Contacts of the helix formed by residues 273 - 294 (chain A) in PDB entry 1J19
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 ARG 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 3.0 48.7 - - - +
55A TYR* 4.0 30.6 + - - -
253A LYS* 4.2 16.4 - - - +
271A ALA* 3.2 10.5 - - - +
272A PRO* 1.3 88.9 - - + +
274A LEU* 1.3 66.3 + - - +
275A ARG* 3.3 27.5 - - + +
276A ILE* 3.4 19.7 + - + +
277A ASN* 3.7 3.1 + - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 3.6 18.4 - - + -
252A ASP* 3.5 38.6 - - - +
253A LYS* 4.3 5.4 - - - +
273A ARG* 1.3 72.3 - - - +
275A ARG* 1.3 66.7 + - - +
277A ASN* 3.1 4.0 + - - +
278A LYS* 3.1 38.6 + - + +
406B ARG* 3.5 47.6 - - + +
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.2 21.4 + - - -
53A LYS* 4.4 17.1 - - - +
55A TYR* 4.2 12.3 - - - -
69A ASP* 3.5 27.1 + - - +
273A ARG* 4.0 27.7 - - + +
274A LEU* 1.3 79.6 - - - +
276A ILE* 1.3 67.9 + - + +
278A LYS* 3.4 11.6 + - - +
279A ARG* 3.1 64.1 + - - +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.8 43.1 - - + +
206A PHE* 4.1 20.1 - - + -
207A GLU 5.3 1.1 - - - +
208A ILE* 5.7 0.2 - - + -
271A ALA* 3.7 17.0 - - + -
272A PRO* 4.3 11.9 - - + -
273A ARG* 3.5 25.8 - - + +
274A LEU 3.1 0.8 - - - -
275A ARG* 1.3 80.9 - - + +
277A ASN* 1.3 58.8 + - - +
279A ARG* 3.2 13.4 + - - +
280A ILE* 2.8 47.4 + - + +
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Residues in contact with ASN 277 (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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250A PHE* 3.6 31.9 - - + +
252A ASP 2.9 23.4 + - - +
253A LYS* 3.2 25.3 + - - +
254A LYS 3.6 2.8 - - - +
255A PHE* 3.7 21.1 - - + +
269A PHE* 4.2 0.9 - - - -
271A ALA* 3.1 20.9 - - - +
273A ARG 3.7 1.6 + - - -
274A LEU 3.1 8.1 + - - +
276A ILE* 1.3 79.1 - - - +
278A LYS* 1.3 62.8 + - - +
280A ILE* 3.3 11.6 + - - +
281A LEU* 3.0 24.9 + - - +
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 3.5 29.4 - - + -
274A LEU* 3.1 36.4 + - + +
275A ARG* 3.6 13.7 - - - +
276A ILE 3.2 0.2 - - - -
277A ASN* 1.3 76.2 - - - +
279A ARG* 1.3 60.7 + - + +
281A LEU* 3.5 3.1 + - - +
282A ALA* 3.1 26.7 + - - +
405B ARG 6.0 0.9 - - - -
406B ARG* 5.8 3.8 - - - +
407B THR 5.6 2.5 - - - -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.7 4.8 + - - -
51A ASP* 3.3 29.3 + - - +
55A TYR* 3.7 21.0 - - - +
57A THR* 3.5 41.5 + - - +
69A ASP* 5.4 2.6 - - - +
206A PHE* 4.9 12.1 - - + -
275A ARG* 3.1 50.1 + - - +
276A ILE* 3.6 13.1 - - - +
278A LYS* 1.3 75.2 - - + +
280A ILE* 1.3 64.3 + - - +
282A ALA* 3.4 6.8 + - - +
283A LEU* 3.0 29.0 + - + +
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Residues in contact with ILE 280 (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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206A PHE* 3.6 37.7 - - + -
208A ILE* 4.9 2.5 - - + -
218A LEU* 3.8 21.8 - - + -
220A VAL* 4.4 1.7 - - + +
225A LEU* 5.0 0.4 - - + -
255A PHE* 3.6 22.9 - - + -
269A PHE* 4.0 17.3 - - + -
271A ALA* 4.9 0.2 - - + -
276A ILE* 2.8 40.8 + - + +
277A ASN* 3.5 19.3 - - - +
279A ARG* 1.3 77.2 - - - +
281A LEU* 1.3 57.8 + - - +
283A LEU* 3.5 2.9 + - - +
284A CYS* 3.0 38.8 + - - -
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Residues in contact with LEU 281 (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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248A ILE* 3.7 47.1 - - + +
