Contacts of the helix formed by residues 325 - 346 (chain A) in PDB entry 2I2X
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 THR 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 3.1 31.4 - - + +
316A GLU 2.8 26.0 + - - +
317A TYR* 3.3 11.7 - - + -
318A HIS* 2.9 29.6 + - - +
320A GLU* 4.2 21.6 + - - +
323A GLY 3.6 1.8 + - - -
324A THR* 1.3 71.1 - - - +
326A VAL* 1.3 66.9 + - + +
328A CYS* 3.4 2.6 + - - -
329A TRP* 3.1 37.4 + - - +
320C GLU* 4.7 0.5 + - - -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.7 10.2 - - + +
44A ASN 4.3 5.2 - - - +
45A TYR* 3.6 34.5 - - + -
65A ILE* 3.8 14.8 - - + +
68A ASP* 3.8 11.7 - - + -
69A VAL* 3.8 24.0 - - + +
315A VAL* 4.7 1.8 - - + -
317A TYR* 3.8 16.4 - - + -
324A THR* 3.2 23.1 - - + -
325A THR* 1.3 87.3 - - + +
327A GLN* 1.3 51.7 + - - +
330A SER* 2.5 38.2 + - - -
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.0 52.8 + - - +
71A GLU* 4.8 7.5 - - - +
72A ARG* 3.6 44.5 + - + +
323A GLY* 3.8 2.9 - - - -
324A THR* 2.7 40.5 + - + +
326A VAL* 1.3 71.7 - - - +
328A CYS* 1.3 65.2 + - - +
330A SER* 3.2 6.1 + - - -
331A GLU* 3.1 24.8 + - - +
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Residues in contact with CYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 4.2 1.8 - - - +
320A GLU* 3.9 30.7 - - + -
322A GLY 4.2 4.9 - - - -
323A GLY 3.9 8.5 - - - -
324A THR 3.0 19.1 + - - -
325A THR* 3.9 3.6 - - - +
327A GLN* 1.3 78.0 - - - +
329A TRP* 1.3 66.5 + - + +
331A GLU 3.4 0.2 + - - -
332A THR* 3.2 12.6 + - - -
292C THR* 2.9 57.4 + - - +
293C CYS* 4.0 5.2 - - - +
329C TRP* 4.5 7.6 - - + -
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Residues in contact with TRP 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.9 16.2 - - + -
290A THR* 3.5 46.3 - - + +
292A THR* 3.2 26.7 - - - -
293A CYS* 3.4 37.0 - - + +
312A ASN* 4.2 7.6 - - + +
315A VAL* 4.1 13.1 - - + +
320A GLU* 6.1 2.0 - - + +
325A THR* 3.1 34.2 + - - +
328A CYS* 1.3 79.8 - - + +
330A SER* 1.3 65.1 + - - +
332A THR* 3.4 4.4 + - - -
333A LEU* 3.0 26.5 + - - +
320C GLU* 5.5 3.7 + - + -
328C CYS* 4.6 4.9 - - + -
329C TRP* 3.7 47.8 - + - +
332C THR* 4.2 7.9 - - + -
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 4.7 2.6 - - - +
43A ILE* 3.6 22.1 - - - +
69A VAL* 4.6 11.8 - - - +
72A ARG* 4.6 9.2 - - - +
73A MET* 4.4 16.5 - - - +
81A ILE* 5.3 2.5 - - - -
326A VAL 2.5 25.8 + - - -
327A GLN* 3.2 12.3 + - - -
329A TRP* 1.3 76.9 - - - +
331A GLU* 1.3 56.7 + - - +
333A LEU* 3.4 6.9 + - - +
334A ALA* 2.8 33.0 + - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.0 20.9 + - + +
73A MET* 5.5 0.2 - - - -
76A VAL* 3.5 7.7 - - - +
78A PHE* 3.9 12.7 - - + -
327A GLN 3.1 17.3 + - - +
328A CYS 3.7 4.0 - - - +
330A SER* 1.3 78.6 + - - +
332A THR* 1.3 56.2 + - - +
334A ALA* 3.8 1.7 - - - +
335A TYR* 2.9 53.5 + - + -
289C LYS* 5.5 0.5 - - - -
292C THR* 3.3 24.6 - - + +
296C SER* 2.7 24.5 + - - -
297C ASP* 3.0 33.9 + - - +
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 3.6 28.3 - - + +
328A CYS 3.2 4.8 + - - -
329A TRP* 3.4 6.7 + - - -
