Contacts of the helix formed by residues 325 - 346 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E VAL* 3.2 30.8 - - + +
316E GLU 2.8 27.2 + - - +
317E TYR* 3.3 17.9 - - + -
318E HIS* 2.6 23.8 + - - -
320E GLU* 4.0 22.1 + - - +
323E GLY 3.6 0.6 + - - -
324E THR* 1.3 73.3 - - - +
326E VAL* 1.3 67.6 + - + +
328E CYS* 3.5 2.4 + - - +
329E TRP* 3.2 36.8 + - - -
320G GLU* 4.5 0.5 + - - -
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Residues in contact with VAL 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ILE* 3.8 11.1 - - + +
44E ASN 4.5 4.5 - - - +
45E TYR* 3.5 33.9 - - + -
65E ILE* 4.1 10.3 - - + +
68E ASP* 4.0 11.0 - - + -
69E VAL* 3.8 24.5 - - + +
315E VAL* 4.5 2.7 - - + -
317E TYR* 4.1 13.9 - - + -
324E THR* 3.2 20.6 - - + -
325E THR* 1.3 91.3 - - + +
327E GLN* 1.3 60.7 + - - +
330E SER* 2.8 31.0 + - - -
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Residues in contact with GLN 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ASP* 3.3 49.8 + - + +
71E GLU* 4.6 10.9 - - - +
72E ARG* 3.1 46.8 + - + +
323E GLY* 3.8 2.9 - - - -
324E THR* 2.8 37.6 + - + +
326E VAL* 1.3 76.9 - - - +
328E CYS* 1.3 64.5 + - - +
330E SER* 3.5 5.4 + - - -
331E GLU* 3.2 23.2 + - - +
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Residues in contact with CYS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 4.9 2.0 - - - +
320E GLU* 3.9 19.7 - - + -
322E GLY 4.3 5.2 - - - -
323E GLY 3.8 17.3 - - - -
324E THR 3.1 13.9 + - - -
325E THR 3.7 5.8 - - - +
327E GLN* 1.3 78.4 - - - +
329E TRP* 1.3 68.8 + - + +
331E GLU* 3.4 0.7 + - - -
332E THR* 3.3 11.3 + - - -
292G THR* 2.8 59.1 + - - +
293G CYS* 4.1 3.8 - - - +
329G TRP* 4.6 3.1 - - + -
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Residues in contact with TRP 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ILE* 4.0 5.4 - - + -
290E THR* 3.5 46.0 - - + +
292E THR* 3.3 27.1 - - - -
293E CYS* 3.4 37.2 - - + +
312E ASN* 4.0 18.4 - - + +
315E VAL* 4.4 7.0 - - + +
320E GLU* 5.9 2.4 - - + +
325E THR* 3.2 36.5 + - - +
326E VAL* 5.0 0.2 - - - -
328E CYS* 1.3 83.2 - - + +
330E SER* 1.3 64.0 + - - +
332E THR* 3.5 5.7 + - - -
333E LEU* 3.1 26.3 + - - +
320G GLU* 5.6 4.3 + - + -
328G CYS* 4.5 4.3 - - + -
329G TRP* 3.4 51.0 - + - +
332G THR* 4.2 8.7 - - + -
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Residues in contact with SER 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO* 4.7 1.4 - - - +
43E ILE* 3.7 27.7 - - - +
69E VAL* 4.5 9.4 - - - +
72E ARG* 4.7 2.6 - - - +
73E MET* 4.1 20.7 - - - +
81E ILE* 5.0 3.4 - - - -
326E VAL 2.8 24.9 + - - -
327E GLN* 3.5 8.1 + - - -
328E CYS 3.4 0.2 - - - -
329E TRP* 1.3 74.1 - - - +
331E GLU* 1.3 57.5 + - - +
333E LEU* 3.1 7.3 + - - +
334E ALA* 2.7 38.0 + - - +
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Residues in contact with GLU 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 2.8 39.0 + - + +
73E MET* 5.4 0.4 - - - -
76E VAL* 3.6 6.9 - - - +
78E PHE* 4.1 15.0 - - + -
327E GLN 3.2 13.3 + - - +
328E CYS 3.6 9.6 - - - +
330E SER* 1.3 76.6 + - - +
332E THR* 1.3 63.5 + - - +
334E ALA* 3.2 1.4 + - - +
335E TYR* 3.0 47.7 + - + -
289G LYS* 5.8 0.2 - - - -
292G THR* 3.6 19.0 - - + +
296G SER* 2.9 15.2 + - - -
297G ASP* 3.2 32.7 + - - +
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Residues in contact with THR 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E THR* 3.5 26.0 - - + +
