Contacts of the helix formed by residues 283 - 305 (chain A) in PDB entry 1J1U
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 HIS 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ARG* 4.9 0.8 - - - +
277A PHE* 4.5 0.4 - - - -
280A LYS 5.1 1.5 + - - +
281A GLU 4.0 3.0 + - - -
282A LEU* 1.4 74.9 - - - +
284A PRO* 1.3 78.4 - - + +
285A MET* 2.9 38.9 + - + +
286A ASP* 3.1 17.6 + - - +
287A LEU* 3.1 11.3 + - - +
535B G 3.3 71.1 + + + +
536B U 3.7 30.0 - + - -
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A CYS* 3.6 17.7 - - - +
233A ALA* 3.8 24.7 - - + -
277A PHE* 4.1 15.9 - - + -
282A LEU 3.9 3.8 - - - +
283A HIS* 1.3 96.7 - - + +
285A MET* 1.4 50.2 + - - +
287A LEU* 3.2 3.6 + - + +
288A LYS* 2.8 40.8 + - - +
536B U 3.1 51.6 - - + +
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Residues in contact with MET 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 2.9 16.1 + - - +
284A PRO* 1.4 76.9 - - - +
286A ASP* 1.4 59.6 + - - +
288A LYS* 3.3 7.0 + - + +
289A ASN* 2.9 47.3 + - - +
535B G 2.9 59.0 - - + +
536B U 3.0 35.6 + - - +
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ILE* 3.8 7.8 - - + +
256A LYS 4.3 3.8 - - - +
257A ARG* 3.7 31.0 + - + +
258A PRO* 3.6 15.0 - - - +
261A PHE* 4.5 1.4 - - - +
282A LEU* 4.1 15.3 - - + -
283A HIS* 3.1 12.2 + - - +
285A MET* 1.4 72.8 - - - +
287A LEU* 1.3 66.1 + - - +
289A ASN* 3.5 11.2 + - - +
290A ALA* 3.0 24.3 + - - +
535B G 2.7 47.8 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A CYS* 4.1 6.5 - - - -
241A ILE* 3.4 28.0 - - + -
242A MET* 3.6 28.0 - - + +
245A ALA* 4.5 1.1 - - + -
249A LEU* 6.2 0.2 - - + -
253A LEU* 6.3 0.9 - - + -
255A ILE* 5.3 3.4 - - + -
273A LEU* 4.1 27.1 - - + -
277A PHE* 3.9 14.6 - - + -
282A LEU* 4.2 20.7 - - + +
283A HIS 3.1 11.0 + - - +
284A PRO* 3.3 8.3 - - + +
286A ASP* 1.3 75.4 - - - +
288A LYS* 1.3 53.9 + - - +
290A ALA* 3.1 5.0 + - + +
291A VAL* 2.7 56.2 + - + +
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.2 37.9 + - + +
227A LYS* 3.0 18.2 + - - +
229A ALA 2.7 28.3 + - - -
231A CYS* 3.7 12.6 - - - -
241A ILE* 4.1 18.8 - - + -
284A PRO 2.8 20.7 + - - +
285A MET* 3.3 6.5 + - + +
287A LEU* 1.3 73.1 - - - +
289A ASN* 1.4 58.8 + - - +
292A ALA* 2.7 34.6 + - - +
536B U 3.0 31.6 + - - +
537B A 3.0 18.4 + - - -
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS 5.3 6.3 + - - +
285A MET* 2.9 39.6 + - - +
286A ASP* 3.8 14.3 + - - +
288A LYS* 1.4 78.9 - - - +
290A ALA* 1.3 62.5 + - - +
292A ALA* 4.0 3.8 - - - +
293A GLU* 3.2 33.7 + - + +
535B G 5.3 0.6 - - - +
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Residues in contact with ALA 290 (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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249A LEU* 5.0 1.1 - - + -
253A LEU* 5.2 6.3 - - + -
254A THR 5.3 2.0 - - - +
255A ILE* 4.0 34.8 - - + -
256A LYS 5.3 2.0 + - - +
286A ASP 3.0 19.2 + - - +
287A LEU* 3.5 6.5 - - + +
289A ASN* 1.3 75.2 - - - +
291A VAL* 1.3 61.6 + - + +
293A GLU* 4.1 2.1 - - - +
