Contacts of the helix formed by residues 222 - 236 (chain A) in PDB entry 1JD7
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ASP 4.3 3.3 - - - +
220A VAL 3.3 0.6 + - - -
221A THR* 1.3 69.4 - - - +
223A PHE* 1.3 62.1 + - - +
224A LYS* 3.1 44.4 + - - +
225A TYR* 3.1 28.4 + - + +
226A SER 4.1 1.4 + - - -
249A GLY 4.9 0.2 - - - +
250A PHE* 3.4 11.1 - - + -
251A MET* 2.9 47.4 + - + +
256A ALA* 3.9 16.6 - - + -
257A VAL 3.0 14.8 + - - +
258A VAL* 4.5 5.0 - - + -
259A PHE* 5.0 3.6 + - - -
296A TYR* 4.0 11.9 - - + +
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLU* 4.0 13.2 - - + -
201A VAL 3.5 16.3 + - - -
202A ILE* 3.6 41.7 - - + -
203A ASP 4.6 4.6 - - - +
204A GLN* 3.3 22.4 + - - +
221A THR* 3.3 29.5 + - + -
222A GLU* 1.3 72.5 + - - +
224A LYS* 1.3 64.6 + - - +
225A TYR 3.1 0.4 - - - -
226A SER* 3.4 5.7 + - - +
227A THR* 3.2 17.8 + - - -
259A PHE* 3.8 28.3 - + - -
262A ASN* 3.9 25.4 - - - -
264A ASP* 5.5 0.7 - - + -
265A ASN* 4.4 8.3 - - + -
269A HIS 5.5 1.6 - - - -
270A GLY 4.1 16.6 - - - -
900A CL 4.3 5.6 - - + -
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASP* 3.2 29.8 + - - +
204A GLN* 3.9 33.9 - - - +
205A GLY* 4.3 4.3 - - - +
222A GLU* 3.1 23.0 + - - +
223A PHE* 1.3 75.0 - - - +
225A TYR* 1.3 56.4 + - - +
227A THR 4.6 0.2 - - - +
228A GLU* 2.7 43.8 + - + +
248A TRP 5.2 2.2 + - - +
249A GLY* 3.2 21.7 + - - +
250A PHE* 3.5 30.7 - - + +
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Residues in contact with TYR 225 (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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222A GLU* 3.1 18.0 + - + +
223A PHE 3.1 0.4 - - - -
224A LYS* 1.3 79.7 - - - +
226A SER* 1.3 56.8 + - - +
229A LEU* 2.8 58.0 + - + +
244A PHE* 3.5 27.0 - + - -
250A PHE* 3.8 13.2 - + + -
258A VAL* 3.4 34.0 - - + +
259A PHE 3.7 11.7 - - - +
290A PHE* 4.3 7.3 - - - -
291A MET* 3.0 48.2 + - + +
294A TYR* 4.7 3.3 - + - +
296A TYR* 3.5 32.6 + + + +
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU 4.1 1.0 + - - -
223A PHE* 3.4 9.9 + - - -
224A LYS 3.4 0.4 - - - -
225A TYR* 1.3 79.0 - - - +
227A THR* 1.3 62.9 + - - +
229A LEU* 4.0 2.4 - - - +
230A GLY* 3.1 19.9 + - - -
259A PHE* 3.4 38.8 + - - -
260A VAL* 2.7 24.7 + - - +
265A ASN* 3.1 23.1 + - - -
275A VAL* 3.8 7.6 - - - +
276A ILE 5.4 0.2 + - - -
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Residues in contact with THR 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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204A GLN* 3.6 31.0 + - - +
223A PHE 3.2 10.6 + - - -
224A LYS 4.1 0.7 - - - -
226A SER* 1.3 76.7 - - - +
228A GLU* 1.3 70.9 + - - +
230A GLY* 3.3 1.4 + - - -
231A ASN* 2.9 28.8 + - + +
265A ASN* 5.5 0.7 + - - -
270A GLY 4.8 1.2 + - - -
271A GLY* 4.7 8.7 - - - -
272A ALA 5.1 0.9 + - - +
274A ASN* 4.1 21.4 + - - +
275A VAL* 4.3 16.8 - - - +
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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
----------------------------------------------------------
204A GLN* 5.1 2.4 - - - +
224A LYS* 2.7 34.1 + - + +
227A THR* 1.3 82.4 - - + +
229A LEU* 1.3 62.0 + - - +
231A ASN* 3.8 8.6 - - - +
232A THR* 2.9 30.8 + - - -
244A PHE* 4.0 8.3 - - + -
248A TRP* 3.2 23.7 - - + -
250A PHE* 3.8 28.7 - - + -
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Residues in contact with LEU 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 TYR* 2.8 48.6 + - + +