328E CYS 3.3 3.6 + - - -
329E TRP* 3.9 7.9 - - + -
330E SER 3.3 0.2 - - - -
331E GLU* 1.3 78.6 - - - +
333E LEU* 1.3 56.7 + - - +
335E TYR* 3.5 1.9 + - - +
336E ASP* 3.0 34.2 + - - +
289G LYS* 2.6 41.2 + - + +
290G THR* 4.3 11.7 - - + +
292G THR* 2.9 16.8 + - - -
329G TRP* 4.4 6.7 - - + -
332G THR* 4.9 7.0 - - + -
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Residues in contact with LEU 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO* 3.8 12.1 - - + -
42E GLU 3.6 30.1 - - - +
43E ILE* 4.0 11.7 - - + +
290E THR* 3.7 21.8 - - + +
310E TRP* 3.6 31.9 - - + +
311E SER 3.6 17.7 - - - +
312E ASN* 3.7 15.3 - - + +
329E TRP 3.1 21.9 + - - +
330E SER* 3.1 9.4 + - - +
332E THR* 1.3 77.1 - - - +
334E ALA* 1.3 56.3 + - - +
336E ASP* 3.2 5.7 + - - +
337E CYS* 3.0 30.1 + - - -
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Residues in contact with ALA 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E PRO* 3.8 13.4 - - + +
73E MET* 3.5 17.0 - - + -
78E PHE* 3.4 41.4 - - + -
330E SER 2.7 19.0 + - - +
333E LEU* 1.3 72.8 - - - +
335E TYR* 1.3 57.5 + - - +
337E CYS* 3.7 4.4 - - - +
338E ALA* 2.8 27.4 + - - +
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Residues in contact with TYR 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E VAL* 3.1 14.9 - - + +
78E PHE* 3.5 17.3 - + - -
331E GLU* 3.0 47.5 + - + +
332E THR 3.8 0.9 - - - +
334E ALA* 1.3 73.4 - - - +
336E ASP* 1.3 66.3 + - - +
337E CYS 3.1 0.9 - - - -
338E ALA* 3.0 2.1 + - + -
339E LEU* 2.9 20.8 + - - +
289G LYS* 3.6 32.8 - - + -
297G ASP* 2.8 21.4 + - - -
298G VAL* 3.3 14.0 - - - -
300G GLY* 3.2 27.8 + - - -
301G ASN* 3.0 27.0 - - - +
360G ASP* 3.4 17.7 - - - -
363G ARG* 3.8 12.4 - - - -
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Residues in contact with ASP 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 3.8 14.9 - - - -
290E THR* 2.5 29.8 + - - +
304E MET* 4.9 7.2 - - - +
310E TRP* 2.9 28.6 + - + +
332E THR* 3.0 19.1 + - - +
333E LEU 3.5 1.6 - - - +
335E TYR* 1.3 74.9 - - - +
337E CYS* 1.3 61.9 + - - +
339E LEU* 3.4 4.8 + - - +
340E MET* 3.2 27.8 + - + +
289G LYS* 2.9 35.7 + - - +
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Residues in contact with CYS 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E THR* 3.3 28.7 + - - +
40E ILE 3.5 30.1 - - - -
41E PRO* 3.6 7.6 - - + -
310E TRP* 3.8 20.0 - - - -
333E LEU 3.0 15.9 + - - +
334E ALA* 3.7 10.3 - - - +
335E TYR 3.1 0.2 - - - -
336E ASP* 1.3 74.1 - - - +
338E ALA* 1.3 61.3 + - - +
339E LEU 3.3 0.2 + - - -
340E MET* 3.3 5.2 + - - -
341E ASN* 2.8 38.4 + - - +
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Residues in contact with ALA 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E PHE* 4.8 3.8 - - + -
334E ALA 2.8 19.6 + - - +
335E TYR* 3.0 10.7 + - + +
337E CYS* 1.3 76.3 - - - +
339E LEU* 1.3 60.4 + - - +
341E ASN* 4.0 7.3 - - - +
342E THR* 2.9 30.3 + - - -
301G ASN* 4.4 0.2 - - - +
359G SER* 4.1 8.1 - - - +
363G ARG* 3.8 26.0 - - - +
12H VAL* 4.4 13.6 - - + +
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Residues in contact with LEU 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E MET* 6.5 0.2 - - + -
335E TYR 2.9 11.8 + - - +
336E ASP* 3.7 9.4 - - - +
338E ALA* 1.3 73.2 - - - +
340E MET* 1.3 66.0 + - + +
342E THR* 3.1 6.4 + - - -
343E ALA* 3.1 19.4 + - - +
352E LEU* 4.2 18.4 - - + -
356E MET* 6.4 0.4 - - - -
