Contacts of the helix formed by residues 226 - 244 (chain A) in PDB entry 3JCK
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 ASP 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ARG* 4.2 13.6 - - - +
177A ASN* 2.8 34.8 - - + +
178A LEU* 3.3 18.3 + - - +
221A ALA* 3.8 7.2 + - + +
224A LYS* 3.3 6.6 - - + +
225A HIS* 1.3 74.5 - - - +
227A ASN* 1.3 67.4 + - - +
228A GLU* 3.5 11.6 + - - +
229A THR* 2.9 16.8 + - - +
230A LYS* 3.1 25.2 + - - +
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Residues in contact with ASN 227 (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 HIS* 3.8 7.1 + - - +
226A ASP* 1.3 75.0 + - - +
228A GLU* 1.3 65.7 + - - +
230A LYS* 3.2 12.3 + - - +
231A ALA* 2.9 21.8 + - - +
260A PRO* 3.4 30.8 - - + +
262A THR* 4.7 5.9 - - - +
263A ASP* 3.1 53.2 + - + +
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Residues in contact with GLU 228 (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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178A LEU* 3.4 32.3 - - + -
181A ALA* 5.0 7.6 - - + -
226A ASP* 3.4 3.1 + - - +
227A ASN* 1.3 81.2 - - - +
229A THR* 1.3 62.8 + - - +
231A ALA* 3.2 4.8 + - - +
232A MET* 2.9 24.7 + - - +
263A ASP 3.8 3.2 + - - +
264A VAL* 3.2 27.0 + - - -
265A SER* 2.9 31.4 - - - -
268A LEU* 3.2 19.6 - - + +
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Residues in contact with THR 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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177A ASN* 2.0 50.8 - - - +
178A LEU* 3.3 8.1 - - - +
180A ASN* 3.4 11.4 - - - +
181A ALA* 3.8 14.6 - - + +
184A TRP* 6.0 0.8 - - - -
221A ALA* 4.6 8.5 - - - +
226A ASP* 2.9 25.5 + - - +
228A GLU* 1.3 74.7 - - - +
230A LYS* 1.3 67.2 + - - +
232A MET* 3.6 1.3 - - - +
233A LEU* 2.9 23.8 + - - +
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Residues in contact with LYS 230 (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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218A LEU* 4.7 9.4 - - + +
221A ALA* 3.9 22.0 - - + +
222A SER* 3.5 35.5 + - - +
225A HIS* 4.5 9.1 + - - +
226A ASP 3.1 25.8 + - - +
227A ASN* 3.2 17.4 + - - +
229A THR* 1.3 80.2 + - - +
231A ALA* 1.3 66.8 + - - +
233A LEU* 2.9 17.5 + - - +
234A ILE* 2.9 22.5 + - + +
258A GLU* 5.1 6.5 + - - -
260A PRO* 3.6 31.7 - - + +
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Residues in contact with ALA 231 (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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227A ASN 2.9 11.4 + - - +
228A GLU* 3.7 5.6 - - - +
230A LYS* 1.3 76.0 - - - +
232A MET* 1.3 63.5 + - - +
234A ILE* 3.3 4.3 + - - +
235A ASN* 2.9 32.2 + - - +
259A TYR* 3.2 38.4 - - + +
260A PRO* 3.6 15.2 - - + +
264A VAL* 5.4 5.2 - - + -
268A LEU* 5.2 6.5 - - + -
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Residues in contact with MET 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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181A ALA* 3.7 41.1 - - + +
182A LYS* 4.9 8.1 - - + +
184A TRP* 4.8 2.2 - - + -
185A PHE* 3.7 37.0 - - + +
228A GLU 2.9 17.4 + - - +
229A THR 3.6 4.7 - - - +
231A ALA* 1.3 75.2 - - - +
233A LEU* 1.3 64.6 + - - +
235A ASN* 3.0 15.3 + - - +
236A LEU* 2.9 35.0 + - + +
268A LEU* 3.6 36.6 - - + +
271A ARG* 5.9 0.7 - - - -
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Residues in contact with LEU 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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184A TRP* 5.0 10.1 - - + -
214A MET* 3.1 66.2 - - + +
217A PHE* 3.6 24.9 - - + +
218A LEU* 3.5 28.7 - - + +
221A ALA* 5.6 2.0 - - + -
229A THR 2.9 17.1 + - - +
230A LYS* 2.9 9.0 + - - +
232A MET* 1.3 74.3 - - - +
234A ILE* 1.3 63.7 + - - +
236A LEU* 2.9 20.8 + - + +
237A ILE* 3.0 16.1 + - + +
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Residues in contact with ILE 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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218A LEU* 3.6 25.1 - - + -
230A LYS* 2.9 23.1 + - + +
231A ALA* 3.4 8.3 - - - +
233A LEU* 1.3 73.9 - - - +
235A ASN* 1.3 67.5 + - - +
237A ILE* 3.0 14.5 - - - +
238A LEU* 2.9 36.3 + - + +
253A PHE* 4.4 4.7 - - + -
257A LEU* 3.9 34.5 - - + -
258A GLU 4.9 4.0 - - - +
259A TYR* 4.3 11.2 - - + -
260A PRO* 4.0 26.0 - - + -
272A TYR* 5.2 2.2 - - + -
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Residues in contact with ASN 235 (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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231A ALA 2.9 19.7 + - - +
232A MET* 3.2 8.7 - - - +
234A ILE* 1.3 77.2 - - - +
236A LEU* 1.3 65.8 + - + +
238A LEU* 3.2 9.7 + - - +
239A ARG* 2.9 25.0 + - - +