226A SER 4.0 2.7 - - - +
228A GLU* 1.3 73.2 - - - +
230A GLY* 1.3 62.0 + - - +
232A THR* 3.4 1.8 + - - -
233A PHE* 3.0 44.4 + - + +
241A LEU* 4.2 7.4 - - + -
244A PHE* 3.8 14.9 - - + -
260A VAL* 4.4 12.3 - - + -
276A ILE* 6.0 0.2 - - + -
287A ALA* 3.9 29.6 - - + +
290A PHE* 3.5 30.7 - - + -
291A MET* 4.4 4.5 - - + -
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Residues in contact with GLY 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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226A SER 3.1 15.8 + - - -
227A THR 3.8 1.8 - - - -
229A LEU* 1.3 74.9 - - - +
231A ASN* 1.3 65.0 + - - +
233A PHE* 3.9 0.5 - - - +
234A ARG* 3.0 30.3 + - - +
260A VAL* 6.4 1.1 - - - +
274A ASN 3.3 21.1 - - - -
276A ILE* 3.8 19.1 - - - -
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Residues in contact with ASN 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 THR* 2.9 19.2 + - + +
228A GLU* 3.8 12.1 - - - +
230A GLY* 1.3 75.5 - - - +
232A THR* 1.3 59.1 + - - +
235A ASN* 2.7 61.3 + - - +
236A GLY 3.4 3.8 + - - -
240A TRP* 6.2 0.3 - - - -
274A ASN* 3.5 24.3 + - - +
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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
----------------------------------------------------------
228A GLU* 2.9 18.8 + - - -
229A LEU 3.9 3.1 - - - -
231A ASN* 1.3 78.7 + - - +
233A PHE* 1.3 61.0 + - - +
236A GLY* 2.8 31.8 + - - +
237A SER* 3.2 34.2 - - - +
238A LEU* 4.2 3.7 - - + +
240A TRP* 4.2 11.4 - - + -
241A LEU* 3.9 26.0 - - + +
248A TRP* 3.4 21.7 - - - -
367A ASN* 5.2 0.2 - - - +
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Residues in contact with PHE 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 LEU* 3.0 32.0 + - + +
232A THR* 1.3 78.0 - - - +
234A ARG* 1.3 59.4 + - - +
236A GLY 5.1 0.2 - - - +
238A LEU* 3.4 40.2 - - + -
241A LEU* 4.1 13.0 - - + -
276A ILE* 3.6 18.4 - - + -
283A LEU* 4.0 14.0 - - + +
286A LEU* 3.5 43.3 - - + -
287A ALA* 3.8 13.9 - - + -
290A PHE* 4.1 13.9 - + + -
381A ILE* 4.4 4.9 - - + -
383A LYS* 2.8 50.7 + - + -
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Residues in contact with ARG 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 GLY 3.0 15.1 + - - +
233A PHE* 1.3 80.8 - - - +
235A ASN* 1.3 76.2 + - - +
236A GLY 3.8 1.0 - - - +
273A GLY 3.4 10.2 + - - -
274A ASN* 2.9 36.7 + - - +
275A VAL 3.0 18.6 + - - -
276A ILE* 3.6 9.5 - - + +
280A ASP* 2.8 41.3 + - - -
283A LEU* 3.8 21.4 - - + +
383A LYS* 4.8 4.3 + - - -
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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 ASN* 2.7 45.3 + - - +
234A ARG* 1.3 92.5 - - - +
236A GLY* 1.3 57.9 + - - +
240A TRP* 4.8 2.8 - - - -
274A ASN* 4.5 6.1 - - - +
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Residues in contact with GLY 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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231A ASN 3.4 3.0 + - - -
232A THR* 2.8 26.5 + - - +
233A PHE 5.1 1.6 - - - +
234A ARG 5.3 0.5 - - - +
235A ASN* 1.3 76.4 - - - +
237A SER* 1.3 63.6 + - - -
240A TRP* 3.4 23.6 - - - -
366A ASN* 4.5 0.9 + - - -
367A ASN* 3.4 16.1 + - - +
383A LYS* 5.3 0.7 + - - -
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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