Contacts of the helix formed by residues 337 - 358 (chain A) in PDB entry 2ZM4
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A LYS 4.6 5.8 - - - +
336A LEU* 1.3 76.4 - - - +
338A ILE* 1.3 66.8 + - - +
339A ASN* 3.3 23.2 - - - +
340A LYS* 3.2 16.6 + - - +
341A LEU* 3.4 9.8 + - - +
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Residues in contact with ILE 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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336A LEU 3.9 0.4 + - - -
337A THR* 1.3 74.8 - - - +
339A ASN* 1.3 64.3 + - - +
341A LEU* 3.1 24.0 + - + +
342A LEU* 3.0 36.9 + - + +
434A VAL* 3.9 28.0 - - + -
464A ASN 5.2 1.3 - - - +
466A PRO* 4.0 27.6 - - + -
469A LEU* 4.6 4.0 - - + -
501A THR* 4.7 13.9 - - + -
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Residues in contact with ASN 339 (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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337A THR* 3.3 15.1 + - - +
338A ILE* 1.3 80.3 - - + +
340A LYS* 1.3 63.5 + - - +
342A LEU* 3.2 7.1 + - - +
343A ASP 2.9 22.5 + - - -
498A PHE* 3.1 39.7 + - - -
501A THR* 2.4 46.3 + - - +
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Residues in contact with LYS 340 (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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336A LEU* 3.6 30.5 - - + -
337A THR* 3.2 15.3 + - - +
339A ASN* 1.3 81.5 + - - +
341A LEU* 1.3 61.8 + - - +
343A ASP* 2.9 32.5 + - - +
344A MET* 2.8 50.7 + - + +
347A GLN* 4.1 4.4 - - - +
375A THR 4.7 2.6 + - - -
376A LEU* 2.9 43.5 + - + +
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Residues in contact with LEU 341 (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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328A LEU* 4.2 16.8 - - + -
336A LEU* 3.9 35.2 - - + +
337A THR 3.6 9.9 - - - +
338A ILE* 3.1 31.2 + - + +
340A LYS* 1.3 75.3 - - - +
342A LEU* 1.3 56.2 + - + +
344A MET* 3.4 7.5 + - - +
345A ALA* 2.8 34.7 + - - +
433A ILE* 3.7 34.9 - - + +
434A VAL* 4.3 11.0 - - - +
436A HIS* 4.4 17.0 - - + +
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Residues in contact with LEU 342 (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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338A ILE* 3.0 34.1 + - + +
339A ASN 3.5 5.6 - - - +
341A LEU* 1.3 71.3 - - - +
343A ASP* 1.3 68.6 + - - +
345A ALA* 2.9 7.9 + - + +
346A ALA* 2.7 24.6 + - - +
466A PRO* 5.5 4.9 - - + -
469A LEU* 3.8 38.1 - - + -
494A LEU* 4.5 14.1 - - + +
497A PHE* 4.0 36.1 - - + +
498A PHE* 4.0 17.3 - - + +
501A THR* 4.1 17.3 - - + +
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Residues in contact with ASP 343 (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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339A ASN 2.9 12.7 + - - +
340A LYS* 2.9 39.5 + - - +
342A LEU* 1.3 77.8 - - - +
344A MET* 1.3 64.3 + - - +
346A ALA* 3.0 12.9 + - - +
347A GLN* 2.8 32.6 + - - +
498A PHE* 3.9 38.7 - - + +
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Residues in contact with MET 344 (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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324A LEU* 4.3 13.9 - - + -
327A PHE* 4.1 17.0 - - + -
328A LEU* 5.0 3.1 - - - -
336A LEU* 4.5 16.8 - - + -
340A LYS* 2.8 39.4 + - - +
341A LEU* 3.7 7.6 - - - +
343A ASP* 1.3 72.9 - - - +
345A ALA* 1.3 62.2 + - - +
347A GLN* 3.0 21.5 + - - +
348A ILE* 3.3 17.5 + - - +
372A VAL* 4.1 15.0 - - + -