294A GLU* 2.9 38.5 + - + +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.3 17.9 - - + -
241A ILE* 3.8 23.3 - - + +
244A ILE* 3.6 34.1 - - + -
245A ALA* 4.4 3.6 - - + -
249A LEU* 4.2 21.7 - - + +
287A LEU* 2.7 44.4 + - + +
288A LYS* 3.9 2.2 - - - +
290A ALA* 1.3 73.8 - - + +
292A ALA* 1.3 58.9 + - - +
294A GLU* 4.0 0.2 - - - +
295A LEU* 2.7 31.5 + - + +
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Residues in contact with ALA 292 (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 ILE* 4.5 2.9 - - + -
223A ARG* 4.4 24.2 - - + -
226A ILE* 4.2 25.7 - - + +
288A LYS 2.7 22.1 + - - +
289A ASN* 4.0 4.7 - - - +
291A VAL* 1.3 75.6 - - - +
293A GLU* 1.3 62.2 + - - +
295A LEU* 3.6 3.9 - - - +
296A ILE* 2.8 37.8 + - - +
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Residues in contact with GLU 293 (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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223A ARG* 2.8 45.3 + - - +
256A LYS* 5.6 10.1 - - - +
289A ASN* 3.2 21.7 + - + +
290A ALA* 4.3 2.5 - - - +
292A ALA* 1.3 79.7 - - + +
294A GLU* 1.3 65.4 + - - +
296A ILE* 3.5 13.0 + - - +
297A LYS* 3.3 32.0 + - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.6 22.7 - - + +
250A GLU* 5.3 5.4 + - - +
253A LEU* 3.7 30.1 - - + +
254A THR 5.2 4.9 - - - +
256A LYS* 5.5 4.5 + - - -
290A ALA* 2.9 23.8 + - + +
291A VAL 4.0 0.2 - - - +
293A GLU* 1.3 75.4 - - + +
295A LEU* 1.3 64.3 + - - +
297A LYS* 3.2 24.9 + - - +
298A ILE* 3.0 32.5 + - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.1 23.8 - - + -
213A ILE* 3.8 34.5 - - + -
222A ILE* 4.1 15.5 - - + -
226A ILE* 4.7 3.6 - - + -
244A ILE* 4.0 25.4 - - + -
248A PHE* 4.8 7.4 - - + -
249A LEU* 4.6 1.1 - - + +
291A VAL 2.7 20.7 + - - +
292A ALA 3.6 3.8 - - - +
294A GLU* 1.3 71.8 - - - +
296A ILE* 1.3 65.7 + - - +
298A ILE* 3.0 14.7 + - + +
299A LEU* 2.9 49.7 + - + +
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Residues in contact with ILE 296 (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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219A PRO* 3.7 49.6 - - + +
222A ILE* 3.9 30.1 - - + -
223A ARG* 3.9 24.0 - - + +
292A ALA 2.8 24.1 + - - +
293A GLU* 3.8 17.0 - - - +
294A GLU 3.3 0.2 - - - -
295A LEU* 1.3 75.8 - - - +
297A LYS* 1.3 66.4 + - + +
299A LEU* 3.9 1.0 - - - +
300A GLU* 3.0 24.7 + - + +
303A ARG* 4.7 3.9 + - - +
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS* 6.0 2.9 - - - +
293A GLU* 3.3 17.6 + - - +
294A GLU* 3.2 29.7 + - - +
295A LEU 3.2 0.6 - - - -
296A ILE* 1.3 82.6 - - + +
298A ILE* 1.3 63.6 + - + +
300A GLU* 3.8 5.3 - - - +
301A PRO* 3.3 18.9 - - - +
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Residues in contact with ILE 298 (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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46A TYR* 4.0 32.2 + - + +
248A PHE* 3.6 29.2 - - + +
249A LEU* 4.0 18.2 - - + -
250A GLU 5.3 1.1 - - - +
294A GLU* 3.0 32.8 + - + +
295A LEU* 3.0 9.8 + - + +
297A LYS* 1.3 78.5 - - + +
299A LEU* 1.3 66.7 + - + +