249A SER* 4.4 1.8 - - - +
250A PHE* 3.5 26.2 - - + -
255A PHE* 4.2 10.3 - - + -
277A ASN 3.0 17.2 + - - +
278A LYS 3.8 4.0 - - - +
280A ILE* 1.3 73.6 - - - +
282A ALA* 1.3 59.6 + - - +
284A CYS* 3.5 4.4 + - - +
285A MET* 3.0 49.3 + - - +
408B GLY* 4.0 1.8 - - - -
409B THR 4.0 22.4 - - - +
410B TYR* 3.9 5.6 - - + -
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Residues in contact with ALA 282 (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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60A LYS* 5.8 5.8 - - - +
83A LYS* 5.8 4.8 + - - +
84A PHE* 5.3 0.5 - - - -
278A LYS 3.1 18.0 + - - +
279A ARG* 3.7 8.3 - - - +
280A ILE 3.3 0.2 - - - -
281A LEU* 1.3 77.0 - - - +
283A LEU* 1.3 57.0 + - - +
285A MET* 3.3 10.1 + - - +
286A GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 283 (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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58A TRP* 4.9 13.5 - - + +
83A LYS* 4.2 28.3 - - + +
84A PHE* 4.0 16.4 - - + -
204A ASN* 3.8 34.5 - - + +
206A PHE* 3.5 30.3 - - + -
220A VAL* 4.2 8.3 - - + -
279A ARG* 3.0 16.1 + - + +
280A ILE* 3.8 4.5 - - - +
282A ALA* 1.3 74.7 - - + +
284A CYS* 1.3 60.1 + - - +
286A GLY* 3.1 2.2 + - - +
287A ASN* 2.8 47.3 + - - +
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Residues in contact with CYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 3.9 16.4 - - - -
225A LEU* 3.7 37.7 - - - -
242A TRP* 3.4 15.7 - - + -
248A ILE* 3.5 26.2 - - + -
255A PHE* 4.8 0.9 - - - -
280A ILE* 3.0 31.6 + - - +
281A LEU* 3.7 3.6 - - - +
283A LEU* 1.3 75.8 - - - +
285A MET* 1.3 58.5 + - - +
287A ASN 3.3 0.2 + - - -
288A HIS* 2.8 32.2 + - - +
410B TYR* 5.4 0.2 - - - -
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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
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281A LEU* 3.0 39.3 + - + +
282A ALA* 3.6 7.9 - - - +
284A CYS* 1.3 78.9 - - + +
286A GLY* 1.3 56.9 + - - +
288A HIS* 3.9 0.7 - - - +
289A GLU* 2.9 30.1 + - - +
409B THR 5.5 1.3 - - - +
410B TYR* 3.6 61.6 + - + -
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Residues in contact with GLY 286 (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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84A PHE* 3.4 27.2 - - - -
282A ALA 2.9 14.1 + - - -
283A LEU 3.1 1.5 + - - -
285A MET* 1.3 77.8 - - - +
287A ASN* 1.3 60.0 + - - +
289A GLU* 3.6 8.8 - - - +
290A LEU* 3.4 26.9 + - - +
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Residues in contact with ASN 287 (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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83A LYS 5.3 0.6 + - - +
84A PHE* 3.5 29.7 - - - +
85A PHE 4.9 2.8 + - - +
204A ASN* 4.4 4.8 + - - +
220A VAL* 4.0 9.5 - - + +
221A ASP* 3.6 22.2 - - - +
222A ALA* 3.5 30.2 - - - +
242A TRP* 3.7 10.3 - - + -
283A LEU* 2.8 31.5 + - - +
284A CYS* 4.6 0.2 - - - -
286A GLY* 1.3 75.2 - - - +
288A HIS* 1.3 59.4 + - - +
289A GLU 3.2 0.2 - - - -
290A LEU* 3.4 5.6 + - - +
291A TYR* 3.0 27.2 + - - +
294A ARG* 5.2 0.9 + - - -
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Residues in contact with HIS 288 (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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242A TRP* 3.4 47.1 - + + +
