Contacts of the helix formed by residues 223 - 243 (chain A) in PDB entry 3J8B
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 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASN 3.7 3.1 - - - +
222A ASN* 1.3 70.0 - - - +
224A GLU* 1.3 60.0 + - - +
226A GLN* 3.3 6.5 + - + +
227A SER* 2.8 31.8 + - - -
264A LYS* 4.8 11.9 - - + +
265A LYS* 4.3 28.3 - - + +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASN* 3.4 2.8 - - + +
223A PRO* 1.3 78.3 - - - +
225A SER* 1.3 63.1 + - - +
227A SER* 3.2 6.9 + - - -
228A MET* 3.1 24.4 + - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 5.9 8.3 - - - -
218A ILE* 5.6 5.2 - - - -
219A ASN* 3.4 30.5 - - - -
220A LEU* 5.2 1.3 - - - -
222A ASN* 3.5 10.1 + - - +
223A PRO 3.3 0.2 - - - -
224A GLU* 1.3 79.3 - - - +
226A GLN* 1.3 61.8 + - - +
228A MET* 3.5 5.9 + - - +
229A HIS* 3.2 20.8 + - - +
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Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 4.9 11.2 - - - +
222A ASN 3.2 10.6 + - - +
223A PRO* 3.8 8.1 - - + +
224A GLU 3.3 0.2 - - - -
225A SER* 1.3 76.6 - - - +
227A SER* 1.3 57.4 + - - +
229A HIS* 3.1 7.1 + - - +
230A LEU* 2.7 39.3 + - + +
259A LEU* 5.6 3.5 - - + +
262A LEU* 5.5 4.7 - - + +
263A SER* 5.0 18.8 - - - +
264A LYS 5.7 1.1 - - - +
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Residues in contact with SER 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO 2.8 22.3 + - - -
224A GLU* 3.2 8.7 + - - -
226A GLN* 1.3 72.6 - - - +
228A MET* 1.3 57.6 + - - +
230A LEU* 3.9 5.4 - - - +
231A GLU* 3.0 28.9 + - - +
265A LYS* 5.6 9.0 - - - -
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Residues in contact with MET 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 5.4 6.7 - - + +
172A ARG* 6.3 0.7 - - - -
175A HIS* 4.3 26.0 - - + +
224A GLU 3.1 15.5 + - - +
225A SER* 3.7 6.5 - - - +
227A SER* 1.3 75.1 - - - +
229A HIS* 1.3 65.5 + - - +
231A GLU* 3.2 8.5 + - - +
232A THR* 3.1 21.1 + - - -
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Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A SER 3.2 11.2 + - - +
226A GLN* 3.1 10.2 + - - +
228A MET* 1.3 78.6 - - - +
230A LEU* 1.3 62.9 + - - +
232A THR* 3.2 9.6 + - - -
233A ARG* 3.1 21.5 + - - +
259A LEU* 5.6 4.5 - - + -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 2.7 21.9 + - + +
227A SER* 4.0 5.4 - - - +
229A HIS* 1.3 70.6 - - - +
231A GLU* 1.3 60.2 + - - +
232A THR 3.3 0.2 + - - -
233A ARG* 3.3 4.6 + - - +
234A LEU* 2.9 30.5 + - - +
256A ILE* 5.9 1.2 - - - +
259A LEU* 4.4 24.8 - - + +
260A PHE* 5.6 1.6 - - - +
263A SER* 5.8 5.6 - - - -
267A PRO* 6.6 0.2 - - + -
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A SER 3.0 19.9 + - - +
228A MET* 3.3 9.0 - - - +
230A LEU* 1.3 77.6 - - - +
232A THR* 1.3 60.6 + - - +
234A LEU* 3.5 7.8 + - - +
235A VAL* 3.3 20.4 + - - +
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A HIS* 5.8 3.8 - - - -
178A ALA* 4.8 18.8 - - - -
228A MET 3.1 11.9 + - - -
229A HIS* 3.4 11.2 - - - -
230A LEU 3.2 0.2 - - - -
231A GLU* 1.3 74.4 - - - +
233A ARG* 1.3 61.6 + - - +
235A VAL* 3.0 9.4 + - - +
236A GLN* 2.9 25.9 + - - +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A HIS 3.1 9.7 + - - +
230A LEU* 3.3 8.5 + - - +
232A THR* 1.3 75.8 - - - +
234A LEU* 1.3 66.8 + - - +
236A GLN* 3.1 11.6 + - + +
237A LEU* 3.0 21.7 + - - +
252A ALA 4.8 4.6 - - - +
255A ASP* 4.7 11.0 - - + +