376A LEU* 3.6 29.2 - - + +
378A CYS* 3.8 29.4 - - - -
433A ILE* 4.8 7.2 - - + -
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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
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341A LEU 2.8 20.6 + - - +
342A LEU* 2.9 8.7 + - + +
344A MET* 1.3 70.3 - - - +
346A ALA* 1.3 60.9 + - - +
348A ILE* 3.7 4.4 + - - +
349A ALA 3.3 14.6 + - - -
426A PHE* 3.5 5.8 - - - -
430A LEU* 3.6 29.8 - - + -
433A ILE* 3.6 17.1 - - + +
469A LEU* 6.2 0.4 - - + -
494A LEU* 3.5 22.5 - - + +
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Residues in contact with ALA 346 (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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342A LEU 2.7 15.9 + - - +
343A ASP* 3.4 11.0 - - - +
345A ALA* 1.3 74.0 - - - +
347A GLN* 1.3 63.4 + - + +
349A ALA* 3.3 4.4 + - - +
350A GLU* 3.1 20.7 + - - +
491A ARG* 4.0 6.2 - - - +
494A LEU* 3.7 26.4 - - + +
495A GLU* 3.8 26.2 - - + -
498A PHE* 5.6 2.5 - - + -
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Residues in contact with GLN 347 (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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299A ARG* 3.5 30.1 + - - +
340A LYS* 4.1 10.5 - - - +
343A ASP* 2.8 40.3 + - - +
344A MET* 3.0 13.3 + - - +
346A ALA* 1.3 73.5 - - + +
348A ILE* 1.3 60.9 + - - +
350A GLU* 3.2 10.4 + - - +
351A GLY* 3.1 24.3 + - - -
376A LEU 4.3 0.4 + - - -
377A SER* 3.2 18.7 - - - +
378A CYS* 2.8 38.1 + - + +
380A ILE* 5.3 0.2 - - - +
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Residues in contact with ILE 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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324A LEU* 4.3 4.7 - - + -
344A MET 3.3 11.9 + - - +
345A ALA* 3.9 6.3 - - - +
346A ALA 3.3 0.4 - - - -
347A GLN* 1.3 77.7 - - - +
349A ALA* 1.3 62.0 + - - +
351A GLY 3.4 1.0 + - - -
352A MET* 3.2 19.6 + - + +
365A LEU* 4.4 3.8 - - + -
370A ILE* 4.0 51.8 - - + -
378A CYS* 4.2 8.7 - - + -
379A LYS* 5.8 1.1 - - - +
380A ILE* 3.6 15.0 - - + +
426A PHE* 3.8 20.9 - - + -
429A LEU* 4.1 13.2 - - + -
433A ILE* 3.8 29.4 - - + -
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Residues in contact with ALA 349 (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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345A ALA 3.3 13.0 + - - +
346A ALA 3.3 3.3 + - - +
347A GLN 3.3 0.4 - - - -
348A ILE* 1.3 81.0 - - - +
350A GLU* 1.3 55.4 + - - +
352A MET* 3.4 7.0 + - - +
353A ALA* 2.8 28.8 + - - +
426A PHE* 3.9 18.6 - - + -
487A PHE* 4.1 7.1 - - + +
490A LEU* 4.2 8.3 - - + -
491A ARG* 3.7 31.9 - - - +
494A LEU* 4.3 1.8 - - + -
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Residues in contact with GLU 350 (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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297A HIS* 4.0 12.6 - - + -
299A ARG* 3.4 29.1 + - + +
346A ALA 3.1 11.6 + - - +
347A GLN* 3.2 14.2 + - - +
349A ALA* 1.3 75.2 - - - +
351A GLY* 1.3 64.2 + - - +
353A ALA* 3.2 14.2 + - + +
354A PHE* 3.5 10.7 + - - +
491A ARG* 4.0 23.0 - - - +
495A GLU* 4.3 11.1 - - - +
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Residues in contact with GLY 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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299A ARG* 3.6 22.2 - - - +
300A LEU* 3.6 18.8 - - - +
347A GLN 3.1 8.4 + - - -
348A ILE 3.7 3.8 - - - -
349A ALA 3.3 0.4 - - - -
350A GLU* 1.3 80.5 - - - +