289G LYS* 4.6 12.8 - - - +
301G ASN* 3.9 14.0 + - - +
304G MET* 5.6 0.4 - - + -
339G LEU* 4.6 15.3 - - + -
352G LEU* 4.5 13.5 - - + -
355G LEU* 3.8 14.3 - - + +
356G MET* 3.6 46.2 - - + +
359G SER* 4.3 4.3 - - - -
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Residues in contact with MET 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.1 44.8 - - + -
39E THR* 3.4 32.1 - - + +
304E MET* 4.2 17.0 - - - +
307E CYS* 3.7 27.8 - - - -
310E TRP* 4.7 8.5 - - + -
336E ASP* 3.2 21.4 + - + +
337E CYS* 3.7 15.0 - - - +
339E LEU* 1.3 79.0 - - + +
341E ASN* 1.3 62.7 + - - +
343E ALA* 2.9 18.7 + - - +
344E LEU 3.1 5.5 + - - -
352E LEU* 4.1 9.6 - - + -
356E MET* 4.5 5.8 - - - -
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Residues in contact with ASN 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E TYR* 3.4 18.5 - - + +
39E THR* 2.6 53.1 + - - +
79E PRO* 5.9 4.0 - - - +
337E CYS* 2.8 27.2 + - - +
338E ALA* 4.0 6.9 - - - +
339E LEU 3.2 0.2 - - - -
340E MET* 1.3 71.6 - - - +
342E THR* 1.3 57.9 + - - +
344E LEU* 3.1 10.1 + - + +
345E GLU* 2.8 36.4 + - + +
11H LYS 5.4 5.1 + - - +
12H VAL* 4.5 17.3 + - + -
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Residues in contact with THR 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E ALA 2.9 18.0 + - - -
339E LEU 3.3 10.1 - - - -
341E ASN* 1.3 75.4 - - - +
343E ALA* 1.3 52.7 + - - +
345E GLU* 3.6 0.9 + - - +
346E THR* 2.7 34.8 + - - +
355G LEU* 3.6 33.2 - - + +
358G LEU* 3.9 19.5 - - + -
359G SER* 3.3 25.8 - - - +
4H PHE* 3.6 19.5 - - + -
12H VAL* 4.0 5.3 - - - +
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Residues in contact with ALA 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.8 8.5 - - + -
339E LEU 3.1 5.1 + - - +
340E MET 2.9 14.2 + - - +
342E THR* 1.3 74.8 - - - +
344E LEU* 1.3 61.5 + - - +
346E THR* 3.1 7.0 + - - -
347E LYS 3.0 3.8 + - - -
348E ASN* 2.7 33.1 + - - +
349E ASP* 3.8 11.2 - - - +
352E LEU* 3.7 28.3 - - + -
355G LEU* 3.9 12.1 - - + +
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Residues in contact with LEU 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.4 41.1 - - + +
20E GLY* 4.0 3.8 - - - -
21E VAL* 3.8 17.9 - - + -
37E GLY* 3.4 33.7 - - - +
38E TYR* 3.8 10.8 - - - -
340E MET 3.1 2.5 + - - +
341E ASN* 3.1 16.7 + - - +
343E ALA* 1.3 77.5 - - - +
345E GLU* 1.3 60.5 + - - +
347E LYS* 2.9 31.7 + - - +
349E ASP* 3.7 27.6 - - + +
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Residues in contact with GLU 345 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLY 4.3 8.5 - - - +
38E TYR* 5.8 0.9 - - - +
341E ASN* 2.8 23.5 + - + +
342E THR 3.9 5.2 - - - +
344E LEU* 1.3 73.3 - - - +
346E THR* 1.3 60.5 + - - +
347E LYS* 3.5 11.2 + - - +
4H PHE* 4.0 9.9 - - + -
5H THR* 6.1 0.5 - - - +
7H ALA 5.1 0.2 - - - -
8H SER* 2.3 54.1 + - - +
11H LYS* 3.7 33.5 + - + +
12H VAL* 3.8 21.8 - - + -
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Residues in contact with THR 346 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E THR* 2.7 22.7 + - + +
343E ALA 3.1 4.3 + - - -
344E LEU 3.1 0.4 - - - -
345E GLU* 1.3 79.3 - - - +
347E LYS* 1.3 71.7 + - - +
348E ASN* 3.0 22.5 + - - +
355G LEU* 3.6 8.5 - - - +
358G LEU* 3.8 27.1 - - + -
2H LEU* 4.5 14.1 - - + +
3H ASP 4.0 13.0 - - - +
4H PHE* 4.5 5.8 - - + -
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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