Contacts of the helix formed by residues 325 - 346 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315K VAL* 3.2 33.8 - - + +
316K GLU 2.8 24.5 + - - +
317K TYR* 3.4 17.3 - - + -
318K HIS* 2.8 20.0 + - - -
320K GLU* 3.8 23.1 + - - +
323K GLY 3.7 0.8 + - - -
324K THR* 1.3 73.0 - - - +
326K VAL* 1.3 65.0 + - + +
328K CYS* 3.4 2.1 + - - +
329K TRP* 3.0 40.9 + - - -
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Residues in contact with VAL 326 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ILE* 3.7 11.3 - - + +
44K ASN 4.2 6.5 - - - +
45K TYR* 3.4 39.9 - - + -
65K ILE* 4.0 10.8 - - + +
68K ASP* 4.1 4.0 - - + -
69K VAL* 3.8 24.6 - - + +
315K VAL* 4.5 1.8 - - + -
317K TYR* 3.9 14.4 - - + -
324K THR* 3.3 20.2 - - + -
325K THR* 1.3 90.6 - - + +
327K GLN* 1.3 52.1 + - - +
330K SER* 2.8 36.8 + - - -
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Residues in contact with GLN 327 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K ASP* 3.1 55.7 + - + +
71K GLU* 4.9 6.7 - - - +
72K ARG* 3.7 44.8 + - + +
323K GLY* 3.7 3.6 - - - -
324K THR* 2.7 34.6 + - + +
326K VAL* 1.3 78.7 - - - +
328K CYS* 1.3 62.8 + - - +
330K SER* 3.2 6.4 + - - -
331K GLU* 3.1 26.2 + - - +
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Residues in contact with CYS 328 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292I THR* 2.7 57.9 + - - +
293I CYS* 4.1 3.8 - - - +
329I TRP* 4.7 4.0 - - + -
72K ARG* 4.3 1.3 - - - +
320K GLU* 3.8 20.6 - - + -
322K GLY 4.2 6.1 - - - -
323K GLY 3.8 17.9 - - - -
324K THR 3.1 16.8 + - - -
325K THR* 3.7 6.5 - - - +
327K GLN* 1.3 79.8 - - - +
329K TRP* 1.3 67.7 + - + +
331K GLU 3.5 0.3 + - - -
332K THR* 3.2 12.5 + - - -
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Residues in contact with TRP 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I GLU* 5.3 4.8 + - + -
328I CYS* 4.6 5.8 - - + -
329I TRP* 3.4 51.8 - + - +
332I THR* 4.4 5.4 - - + -
43K ILE* 4.0 7.2 - - + -
290K THR* 3.6 40.1 - - + +
292K THR* 3.4 25.6 - - - -
293K CYS* 3.3 36.3 - - + +
312K ASN* 4.0 17.7 - - + +
315K VAL* 4.2 10.7 - - + +
320K GLU* 5.7 3.0 + - - +
325K THR* 3.0 38.7 + - - +
328K CYS* 1.3 78.1 - - + +
330K SER* 1.3 60.4 + - - +
332K THR* 3.3 4.6 + - - +
333K LEU* 2.9 33.0 + - - +
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Residues in contact with SER 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K PRO* 4.7 2.9 - - - +
43K ILE* 3.7 22.1 - - - +
69K VAL* 4.7 10.4 - - - +
72K ARG* 4.4 6.8 - - - +
73K MET* 4.3 19.7 - - - +
81K ILE* 5.3 2.7 - - - -
326K VAL 2.8 25.3 + - - -
327K GLN* 3.2 10.2 + - - -
329K TRP* 1.3 76.3 - - - +
331K GLU* 1.3 60.8 + - - +
333K LEU* 3.4 7.6 + - - +
334K ALA* 2.9 31.6 + - - +
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Residues in contact with GLU 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I GLY 5.7 0.3 - - - +
289I LYS* 5.5 0.2 - - - -
292I THR* 3.6 20.7 - - + +
296I SER* 2.5 25.9 + - - -
297I ASP* 3.3 30.5 + - - +
72K ARG* 2.8 27.4 + - + +
73K MET* 5.3 0.2 - - - -
76K VAL* 3.8 6.6 - - + +
78K PHE* 3.8 16.9 - - + -
327K GLN 3.1 14.1 + - - +
328K CYS 3.7 4.7 - - - +
330K SER* 1.3 83.4 + - - +
332K THR* 1.3 61.5 + - - +
334K ALA 3.5 0.3 + - - -
335K TYR* 3.0 42.9 + - + -
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Residues in contact with THR 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I LYS* 2.7 32.6 + - + +
