Contacts of the helix formed by residues 344 - 368 (chain A) in PDB entry 2JI8
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 ASP 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ALA 4.5 6.3 + - - +
214A LYS* 3.2 43.6 - - - +
216A PRO* 5.1 2.6 - - - +
342A LYS 3.7 1.6 + - - -
343A ALA* 1.3 71.6 - - - +
345A ALA* 1.3 61.2 + - - +
346A GLU* 3.3 25.1 + - - +
347A TRP* 3.2 7.9 + - + +
348A THR* 3.1 24.8 + - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 3.1 5.9 + - - +
344A ASP* 1.3 73.9 + - - +
346A GLU* 1.3 57.4 + - - +
348A THR* 3.2 9.2 + - - -
349A GLY* 2.9 25.5 + - - -
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASP* 3.8 18.6 + - - +
345A ALA* 1.3 75.0 - - - +
347A TRP* 1.3 63.2 + - + +
349A GLY* 4.6 0.7 - - - +
350A ALA* 3.2 26.9 + - - +
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Residues in contact with TRP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LYS 3.7 14.6 - - - +
215A ARG* 3.5 54.8 - - + -
216A PRO* 3.1 31.9 + - + -
217A VAL* 5.2 1.6 - - + -
243A PRO* 3.7 17.0 - - + +
268A PHE* 4.1 15.5 - + - -
269A ALA* 3.8 25.4 - - + -
272A GLN* 4.0 14.6 - - + -
273A CYS* 4.0 11.7 - - + -
343A ALA* 5.2 0.4 - - + -
344A ASP* 3.2 10.4 + - + +
346A GLU* 1.3 81.4 - - + +
348A THR* 1.3 69.1 + - + +
350A ALA* 3.2 6.1 + - + +
351A LEU* 3.0 50.2 + - + +
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Residues in contact with THR 348 (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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241A GLY 3.5 25.1 - - - +
243A PRO* 3.7 25.6 - - + -
260A GLN* 6.5 0.2 - - + -
343A ALA* 4.1 9.9 + - + +
344A ASP 3.1 13.0 + - - +
345A ALA* 3.2 14.9 + - - +
347A TRP* 1.3 77.4 - - + +
349A GLY* 1.3 58.7 + - - +
351A LEU* 3.5 2.6 + - - +
352A LYS* 2.9 29.7 + - - +
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA 2.9 19.2 + - - -
346A GLU* 4.4 0.9 - - - -
348A THR* 1.3 75.8 + - - +
350A ALA* 1.3 64.1 + - - +
352A LYS* 3.3 6.9 + - - +
353A ALA* 3.0 26.2 + - - +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 4.9 15.3 - - + -
346A GLU 3.2 22.1 + - - +
347A TRP* 3.2 10.1 + - + +
349A GLY* 1.3 74.7 - - - +
351A LEU* 1.3 60.7 + - - +
353A ALA* 3.6 5.3 + - - +
354A LYS* 3.1 33.1 + - + +
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Residues in contact with LEU 351 (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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217A VAL* 5.1 0.4 - - + -
243A PRO* 3.7 35.9 - - + -
262A ALA* 4.0 14.6 - - + -
265A THR* 3.7 16.7 - - + +
268A PHE* 3.6 34.1 - - + -
269A ALA* 4.2 9.9 - - + -
347A TRP* 3.0 45.2 + - + +
348A THR* 3.8 4.7 - - - +
350A ALA* 1.3 74.1 - - - +
352A LYS* 1.3 60.6 + - - +
354A LYS* 3.3 3.1 + - - +
355A VAL* 2.9 34.8 + - + +
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Residues in contact with LYS 352 (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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258A HIS 5.5 0.4 + - - -
259A PRO* 3.7 36.0 + - + +
261A SER 5.4 1.5 + - - +
348A THR 2.9 18.8 + - - +
349A GLY* 3.3 8.3 + - - +
351A LEU* 1.3 76.4 - - - +
353A ALA* 1.3 62.4 + - - +
355A VAL* 3.5 21.8 + - + +
356A ASP* 3.1 60.7 + - - +
359A LYS* 5.5 3.6 - - - +
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Residues in contact with ALA 353 (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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349A GLY 3.0 16.4 + - - +
350A ALA* 3.8 6.5 - - - +
352A LYS* 1.3 78.1 - - - +
354A LYS* 1.3 61.9 + - + +
356A ASP* 3.5 7.1 + - - +
357A GLY* 3.1 20.8 + - - -
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Residues in contact with LYS 354 (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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265A THR* 3.2 24.2 - - + +
268A PHE* 3.6 50.7 - - + -
350A ALA* 3.1 25.0 + - - +
351A LEU* 3.3 7.2 + - - +
353A ALA* 1.3 75.6 - - + +
355A VAL* 1.3 61.5 + - - +
357A GLY* 3.4 1.4 + - - -
358A ASN* 2.9 42.0 + - - +
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Residues in contact with VAL 355 (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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261A SER 3.5 24.2 - - - +
262A ALA* 3.9 4.5 - - + -
264A ALA* 4.0 18.5 - - + +
265A THR* 3.6 20.4 - - + -
351A LEU 2.9 22.9 + - - +
352A LYS* 3.6 27.6 - - - +
354A LYS* 1.3 76.4 - - - +
356A ASP* 1.3 58.3 + - - +
358A ASN* 3.9 0.3 - - - -
359A LYS* 3.0 53.2 + - + +
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Residues in contact with ASP 356 (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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352A LYS* 3.1 50.4 + - - +
353A ALA* 3.8 7.2 - - - +
354A LYS 3.3 0.2 - - - -
355A VAL* 1.3 72.9 - - - +
357A GLY* 1.3 66.3 + - - +
359A LYS* 3.4 6.5 + - - +
360A ALA* 3.0 25.9 + - - +
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Residues in contact with GLY 357 (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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353A ALA 3.1 12.6 + - - -