331A GLU* 1.3 73.4 - - - +
333A LEU* 1.3 67.8 + - - +
335A TYR* 3.2 5.9 + - - +
336A ASP* 2.9 30.2 + - - +
289C LYS* 2.8 35.2 + - + +
290C THR* 4.2 13.0 - - + +
292C THR* 2.9 17.2 + - - -
329C TRP* 4.2 8.1 - - + -
332C THR* 4.9 5.8 - - + -
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.7 13.9 - - + -
42A GLU 3.6 27.1 - - - +
43A ILE* 4.0 12.3 - - + -
290A THR* 3.6 20.9 - - + -
310A TRP* 3.6 25.9 - - + +
311A SER 3.5 26.2 - - - +
312A ASN* 3.7 15.9 - - + +
329A TRP 3.0 22.5 + - - +
330A SER* 3.6 5.4 - - - +
332A THR* 1.3 75.1 - - - +
334A ALA* 1.3 59.0 + - - +
336A ASP* 3.1 5.5 + - - +
337A CYS* 2.9 30.5 + - - -
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.7 12.7 - - + +
73A MET* 3.7 15.0 - - + -
78A PHE* 3.4 42.9 - - + -
330A SER 2.8 21.0 + - - +
332A THR 3.3 0.2 - - - -
333A LEU* 1.3 74.3 - - - +
335A TYR* 1.3 57.8 + - - +
337A CYS* 3.3 4.2 + - - +
338A ALA* 2.9 27.0 + - - +
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Residues in contact with TYR 335 (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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76A VAL* 3.5 9.4 - - + +
78A PHE* 3.6 13.7 - + - -
331A GLU* 2.9 52.5 + - + +
332A THR 3.7 1.8 - - - +
333A LEU 3.2 0.2 - - - -
334A ALA* 1.3 74.7 - - - +
336A ASP* 1.3 65.1 + - - +
338A ALA* 3.0 11.3 + - + +
339A LEU 3.1 2.6 + - - -
289C LYS* 3.6 32.1 - - + -
297C ASP* 2.7 20.2 + - - -
298C VAL* 3.1 21.0 - - - -
300C GLY* 3.2 21.4 + - - -
301C ASN* 2.8 34.8 + - - +
360C ASP* 3.3 22.9 - - - -
363C ARG* 3.8 10.7 - - - -
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 4.0 12.9 - - - -
290A THR* 2.6 30.8 + - - +
304A MET* 4.6 7.3 - - - +
310A TRP* 2.8 28.5 + - + +
332A THR* 2.9 19.4 + - - +
333A LEU 3.4 4.0 - - - +
335A TYR* 1.3 74.7 - - - +
337A CYS* 1.3 62.2 + - - +
339A LEU* 3.5 5.7 + - - +
340A MET* 3.3 25.1 + - - +
289C LYS* 2.7 41.4 + - - +
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Residues in contact with CYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.3 29.4 + - - +
40A ILE 3.4 11.7 - - - -
41A PRO* 3.3 35.9 - - + -
310A TRP* 3.9 17.5 - - - -
333A LEU 2.9 15.4 + - - +
334A ALA 3.6 8.1 - - - +
335A TYR 3.1 0.4 - - - -
336A ASP* 1.3 78.4 - - - +
338A ALA* 1.3 56.6 + - - +
340A MET* 3.1 5.0 + - - -
341A ASN* 2.8 37.1 + - - +
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Residues in contact with ALA 338 (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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78A PHE* 4.8 4.0 - - + -
334A ALA 2.9 15.5 + - - +
335A TYR* 3.0 12.0 + - + +
337A CYS* 1.3 75.0 - - - +
339A LEU* 1.3 57.4 + - - +
341A ASN* 3.3 8.3 + - - +
342A THR* 2.8 34.5 + - - -
301C ASN* 4.1 1.3 - - - +
359C SER* 4.0 9.9 - - - +
363C ARG* 3.8 25.6 - - - +
12D VAL* 4.5 12.8 - - + +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 6.2 0.2 - - - +
335A TYR 3.1 10.8 + - - +
336A ASP* 3.6 10.8 - - - +
338A ALA* 1.3 71.8 - - - +
340A MET* 1.3 68.9 + - + +
342A THR* 3.3 7.0 + - - -
343A ALA* 3.1 20.4 + - - +
352A LEU* 4.2 15.1 - - + +