290I THR* 4.2 14.8 - - + +
292I THR* 2.8 21.3 + - - -
329I TRP* 4.3 7.2 - - + -
332I THR* 4.8 7.0 - - + -
290K THR* 3.6 25.6 - - + +
328K CYS 3.2 5.0 + - - -
329K TRP* 3.3 11.6 + - + -
330K SER 3.3 0.2 - - - -
331K GLU* 1.3 74.7 - - - +
333K LEU* 1.3 65.3 + - - +
335K TYR* 3.2 7.3 + - - +
336K ASP* 3.0 24.6 + - - +
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Residues in contact with LEU 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K PRO* 3.8 12.3 - - + -
42K GLU 3.6 21.1 - - - +
43K ILE* 4.2 8.1 - - + +
290K THR* 3.6 18.6 - - + +
310K TRP* 3.4 31.4 - - + +
311K SER 3.4 25.4 - - - +
312K ASN* 3.6 27.6 - - + +
329K TRP 2.9 21.0 + - - +
330K SER* 3.7 5.2 - - - +
332K THR* 1.3 75.9 - - - +
334K ALA* 1.3 64.4 + - - +
336K ASP* 3.2 6.3 + - - +
337K CYS* 3.1 26.0 + - - -
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Residues in contact with ALA 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K PRO* 3.8 15.7 - - + +
73K MET* 3.9 12.3 - - + -
78K PHE* 3.5 43.3 - - + -
330K SER 2.9 17.5 + - - +
333K LEU* 1.3 75.8 - - - +
335K TYR* 1.3 57.1 + - - +
337K CYS* 3.3 4.7 + - - +
338K ALA* 2.9 26.7 + - - +
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Residues in contact with TYR 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I LYS* 3.4 33.7 - - + -
297I ASP* 2.7 21.1 + - - -
298I VAL* 3.2 18.9 + - - -
300I GLY* 3.3 19.5 - - - -
301I ASN* 2.7 40.3 - - - +
359I SER* 4.7 1.1 - - - -
360I ASP* 3.3 22.7 - - - -
363I ARG* 3.8 8.5 - - - -
76K VAL* 3.5 10.6 - - + +
78K PHE* 3.7 12.1 - + - -
331K GLU* 3.0 52.7 + - + +
332K THR 3.5 2.0 - - - +
334K ALA* 1.3 74.9 - - - +
336K ASP* 1.3 64.8 + - - +
338K ALA* 3.1 10.1 + - + +
339K LEU 3.2 2.4 + - - -
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Residues in contact with ASP 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I LYS* 2.8 35.8 + - - +
289K LYS* 3.9 13.5 - - - -
290K THR* 2.7 29.3 + - - +
304K MET* 4.6 4.2 - - - +
310K TRP* 2.7 28.6 + - + +
332K THR* 3.0 18.6 + - - +
333K LEU 3.2 4.0 + - - +
335K TYR* 1.3 74.4 - - - +
337K CYS* 1.3 61.8 + - - +
339K LEU* 3.4 7.3 + - - +
340K MET* 3.2 30.8 + - + +
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Residues in contact with CYS 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K THR* 3.1 30.8 + - - +
40K ILE 3.6 7.0 - - - -
41K PRO* 3.5 31.2 - - + -
310K TRP* 3.7 22.0 - - - -
333K LEU 3.1 17.1 + - - +
334K ALA 3.6 8.1 - - - +
335K TYR 3.2 0.2 - - - -
336K ASP* 1.3 74.7 - - - +
338K ALA* 1.3 59.2 + - - +
340K MET* 3.3 4.1 + - - -
341K ASN* 2.8 37.3 + - - +
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Residues in contact with ALA 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I ASN* 4.3 0.4 - - - +
359I SER* 3.6 17.9 - - - +
363I ARG* 3.8 20.6 - - - +
12J VAL* 4.6 13.1 - - + +
78K PHE* 5.0 2.9 - - + -
334K ALA 2.9 14.7 + - - +
335K TYR* 3.1 10.7 + - + +
337K CYS* 1.3 75.5 - - - +
339K LEU* 1.3 57.6 + - - +
341K ASN* 3.8 7.2 - - - +
342K THR* 2.8 35.8 + - - -
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Residues in contact with LEU 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I LYS* 4.2 17.3 - - - +
301I ASN* 3.8 13.3 + - + +
304I MET* 5.1 2.2 - - + -
339I LEU* 4.5 21.1 - - + -