301A PRO* 3.5 15.3 - - - +
302A ILE* 4.4 6.6 - - - +
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Residues in contact with LEU 299 (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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43A LEU* 4.4 9.2 - - + -
46A TYR* 4.0 22.9 - - + -
213A ILE* 4.7 1.8 - - + -
214A ALA 4.6 2.5 - - - +
215A VAL* 3.8 36.0 - - + +
222A ILE* 3.9 23.3 - - + -
295A LEU* 2.9 37.3 + - + +
296A ILE 4.3 2.0 - - - +
298A ILE* 1.3 78.1 - - - +
300A GLU* 1.3 65.2 + - - +
301A PRO 3.4 0.4 - - - -
302A ILE* 3.0 26.4 + - + +
303A ARG* 2.9 28.2 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.0 18.1 + - + +
297A LYS* 3.8 7.0 - - - +
299A LEU* 1.3 78.4 - - - +
301A PRO* 1.4 67.6 - - + +
303A ARG* 3.2 26.2 + - - +
304A LYS* 2.8 60.9 + - + +
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Residues in contact with PRO 301 (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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95A ALA 5.2 0.9 - - - -
297A LYS 3.3 15.7 - - - +
298A ILE* 3.5 14.6 - - - +
300A GLU* 1.4 96.5 - - + +
302A ILE* 1.3 61.8 + - + +
304A LYS* 3.2 20.9 - - + +
305A ARG* 3.2 37.7 + - - +
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Residues in contact with ILE 302 (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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46A TYR* 3.8 32.8 - - + +
92A VAL* 4.6 2.2 - - + -
95A ALA* 3.9 33.8 - - + +
96A MET* 3.9 21.3 - - + -
215A VAL* 4.2 25.1 - - + +
298A ILE 4.4 4.9 - - - +
299A LEU* 3.0 29.5 + - + +
300A GLU 3.0 0.6 - - - -
301A PRO* 1.3 76.5 - - + +
303A ARG* 1.3 69.8 + - - +
304A LYS 3.0 1.1 - - - -
305A ARG* 3.0 15.1 + - - +
306A LEU* 3.5 18.0 - - + +
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Residues in contact with ARG 303 (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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215A VAL 4.6 0.6 + - - -
216A ASP* 3.6 28.9 - - + +
217A ASP 3.4 25.8 + - - -
218A SER* 4.6 2.4 - - - +
219A PRO* 3.6 33.2 - - - +
222A ILE* 5.8 2.3 - - - +
296A ILE* 4.7 4.8 + - - +
299A LEU* 2.9 15.3 + - - +
300A GLU* 3.2 42.8 - - - +
302A ILE* 1.3 80.6 - - - +
304A LYS* 1.3 58.8 + - - +
306A LEU* 3.3 22.3 + - - +
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 2.8 43.9 + - + +
301A PRO* 3.2 17.7 - - + +
303A ARG* 1.3 77.9 - - - +
305A ARG* 1.3 61.9 + - + +
306A LEU 3.3 5.8 + - - +
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Residues in contact with ARG 305 (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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94A GLU 4.4 4.2 + - - -
95A ALA* 3.1 43.2 + - + +
96A MET 5.0 0.2 - - - -
97A GLY* 4.5 7.7 - - - +
301A PRO* 3.2 26.0 + - - +
302A ILE 3.0 8.0 + - - +
304A LYS* 1.3 77.7 - - + +
306A LEU* 1.3 66.3 + - - +
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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
------------------------------------------------------------
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