CYS* 1.3 57.4 + - - -
475A LEU* 3.5 31.2 - - + +
478A ARG* 6.1 2.8 - - - +
479A GLU* 3.3 39.4 + - + +
482A LEU 4.9 9.6 - - - -
----------------------------------------------------------
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