352I LEU* 4.6 7.0 - - + -
355I LEU* 3.9 13.9 - - + +
356I MET* 3.7 44.0 - - + +
359I SER* 4.5 2.0 - - - -
289K LYS* 6.1 0.4 - - - +
335K TYR 3.2 11.7 + - - +
336K ASP* 3.5 10.1 - - - +
338K ALA* 1.3 77.9 - - - +
340K MET* 1.3 63.8 + - + +
342K THR* 3.3 5.4 + - - -
343K ALA* 2.9 21.1 + - - +
352K LEU* 4.2 15.4 - - + +
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Residues in contact with MET 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K PHE* 3.2 51.7 - - + -
39K THR* 3.8 11.4 - - - +
304K MET* 4.0 27.6 - - + +
307K CYS* 3.8 31.4 - - - -
310K TRP* 4.6 3.6 - - + -
336K ASP* 3.2 26.9 + - + +
337K CYS* 3.7 18.4 - - - +
339K LEU* 1.3 81.1 - - + +
341K ASN* 1.3 57.2 + - - +
343K ALA* 3.1 6.0 + - - +
344K LEU* 2.8 24.8 + - - +
352K LEU* 4.3 7.9 - - + -
356K MET* 4.6 3.8 - - - -
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Residues in contact with ASN 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LYS 5.7 1.4 + - - -
12J VAL* 4.2 22.0 + - + +
38K TYR* 3.6 18.4 - - + +
39K THR* 2.8 54.6 + - - +
79K PRO* 5.7 5.9 - - - +
337K CYS* 2.8 25.2 + - - +
338K ALA* 3.9 6.5 - - - +
340K MET* 1.3 70.6 - - - +
342K THR* 1.3 61.1 + - - +
344K LEU* 3.5 8.3 - - + +
345K GLU* 2.9 38.7 + - + +
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Residues in contact with THR 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I LEU* 3.6 33.9 - - + +
358I LEU* 3.8 17.3 - - + -
359I SER* 3.4 17.0 - - - +
4J PHE* 3.4 30.1 - - + -
12J VAL* 4.0 4.2 - - - +
338K ALA 2.8 22.9 + - - -
339K LEU 3.5 4.9 - - - -
341K ASN* 1.3 74.5 - - - +
343K ALA* 1.3 57.4 + - - +
345K GLU* 3.3 1.9 + - - +
346K THR* 2.8 34.2 + - - +
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Residues in contact with ALA 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I LEU* 3.8 13.1 - - + +
19K PHE* 3.9 1.8 - - + -
339K LEU 2.9 13.1 + - - +
340K MET 3.1 10.3 - - - +
342K THR* 1.3 75.0 - - - +
344K LEU* 1.3 58.6 + - - +
346K THR* 3.1 11.2 + - - -
348K ASN* 2.7 33.5 + - - +
349K ASP* 3.7 21.5 - - - +
352K LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K PHE* 3.7 36.6 - - + +
20K GLY* 4.1 6.1 - - - -
21K VAL* 3.9 17.3 - - + -
37K GLY* 3.7 30.5 - - - +
340K MET 2.8 15.1 + - - +
341K ASN* 3.5 27.1 - - - +
343K ALA* 1.3 74.4 - - - +
345K GLU* 1.3 63.8 + - - +
347K LYS* 3.3 17.5 + - - +
349K ASP* 3.9 25.5 - - + +
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Residues in contact with GLU 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 3.9 13.5 - - + -
5J THR* 5.9 1.6 - - - +
8J SER* 2.9 46.8 + - - +
11J LYS* 3.1 43.7 + - - +
12J VAL* 3.8 19.2 - - + +
37K GLY 3.8 9.9 - - - +
38K TYR* 5.6 0.5 - - - +
341K ASN* 2.9 28.9 + - - +
342K THR 3.3 0.6 + - - +
344K LEU* 1.3 75.9 - - - +
346K THR* 1.3 59.5 + - - +
347K LYS* 3.4 12.3 + - - +
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Residues in contact with THR 346 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355I LEU* 3.5 8.8 - - - +
358I LEU* 3.9 26.7 - - + -
2J LEU* 4.5 14.7 - - + +
3J ASP 4.1 12.1 - - - +
4J PHE* 4.5 6.7 - - + -
342K THR* 2.8 22.9 + - + +
343K ALA 3.1 5.7 + - - -
344K LEU 3.2 0.2 - - - -
345K GLU* 1.3 77.6 - - - +
347K LYS* 1.3 74.5 + - - +
348K ASN* 3.2 22.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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