Contacts of the helix formed by residues 344 - 368 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B ALA 4.1 13.2 - - - +
214B LYS* 3.6 36.3 + - - +
216B PRO* 5.3 1.4 - - - +
342B LYS 3.6 3.7 + - - +
343B ALA* 1.3 71.8 - - - +
345B ALA* 1.3 65.7 + - - +
346B GLU* 3.3 4.9 - - + +
347B TRP* 3.1 18.8 + - + +
348B THR* 3.2 10.9 + - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA 3.2 5.0 + - - -
344B ASP* 1.3 71.4 - - - +
346B GLU* 1.3 62.9 + - + +
348B THR* 3.2 9.2 + - - +
349B GLY* 2.8 29.3 + - - -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ASP* 3.3 3.9 - - + +
345B ALA* 1.3 81.6 - - + +
347B TRP* 1.3 56.7 + - - +
349B GLY* 5.1 0.4 - - - -
350B ALA* 3.1 28.3 + - - +
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Residues in contact with TRP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LYS 3.9 12.3 - - - +
215B ARG* 3.5 50.5 - - + -
216B PRO* 2.9 32.5 + - + -
217B VAL* 5.1 2.2 - - + -
243B PRO* 3.6 17.1 - - + +
268B PHE* 4.5 7.2 - + - -
269B ALA* 3.8 25.4 - - + -
272B GLN* 3.9 20.2 - - + -
273B CYS* 3.8 11.2 - - + -
343B ALA* 5.0 1.8 - - + -
344B ASP* 3.1 11.8 + - + +
346B GLU* 1.3 77.8 - - - +
348B THR* 1.3 67.9 + - + +
350B ALA* 3.3 6.5 + - + +
351B LEU* 3.1 59.1 + - + +
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Residues in contact with THR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLY 3.4 25.4 - - - +
243B PRO* 3.6 28.0 - - + -
343B ALA* 3.9 16.3 + - + +
344B ASP 3.2 2.9 + - - +
345B ALA* 3.2 17.5 + - - -
347B TRP* 1.3 76.9 - - + +
349B GLY* 1.3 59.0 + - - +
351B LEU* 3.5 2.6 + - - +
352B LYS* 3.0 30.0 + - - +
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Residues in contact with GLY 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 2.8 19.1 + - - -
346B GLU* 4.4 0.9 - - - -
348B THR* 1.3 76.8 + - - +
350B ALA* 1.3 60.3 + - - -
352B LYS* 3.9 6.3 - - - +
353B ALA* 3.2 23.0 + - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 5.3 10.8 - - + -
346B GLU 3.1 22.6 + - - +
347B TRP* 3.3 9.1 + - + +
349B GLY* 1.3 74.1 - - - +
351B LEU* 1.3 67.1 + - + +
353B ALA* 3.6 6.0 + - - +
354B LYS* 3.3 27.8 + - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 5.6 0.2 - - + -
243B PRO* 3.6 35.9 - - + -
262B ALA* 4.2 12.3 - - + -
265B THR* 3.6 19.4 - - + +
268B PHE* 3.7 30.7 - - + -
269B ALA* 4.3 9.9 - - + -
347B TRP* 3.1 48.2 + - + +
348B THR* 4.0 3.4 - - - +
349B GLY 3.4 0.2 - - - -
350B ALA* 1.3 73.8 - - + +
352B LYS* 1.3 61.4 + - - +
354B LYS* 3.2 2.5 + - - +
355B VAL* 2.9 35.3 + - - +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASN 5.8 0.2 + - - -
259B PRO* 3.9 38.8 + - + +
261B SER 6.0 0.7 - - - +
348B THR 3.0 19.3 + - - +
349B GLY* 3.9 8.1 - - - +
351B LEU* 1.3 77.8 - - - +
353B ALA* 1.3 55.7 + - - +
355B VAL* 3.4 14.9 + - + +
356B ASP* 3.0 61.2 + - - +
359B LYS* 6.0 2.0 - - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLY 3.2 16.2 + - - +
350B ALA* 3.7 7.6 - - - +
351B LEU 3.3 0.2 - - - -
352B LYS* 1.3 80.7 - - - +
354B LYS* 1.3 59.9 + - - +
356B ASP* 3.5 8.0 + - - +
357B GLY* 3.2 19.1 + - - -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B THR* 3.6 26.9 - - + +
268B PHE* 3.7 48.9 - - + -
350B ALA* 3.3 12.8 + - - +
351B LEU* 3.2 7.8 + - - +
353B ALA* 1.3 75.2 - - - +
355B VAL* 1.3 60.2 + - - +
357B GLY* 4.1 0.8 - - - +
358B ASN* 3.1 41.7 + - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B SER 3.8 24.5 - - - +
262B ALA* 4.1 4.5 - - - -
264B ALA* 3.8 19.5 - - + +
265B THR* 3.3 27.8 - - + +
351B LEU 2.9 22.8 + - - +
352B LYS* 3.6 15.5 - - + +
354B LYS* 1.3 76.6 - - - +
356B ASP* 1.3 62.3 + - - +
358B ASN* 3.5 1.2 + - - +
359B LYS* 2.9 55.1 + - + +
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LYS* 3.0 54.3 + - - +
353B ALA* 3.7 8.5 - - - +
354B LYS 3.3 0.2 - - - -
355B VAL* 1.3 79.3 - - - +
357B GLY* 1.3 56.9 + - - +
359B LYS* 3.4 8.6 + - - +
360B ALA* 3.1 27.9 + - - +