354A LYS* 3.8 3.4 - - - -
356A ASP* 1.3 80.0 - - - +
358A ASN* 1.3 63.2 + - - +
360A ALA* 3.8 6.4 + - - +
361A LYS* 3.4 25.9 + - - +
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Residues in contact with ASN 358 (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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264A ALA 2.6 30.8 + - - +
265A THR* 4.1 10.1 + - - +
354A LYS* 2.9 24.9 + - - +
355A VAL 4.0 2.2 - - - +
357A GLY* 1.3 74.9 - - - +
359A LYS* 1.3 64.5 + - - +
361A LYS* 3.4 22.8 + - - +
362A LEU* 3.2 16.6 + - - +
1569A FYN 3.6 26.4 + - + +
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Residues in contact with LYS 359 (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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256A ASP 4.4 14.5 + - - -
257A ASN* 4.6 13.1 - - - +
258A HIS 5.6 1.8 + - - -
261A SER* 5.9 2.6 - - - -
264A ALA* 4.0 6.5 - - + -
352A LYS* 5.5 3.4 - - - +
355A VAL* 3.0 40.2 + - + +
356A ASP* 3.4 6.9 + - - +
358A ASN* 1.3 74.2 - - - +
360A ALA* 1.3 59.6 + - - +
362A LEU* 3.3 3.5 + - - +
363A ALA* 2.9 27.5 + - - +
366A MET* 5.5 0.5 - - - +
412A ASP* 5.1 8.2 + - - -
1569A FYN 3.6 36.3 - - - +
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Residues in contact with ALA 360 (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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356A ASP 3.0 17.3 + - - +
357A GLY* 3.8 7.9 - - - +
359A LYS* 1.3 76.7 - - - +
361A LYS* 1.3 60.9 + - - +
363A ALA* 3.4 8.9 + - - +
364A GLY* 3.2 18.4 + - - -
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Residues in contact with LYS 361 (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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357A GLY 3.4 12.9 + - - +
358A ASN* 3.4 26.4 + - - +
359A LYS 3.2 0.4 - - - -
360A ALA* 1.3 77.4 - - - +
362A LEU* 1.3 62.0 + - - +
364A GLY* 3.6 3.5 + - - +
365A LYS* 3.5 28.4 + - + +
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Residues in contact with LEU 362 (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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358A ASN 3.2 12.8 + - - +
359A LYS 3.3 7.6 + - - +
361A LYS* 1.3 76.5 - - - +
363A ALA* 1.3 63.5 + - - +
364A GLY 3.2 0.2 - - - -
365A LYS* 3.2 14.2 + - + +
366A MET* 3.1 43.9 + - + +
378A SER* 4.5 10.3 - - - +
385A ARG* 6.2 0.7 - - - -
409A MET* 3.8 30.5 - - + +
410A ILE* 4.0 28.3 - - + -
1569A FYN 3.4 35.4 - - + +
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Residues in contact with ALA 363 (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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359A LYS 2.9 14.1 + - - +
360A ALA* 3.6 12.8 - - - +
361A LYS 3.4 0.2 - - - -
362A LEU* 1.3 76.4 - - - +
364A GLY* 1.3 61.5 + - - +
366A MET* 3.5 18.7 + - + +
367A THR* 3.2 25.5 + - - -
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Residues in contact with GLY 364 (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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360A ALA 3.2 10.3 + - - -
361A LYS* 3.6 5.3 + - - -
362A LEU 3.2 0.6 - - - -
363A ALA* 1.3 80.0 - - - +
365A LYS* 1.3 59.7 + - - +
367A THR* 3.8 10.5 - - - +
368A ALA* 3.6 16.8 + - - +
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Residues in contact with LYS 365 (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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361A LYS* 3.5 17.9 + - + +
362A LEU* 3.2 21.1 + - + +
364A GLY* 1.3 75.4 - - - +
366A MET* 1.3 60.4 + - - +
367A THR 3.1 5.2 + - - -
368A ALA* 3.3 19.6 + - - +
376A ASN* 4.7 3.5 + - - -
378A SER* 3.7 30.0 + - - +
379A ASN* 4.3 3.3 + - - +
409A MET* 6.2 2.2 - - - +
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Residues in contact with MET 366 (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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359A LYS 5.5 0.4 - - - +
362A LEU* 3.1 32.6 + - + +
363A ALA* 3.5 20.2 + - + +
365A LYS* 1.3 75.6 - - - +
367A THR* 1.3 57.2 + - - +
378A SER* 3.4 28.9 - - - +
379A ASN* 3.5 20.4 - - - +
382A GLY* 3.8 14.3 - - - +
385A ARG* 3.9 29.4 - - - +
410A ILE* 3.6 30.1 - - + -
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Residues in contact with THR 367 (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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363A ALA 3.2 17.6 + - - -
364A GLY* 3.8 11.4 - - - +
365A LYS 3.1 0.2 - - - -
366A MET* 1.3 77.2 - - - +
368A ALA* 1.3 70.7 + - - +
369A GLU* 4.6 2.6 - - - +
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 3.6 9.2 + - - +
365A LYS* 3.3 16.3 + - - +
367A THR* 1.3 87.5 - - - +
369A GLU* 1.3 61.6 + - - +
370A THR* 5.3 0.9 - - + -
376A ASN* 5.2 7.2 - - - +
379A ASN* 3.4 25.2 + - - +
522A PRO* 5.6 1.0 - - - +
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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
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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