256A ILE* 4.4 26.2 - - - +
259A LEU* 5.7 2.5 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU 2.9 17.5 + - - +
231A GLU* 3.5 10.3 - - - +
232A THR 3.2 0.2 - - - -
233A ARG* 1.3 74.7 - - - +
235A VAL* 1.3 61.5 + - - +
237A LEU* 3.3 9.1 + - - +
238A ASP* 3.1 19.4 + - - +
256A ILE* 5.1 7.2 - - - +
271A LEU* 5.2 15.7 - - + +
275A TYR* 5.6 10.3 - - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLN* 6.1 4.9 - - + -
182A PHE* 5.3 12.5 - - + +
231A GLU 3.3 9.7 + - - +
232A THR* 3.0 11.3 + - - +
234A LEU* 1.3 76.3 - - - +
236A GLN* 1.3 61.8 + - - +
238A ASP* 3.0 8.6 + - - +
239A SER* 2.9 32.1 + - - -
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PHE* 5.8 3.3 - - - +
198A CYS* 5.8 8.3 - - + -
232A THR 2.9 13.4 + - - +
233A ARG* 3.2 14.8 - - - +
235A VAL* 1.3 77.2 - - - +
237A LEU* 1.3 62.2 + - - +
239A SER* 3.6 4.1 + - - -
240A ALA* 3.1 24.4 + - - +
252A ALA* 4.4 12.7 - - + +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ARG 3.0 11.3 + - - +
234A LEU* 3.6 10.3 - - - +
235A VAL 3.2 0.2 - - - -
236A GLN* 1.3 76.8 - - - +
238A ASP* 1.3 62.6 + - - +
240A ALA* 3.3 5.7 + - - +
241A ILE* 3.1 22.7 + - - +
249A ALA* 4.9 6.3 - - + +
252A ALA* 4.1 23.0 - - + +
253A VAL* 5.1 4.3 - - + +
256A ILE* 5.7 3.4 - - + -
275A TYR* 6.4 2.9 - - + -
278A LYS* 5.2 10.3 - - + +
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU 3.1 12.6 + - - +
235A VAL* 3.0 12.0 + - - +
237A LEU* 1.3 76.7 - - - +
239A SER* 1.3 62.4 + - - +
241A ILE* 3.2 8.7 + - - +
242A SER* 3.1 22.0 + - - -
278A LYS* 5.3 7.6 - - + -
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PHE* 4.8 20.4 - - - -
185A CYS* 6.1 2.5 - - - -
186A LEU* 4.9 13.8 - - - +
194A PHE* 6.3 2.5 - - - -
235A VAL 2.9 18.1 + - - -
236A GLN* 4.2 5.2 - - - -
238A ASP* 1.3 72.4 - - - +
240A ALA* 1.3 53.6 + - - +
242A SER* 3.1 8.1 + - - -
243A MET* 2.8 38.3 + - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN 3.1 19.9 + - - +
237A LEU 3.3 6.1 - - - +
238A ASP 3.2 0.2 - - - -
239A SER* 1.3 77.4 - - - +
241A ILE* 1.3 59.7 + - - +
243A MET* 3.4 2.3 + - - -
244A GLU 3.2 3.1 + - - -
245A LEU* 3.0 37.9 + - - +
248A GLU* 4.3 6.7 - - + +
249A ALA* 3.5 34.1 - - + +
252A ALA* 5.2 1.1 - - + -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU 3.1 9.3 + - - +
238A ASP* 3.2 9.2 + - - +
240A ALA* 1.3 79.1 - - - +
242A SER* 1.3 58.7 + - - +
244A GLU* 3.0 20.0 + - - +
245A LEU 5.9 0.2 - - - -
246A TRP* 6.3 0.4 - - - +
249A ALA* 4.5 8.3 - - + +
278A LYS* 4.9 19.7 - - + +
281A THR* 5.5 8.1 - - - -
282A VAL* 6.1 2.7 - - + +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.8 6.1 - - - -
238A ASP 3.1 12.6 + - - -
239A SER* 3.1 10.5 + - - -
241A ILE* 1.3 78.1 - - - +
243A MET* 1.3 57.8 + - - +
244A GLU* 3.2 2.2 + - - +
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU* 6.2 4.5 - - - -
189A THR* 6.4 2.9 - - - -
191A LYS* 5.2 16.5 - - + +
194A PHE* 6.3 3.4 - - + -
239A SER* 2.8 16.9 + - - +
240A ALA* 4.1 4.0 - - - +
241A ILE 3.2 0.2 - - - -
242A SER* 1.3 76.2 - - - +
244A GLU* 1.3 69.8 + - - +
245A LEU* 3.0 10.8 + - + +
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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
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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) + - + + + + + -
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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