284A CYS 2.8 17.2 + - - +
285A MET 4.1 2.9 - - - +
287A ASN* 1.3 73.2 - - - +
289A GLU* 1.3 65.7 + - - +
291A TYR* 3.1 10.5 + + - +
292A MET* 2.9 48.7 + - - +
410B TYR* 2.7 32.0 + + + +
412B VAL* 3.4 33.8 - - + +
415B ALA* 4.0 0.4 - - + -
416B TRP* 3.6 17.5 + - - -
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Residues in contact with GLU 289 (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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285A MET 2.9 20.7 + - - +
286A GLY* 3.6 9.9 - - - +
287A ASN 3.2 0.2 - - - -
288A HIS* 1.3 76.7 - - - +
290A LEU* 1.3 70.5 + - - +
292A MET* 3.3 20.6 + - + +
293A ARG* 2.9 36.6 + - - +
410B TYR* 5.2 0.4 + - - -
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Residues in contact with LEU 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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43A TRP* 3.7 33.9 - - + +
44A PHE* 4.6 8.5 - - + -
84A PHE* 3.6 34.8 - - + -
286A GLY 3.4 14.1 + - - +
287A ASN* 4.0 4.9 - - - +
288A HIS 3.3 0.2 - - - -
289A GLU* 1.3 86.0 - - - +
291A TYR* 1.3 64.7 + - - +
292A MET 3.2 0.7 - - - -
293A ARG* 3.6 28.4 - - - +
294A ARG* 3.0 50.8 + - - +
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Residues in contact with TYR 291 (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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87A GLU* 3.4 18.4 - - - -
222A ALA 3.6 8.3 - - - +
223A LEU* 4.1 13.5 - - + -
242A TRP* 3.3 41.1 - + + +
243A SER* 5.3 9.5 + - - -
287A ASN 3.0 18.2 + - - +
288A HIS* 3.1 16.4 + + - +
290A LEU* 1.3 77.5 - - - +
292A MET* 1.3 66.2 + - + +
294A ARG* 3.7 11.0 - - - +
295A ARG* 2.9 64.8 + - - +
416B TRP* 4.8 17.2 - + - -
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Residues in contact with MET 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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288A HIS* 2.9 53.0 + - + +
289A GLU* 3.6 19.1 - - + +
291A TYR* 1.3 80.5 - - + +
293A ARG* 1.3 63.8 - - - +
295A ARG* 3.0 17.6 + - - +
296A LYS* 3.4 36.5 + - - +
410B TYR* 4.1 2.9 - - - +
415B ALA* 3.7 30.5 - - + +
416B TRP* 3.9 18.8 - - + +
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.7 57.9 - - - +
289A GLU* 2.9 26.1 + - - +
290A LEU* 3.6 27.9 - - - +
292A MET* 1.3 76.9 - - - +
294A ARG* 1.3 61.0 + - - +
295A ARG 3.1 0.2 - - - -
296A LYS* 3.1 33.6 + - - +
297A PRO 4.9 0.5 - - - +
298A ASP* 5.7 2.2 + - - +
299A THR* 4.2 18.9 + - + +
301A GLU* 5.5 0.4 + - - -
302A VAL* 3.8 17.1 - - - +
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Residues in contact with ARG 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.6 3.2 - - - -
85A PHE 4.1 4.8 + - - -
86A PRO* 3.8 13.3 - - - +
87A GLU* 2.8 53.8 + - - +
92A GLU* 2.8 42.2 + - + +
222A ALA* 4.3 10.3 + - - +
287A ASN 5.2 0.6 + - - -
290A LEU* 3.0 48.4 + - - +
291A TYR* 3.7 7.9 - - - +
293A ARG* 1.3 80.5 - - - +
295A ARG* 1.3 73.5 + - + +
296A LYS 3.3 6.3 + - - +
298A ASP* 5.5 5.0 - - - +
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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) + - + + + + + -
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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