259A TYR* 4.5 3.3 + - - -
268A LEU* 3.4 47.2 + - - +
271A ARG* 4.1 8.4 - - + +
272A TYR* 3.9 29.2 - - - +
275A TYR* 4.1 13.8 - - + -
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Residues in contact with LEU 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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184A TRP* 3.4 42.6 - - + +
185A PHE* 4.0 20.9 - - + +
188A TYR* 4.0 30.6 - - + -
214A MET* 3.4 21.8 - - + -
232A MET* 2.9 26.4 + - + +
233A LEU* 2.9 11.8 + - + +
235A ASN* 1.3 78.6 - - + +
237A ILE* 1.3 58.1 + - - +
239A ARG* 3.3 11.8 + - - +
240A ASP* 2.9 24.6 + - - +
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Residues in contact with ILE 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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211A ARG* 4.5 17.9 - - + +
214A MET* 3.5 45.3 - - + -
215A MET* 5.0 3.8 - - + -
218A LEU* 5.0 5.2 - - + -
233A LEU* 3.0 11.3 + - + +
234A ILE* 3.0 24.5 - - - +
236A LEU* 1.3 71.5 - - - +
238A LEU* 1.3 75.0 + - + +
240A ASP* 2.9 10.2 + - + +
241A PHE* 2.9 40.4 + - + -
253A PHE* 3.3 41.5 - - + -
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Residues in contact with LEU 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 ILE* 2.9 31.5 + - + +
235A ASN* 3.5 10.8 - - - +
237A ILE* 1.3 77.0 - - + +
239A ARG* 1.3 64.5 + - - +
241A PHE* 2.8 23.1 + - + +
242A LEU* 3.0 17.6 + - + +
250A ALA* 4.0 23.3 - - + -
253A PHE* 4.2 8.7 - - + -
254A ILE* 3.9 32.1 - - + -
272A TYR* 4.6 16.4 - - + -
275A TYR* 4.5 24.9 - - + -
276A LEU* 5.5 2.5 - - - +
279A ILE* 6.4 2.7 - - + -
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Residues in contact with ARG 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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188A TYR* 3.8 10.1 - - - +
189A LEU* 5.8 0.4 - - - +
192A GLU* 2.9 35.1 + - - -
196A ARG* 5.3 1.8 - - - +
235A ASN 2.9 13.2 + - - +
236A LEU* 3.5 15.9 - - - +
238A LEU* 1.3 75.9 - - - +
240A ASP* 1.3 52.6 + - - +
242A LEU* 3.4 3.8 + - - +
243A ASN* 2.2 48.4 + - - +
275A TYR* 2.4 55.0 + - + +
37I ASP* 3.2 44.3 + - - +
38I PHE* 4.0 18.4 - - - -
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Residues in contact with ASP 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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188A TYR* 3.0 27.4 + - + +
207A ASN* 5.1 14.4 - - - +
210A LEU* 5.6 2.4 - - - +
211A ARG* 2.4 47.3 + - - +
214A MET* 6.2 0.9 - - - -
236A LEU 2.9 12.6 + - - +
237A ILE* 2.9 14.5 + - + +
239A ARG* 1.3 74.8 - - - +
241A PHE* 1.3 65.5 + - - +
243A ASN* 3.1 4.9 + - - +
244A ASN* 2.8 33.1 + - - +
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Residues in contact with PHE 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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211A ARG* 3.2 39.3 - - + -
215A MET* 5.3 4.9 - - - -
237A ILE* 2.9 50.2 + - + -
238A LEU* 2.8 12.6 + - + +
240A ASP* 1.3 72.7 - - - +
242A LEU* 1.3 59.7 + - + +
244A ASN* 2.9 30.0 - - - +
246A GLU* 3.2 38.9 + - + +
249A SER* 3.3 28.5 - - - -
250A ALA* 3.7 27.6 - - + -
253A PHE* 4.5 14.6 - + - -
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Residues in contact with LEU 242 (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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238A LEU* 3.0 20.1 + - + +
239A ARG* 4.1 5.8 - - - +
241A PHE* 1.3 83.5 - - + +
243A ASN* 1.3 57.8 + - - +
244A ASN 2.8 15.8 - - - +
245A GLY 5.7 0.2 - - - -
246A GLU 4.1 13.0 - - - +
247A VAL* 5.0 6.7 - - + -
250A ALA* 4.7 3.8 - - + -
275A TYR* 4.5 17.3 - - + -
278A LYS* 3.6 40.0 + - + +
279A ILE* 3.4 35.0 - - + -
282A ILE* 5.3 2.9 - - + -
375A ASP* 5.2 4.1 - - - +
127H GLN* 5.9 0.9 + - - -
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Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR* 2.8 20.7 + - - +
192A GLU* 2.9 29.0 + - + +
196A ARG* 4.1 6.6 + - - -
239A ARG* 2.2 50.7 + - - +
240A ASP* 3.6 6.3 - - - +
242A LEU* 1.3 73.9 - - - +
244A ASN* 1.3 67.8 + - - +
131H LYS* 3.8 10.6 - - - +
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Residues in contact with ASN 244 (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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207A ASN* 5.7 5.7 + - - +
211A ARG* 2.4 34.1 + - - +
240A ASP* 2.8 21.7 + - - +
241A PHE* 2.9 18.2 - - - +
242A LEU* 2.8 20.4 - - - +
243A ASN* 1.3 79.8 - - - +
245A GLY* 1.3 59.0 + - - +
246A GLU* 4.0 12.8 - - + +
127H GLN* 5.4 2.1 + - - +
131H LYS* 3.5 21.9 - - - +
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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
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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