289C LYS* 4.5 13.9 - - - +
301C ASN* 3.8 14.0 + - + +
304C MET* 5.4 2.5 - - + -
339C LEU* 4.4 17.7 - - + -
352C LEU* 4.3 17.0 - - + -
355C LEU* 3.9 15.7 - - + +
356C MET* 3.9 41.7 - - + +
359C SER* 4.7 1.8 - - - -
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Residues in contact with MET 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.4 43.2 - - + -
39A THR* 3.7 24.2 - - + +
304A MET* 4.0 28.0 - - - +
307A CYS* 3.8 31.4 - - - -
310A TRP* 4.5 5.8 - - + -
336A ASP 3.3 20.1 + - - +
337A CYS* 3.1 16.0 + - - +
339A LEU* 1.3 83.2 - - + +
341A ASN* 1.3 61.6 + - - +
343A ALA* 3.0 15.2 + - - +
344A LEU* 3.1 10.3 + - - +
352A LEU* 4.3 7.4 - - + -
356A MET* 4.6 4.7 - - - -
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 5.6 0.4 - - - +
38A TYR* 3.5 19.1 - - + +
39A THR* 2.7 53.8 + - - +
79A PRO* 5.6 5.9 - - - +
337A CYS* 2.8 26.5 + - - +
338A ALA* 3.3 7.1 + - - +
339A LEU 3.2 0.2 - - - -
340A MET* 1.3 74.1 - - - +
342A THR* 1.3 57.5 + - - +
344A LEU* 3.3 9.3 + - - +
345A GLU* 3.0 35.6 + - + +
11D LYS 5.5 4.2 + - - -
12D VAL* 4.4 19.2 + - + -
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA 2.8 20.9 + - - -
339A LEU 3.6 6.1 - - - -
340A MET 3.2 0.2 - - - -
341A ASN* 1.3 74.5 - - - +
343A ALA* 1.3 56.9 + - - +
345A GLU* 3.4 0.9 + - - +
346A THR* 2.8 35.0 + - - +
355C LEU* 3.7 31.9 - - + +
358C LEU* 3.9 17.0 - - + -
359C SER* 3.4 16.8 - - - -
4D PHE* 3.6 33.0 - - + -
12D VAL* 4.2 3.3 - - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.9 1.6 - - + -
339A LEU 3.1 11.7 + - - +
340A MET 3.0 10.9 + - - +
342A THR* 1.3 71.4 - - - +
344A LEU* 1.3 66.2 + - - +
346A THR* 3.3 5.9 + - - -
347A LYS 2.9 3.5 + - - -
348A ASN 2.6 31.2 + - - +
349A ASP* 3.2 24.4 + - - +
352A LEU* 3.8 20.4 - - + -
355C LEU* 3.9 12.3 - - + +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.5 37.2 - - + +
20A GLY* 4.4 1.8 - - - -
21A VAL* 3.9 17.7 - - + -
37A GLY* 3.8 28.3 - - - +
38A TYR* 4.1 2.7 - - - -
39A THR 4.6 0.2 - - - +
340A MET 3.1 12.9 + - - +
341A ASN* 3.5 25.6 - - - +
342A THR 3.3 0.2 - - - -
343A ALA* 1.3 77.4 - - - +
345A GLU* 1.3 66.3 + - - +
347A LYS* 3.0 21.0 + - - +
349A ASP* 3.7 27.6 - - + +
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 4.2 4.9 - - - +
341A ASN* 3.0 19.3 + - + +
342A THR 3.8 4.5 - - - +
343A ALA 3.3 0.2 - - - -
344A LEU* 1.3 79.9 - - - +
346A THR* 1.3 60.1 + - - +
347A LYS* 3.7 10.0 + - - +
4D PHE* 3.9 10.1 - - + -
8D SER* 2.6 50.5 + - - +
11D LYS* 2.7 40.6 + - - +
12D VAL* 3.7 19.3 - - + -
12I ALA* 5.9 3.6 - - - +
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Residues in contact with THR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A THR* 2.8 22.5 + - + +
343A ALA 3.5 2.4 + - - -
344A LEU 3.1 0.6 - - - -
345A GLU* 1.3 79.9 - - - +
347A LYS* 1.3 71.5 + - - +
348A ASN* 3.0 24.2 + - - +
355C LEU* 3.4 11.3 - - - +
358C LEU* 3.8 28.0 - - + -
2D LEU* 4.5 12.8 - - + +
3D ASP 4.1 12.3 - - - +
4D PHE* 4.4 6.5 - - + -
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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