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Residues in contact with GLY 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ALA 3.2 12.6 + - - -
354B LYS* 4.1 1.6 - - - -
356B ASP* 1.3 79.3 - - - +
358B ASN* 1.3 61.9 + - - +
360B ALA* 3.4 7.5 + - - +
361B LYS* 3.2 26.9 + - - +
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Residues in contact with ASN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B ALA 2.7 28.8 + - - +
265B THR* 4.1 10.7 + - - +
354B LYS* 3.1 27.0 + - - +
355B VAL 3.9 2.2 - - - +
357B GLY* 1.3 74.0 - - - +
359B LYS* 1.3 64.9 + - - +
361B LYS* 3.4 18.0 + - - +
362B LEU* 3.2 17.3 + - - +
1566B FYN 3.5 26.1 + - + +
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ASP 4.4 5.8 + - - -
257B ASN* 4.3 26.1 + - - +
258B HIS 5.8 0.4 + - - -
261B SER* 6.1 1.0 - - - -
264B ALA* 4.1 6.1 - - + -
352B LYS* 6.0 1.6 - - - +
355B VAL* 2.9 40.2 + - + +
356B ASP* 3.7 9.2 - - - +
358B ASN* 1.3 75.4 - - - +
360B ALA* 1.3 58.2 + - - +
362B LEU* 3.4 4.3 + - - +
363B ALA* 3.1 26.3 + - - +
366B MET* 5.4 0.7 - - - +
385B ARG* 6.1 4.2 - - - +
412B ASP* 5.1 7.5 + - - -
1566B FYN 3.8 33.9 - - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ASP 3.1 14.3 + - - +
357B GLY* 3.6 11.9 - - - +
358B ASN 3.3 0.2 - - - -
359B LYS* 1.3 74.5 - - - +
361B LYS* 1.3 64.8 + - - +
363B ALA* 3.3 8.9 + - - +
364B GLY* 3.3 17.5 + - - -
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Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B GLY 3.2 14.3 + - - +
358B ASN* 3.6 20.1 + - - +
359B LYS 3.4 0.2 - - - -
360B ALA* 1.3 77.5 - - - +
362B LEU* 1.3 61.2 + - - +
364B GLY* 3.5 3.2 + - - -
365B LYS* 3.5 27.6 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ASN 3.2 13.4 + - - +
359B LYS* 3.6 8.1 - - - +
360B ALA 3.2 0.2 - - - -
361B LYS* 1.3 73.8 - - - +
363B ALA* 1.3 65.8 - - - +
365B LYS* 3.0 16.7 + - + +
366B MET* 3.0 38.8 + - + +
378B SER* 4.7 7.6 - - - +
385B ARG* 5.9 1.8 - - - +
409B MET* 3.5 34.1 - - + +
410B ILE* 4.1 25.4 - - + +
1566B FYN 3.2 37.7 - - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LYS 3.1 13.4 + - - +
360B ALA* 3.5 12.8 - - - +
362B LEU* 1.3 76.3 - - - +
364B GLY* 1.3 56.4 + - - +
366B MET* 3.3 17.5 + - + +
367B THR* 2.9 33.6 + - - +
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Residues in contact with GLY 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ALA 3.3 9.7 + - - -
361B LYS* 3.5 4.2 + - - -
362B LEU 3.2 0.8 - - - -
363B ALA* 1.3 79.0 - - - +
365B LYS* 1.3 60.5 + - - +
367B THR* 4.1 8.4 - - - +
368B ALA* 3.4 21.7 + - - +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B LYS* 3.5 19.6 + - - +
362B LEU* 3.0 18.4 + - + +
364B GLY* 1.3 74.4 - - - +
366B MET* 1.3 62.3 + - - +
368B ALA* 3.5 17.2 + - - +
376B ASN* 4.7 4.3 + - - +
378B SER* 3.4 31.5 - - - +
379B ASN* 4.2 4.9 + - - +
409B MET* 6.2 0.9 - - + -
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Residues in contact with MET 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LYS 5.4 0.4 - - - +
362B LEU* 3.0 30.0 + - + +
363B ALA* 3.7 29.4 - - + +
365B LYS* 1.3 75.1 - - - +
367B THR* 1.3 61.7 + - - +
368B ALA 4.0 0.2 - - - +
378B SER* 3.5 28.7 - - - +
379B ASN* 3.3 21.3 - - - +
382B GLY* 3.7 24.3 - - - -
385B ARG* 3.8 29.6 - - - +
410B ILE* 3.8 19.5 - - + -
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ALA* 2.9 18.8 + - - +
364B GLY* 4.1 8.1 - - - +
365B LYS 3.4 0.2 - - - -
366B MET* 1.3 75.1 - - - +
368B ALA* 1.3 67.9 + - - +
369B GLU* 5.2 0.7 - - - +
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B GLY 3.4 12.2 + - - +
365B LYS* 3.5 15.0 + - - +
366B MET 3.3 2.2 - - - -
367B THR* 1.3 86.5 - - - +
369B GLU* 1.3 61.4 + - - +
370B THR* 5.3 1.1 - - + -
376B ASN* 5.6 4.3 - - - +
379B ASN* 3.4 24.2 + - - +
522B 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
------------------------------------------------------------
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