352A MET* 1.3 62.3 + - - +
354A PHE* 3.2 7.0 + - - +
355A ILE* 3.2 16.4 + - - +
380A ILE* 4.0 8.7 - - - -
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Residues in contact with MET 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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348A ILE* 3.2 16.3 + - + +
349A ALA 3.7 2.7 - - - +
351A GLY* 1.3 74.6 - - - +
353A ALA* 1.3 56.3 + - - +
355A ILE* 3.1 29.9 + - + +
356A GLU* 2.8 31.9 + - - +
362A HIS* 3.6 16.8 - - + -
365A LEU* 3.6 33.2 - - + -
380A ILE* 4.0 9.6 - - + -
419A ILE* 4.5 0.9 - - + -
422A ASP* 3.5 25.6 - - - +
426A PHE* 5.0 0.4 - - + -
487A PHE* 3.4 48.0 - - + -
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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 ALA 2.8 17.5 + - - +
350A GLU* 3.2 13.3 + - - +
352A MET* 1.3 72.3 - - - +
354A PHE* 1.4 56.4 + - - +
356A GLU* 3.6 6.5 - - - +
357A GLU* 3.0 28.2 + - - +
487A PHE* 3.6 11.8 - - - +
488A ASP* 3.9 30.7 - - + +
491A ARG* 5.2 4.0 - - + +
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Residues in contact with PHE 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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294A GLN 5.2 1.8 - - - -
295A LEU* 3.6 23.6 - - + -
296A GLN 3.1 34.8 - - - -
297A HIS* 3.6 38.8 - + + +
300A LEU* 4.0 12.6 - - + -
350A GLU 3.5 6.5 + - - +
351A GLY 3.2 9.1 + - - +
352A MET 3.1 0.4 - - - -
353A ALA* 1.4 76.3 - - - +
355A ILE* 1.3 66.2 + - - +
356A GLU 3.3 0.2 - - - -
357A GLU* 3.5 11.9 + - - +
358A ARG* 3.0 57.2 + - + +
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Residues in contact with ILE 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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295A LEU* 3.9 15.0 - - + -
300A LEU* 3.7 30.1 - - + -
351A GLY 3.2 7.5 + - - +
352A MET* 3.1 44.5 + - + +
354A PHE* 1.3 75.4 - - - +
356A GLU* 1.3 65.5 + - - +
358A ARG* 3.3 5.7 + - - -
360A TYR* 3.1 53.5 + - + +
361A ILE* 4.1 8.5 - - - +
362A HIS* 4.5 3.8 - - + -
380A ILE* 4.2 10.5 - - + -
383A PHE* 4.3 12.1 - - + -
419A ILE* 4.4 1.1 - - + -
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Residues in contact with GLU 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 MET 2.8 19.7 + - - +
353A ALA 3.6 5.7 - - - +
355A ILE* 1.3 72.0 - - - +
357A GLU* 1.3 65.2 + - - +
359A ASN* 3.2 19.2 + - - +
360A TYR 4.2 1.9 + - - +
419A ILE* 3.5 38.8 - - + +
420A LYS* 5.1 1.4 + - - -
423A VAL* 4.9 1.7 - - - +
486A THR* 3.7 17.2 - - - +
487A PHE* 2.8 43.9 + - + +
488A ASP* 3.3 14.2 + - - +
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Residues in contact with GLU 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 3.0 19.6 + - - +
354A PHE* 3.8 14.0 - - - +
355A ILE 3.3 0.4 - - - -
356A GLU* 1.3 78.4 - - + +
358A ARG* 1.3 97.0 + - - +
359A ASN* 3.3 8.0 + - - +
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Residues in contact with ARG 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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294A GLN 5.5 4.2 + - - +
295A LEU* 3.9 8.7 - - + -
354A PHE* 3.0 50.3 + - + +
355A ILE 3.3 1.1 + - - +
356A GLU 3.2 0.8 + - - -
357A GLU* 1.3 105.0 + - - +
359A ASN* 1.3 70.5 + - - +
360A TYR* 3.3 26.6 - - + -
388A LEU* 4.1 3.6 - - - +
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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
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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