Contacts of the helix formed by residues 336 - 357 (chain A) in PDB entry 3MSS
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 SER 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ARG 4.0 6.7 - - - -
333A GLN 4.1 14.6 - - - -
334A GLU 3.1 3.2 + - - -
335A VAL* 1.3 77.2 - - - +
337A ALA* 1.3 66.1 + - - +
338A VAL* 3.3 24.9 - - - +
339A VAL* 3.0 10.2 + - - +
340A LEU* 3.0 20.2 + - - +
435A TYR* 4.1 5.4 - - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 1.3 73.5 - - - +
338A VAL* 1.3 57.9 + - - +
340A LEU* 3.2 11.0 + - + +
341A LEU 2.8 24.8 + - - -
435A TYR* 4.6 2.0 + - - -
463A GLY 5.6 5.4 - - - +
465A PRO* 5.9 1.1 - - + -
516A MS7 3.3 34.2 - - + +
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER* 3.3 18.1 - - - +
337A ALA* 1.3 80.0 - - - +
339A VAL* 1.3 62.4 + - + +
341A LEU* 3.4 11.8 + - + +
342A TYR* 2.9 25.8 + - - +
497A PHE* 4.1 19.9 - - + +
516A MS7 4.4 9.1 - - + -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU 3.5 21.3 - - - +
335A VAL* 4.0 15.0 - - + -
336A SER* 3.0 19.0 + - - +
338A VAL* 1.3 78.0 - - + +
340A LEU* 1.3 67.5 + - - +
342A TYR* 3.1 8.9 + - + +
343A MET* 2.9 27.4 + - + +
375A HIS* 3.5 49.4 - - + +
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Residues in contact with LEU 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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327A LEU* 3.8 13.2 - - + -
335A VAL* 3.7 24.0 - - + -
336A SER 3.0 15.6 + - - +
337A ALA* 3.5 10.8 - - - +
339A VAL* 1.3 77.7 - - - +
341A LEU* 1.4 62.0 + - - +
343A MET* 3.3 6.8 + - - +
344A ALA* 3.0 23.9 + - - +
432A ILE* 3.6 45.3 - - + +
433A ALA* 4.3 5.4 - - - +
435A TYR* 4.0 27.6 - - + +
516A MS7 3.9 24.9 - - + -
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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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337A ALA 2.8 14.0 + - - +
338A VAL* 3.4 12.6 - - + +
340A LEU* 1.4 74.2 - - - +
342A TYR* 1.3 57.4 + - - +
344A ALA* 3.3 2.3 + - - +
345A THR* 2.8 37.2 + - - +
493A PHE* 3.6 31.9 - - + +
496A MET* 3.9 19.3 - - + +
497A PHE* 3.7 36.8 - - + +
516A MS7 3.6 49.6 - - + +
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Residues in contact with TYR 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 VAL* 2.9 17.4 + - + +
339A VAL* 3.1 11.2 + - + +
341A LEU* 1.3 73.8 - - - +
343A MET* 1.4 61.9 + - - +
345A THR* 3.4 5.4 + - + -
346A GLN* 3.0 65.6 + - + +
374A ASN 3.7 15.8 + - - -
375A HIS* 3.5 23.6 - - + -
376A LEU* 4.9 5.7 - - - +
497A PHE* 3.4 39.7 - + + -
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Residues in contact with MET 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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323A LEU* 3.9 24.5 - - + -
326A TYR* 3.8 30.1 - - + -
327A LEU* 4.2 16.2 - - - -
335A VAL* 4.5 3.8 - - + -
339A VAL* 2.9 34.9 + - + +
340A LEU* 3.6 18.4 - - - +
342A TYR* 1.4 73.0 - - - +
344A ALA* 1.4 58.4 + - - +
346A GLN* 3.3 9.7 + - - +
347A ILE* 3.1 35.7 + - + +
371A VAL* 4.8 2.7 - - + -
375A HIS* 4.6 11.0 - - + +
377A VAL* 3.7 22.6 - - + +
432A ILE* 4.7 11.4 - - + -
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Residues in contact with ALA 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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340A LEU 3.0 13.8 + - - +
341A LEU 3.7 7.0 - - - +
343A MET* 1.4 73.7 - - - +
345A THR* 1.3 64.3 + - - +
347A ILE* 3.5 4.4 + - - +
348A SER* 3.0 25.3 + - - -
425A PHE* 4.0 4.9 - - + -
429A LEU* 3.5 31.4 - - + -
432A ILE* 4.3 12.0 - - + +
493A PHE* 4.0 15.9 - - + -
516A MS7 4.2 4.9 - - + -
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Residues in contact with THR 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 24.6 + - - +
342A TYR* 3.7 9.0 - - + -
343A MET 3.4 0.2 - - - -
344A ALA* 1.3 74.7 - - - +
346A GLN* 1.3 65.3 + - + +
348A SER* 2.9 20.2 + - - -
349A SER* 2.9 12.4 + - - -
490A HIS* 3.5 10.0 + - + +
493A PHE* 3.4 19.6 + - - +
494A GLU* 3.3 39.7 - - - +
497A PHE* 4.0 13.7 - - + +
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Residues in contact with GLN 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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297A ASN* 3.2 35.9 + - - +
342A TYR* 3.0 59.7 + - + +
343A MET* 3.3 10.0 + - - +
345A THR* 1.3 76.8 - - + +
347A ILE* 1.3 64.5 + - - +
349A SER* 3.2 14.0 + - - -
350A ALA 3.2 10.2 + - - -
375A HIS 3.0 22.4 + - - -
376A LEU* 3.5 10.9 - - - +
377A VAL* 2.9 29.5 + - + +
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Residues in contact with ILE 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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297A ASN* 5.4 0.2 - - - -
323A LEU* 3.9 20.4 - - + -
343A MET 3.1 19.2 + - - +
344A ALA 4.0 2.7 - - - +
345A THR 3.3 0.4 - - - -
346A GLN* 1.3 77.9 - - - +
348A SER* 1.3 63.6 + - - +
350A ALA* 3.2 3.3 + - - +
351A MET* 3.0 22.8 + - + +
364A LEU* 4.3 4.7 - - + -
369A CYS* 4.1 2.2 - - - -
377A VAL* 3.8 19.1 - - + +
379A VAL* 3.6 26.7 - - + -
425A PHE* 3.8 20.4 - - + -
428A LEU* 4.0 21.8 - - + -
432A ILE* 3.9 26.2 - - + -
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Residues in contact with SER 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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344A ALA 3.0 16.2 + - - -
345A THR* 2.9 20.4 + - - -
347A ILE* 1.3 76.7 - - - +
349A SER* 1.3 55.9 + - - +
351A MET* 3.9 6.3 - - - +
352A GLU* 2.8 30.5 + - - +
425A PHE* 4.0 11.1 - - - -
486A PHE* 4.4 4.4 - - - +
489A ILE* 3.9 27.6 - - - -
490A HIS* 3.2 25.1 + - - +
493A PHE* 3.9 2.8 - - - -
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Residues in contact with SER 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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295A HIS* 3.2 28.1 + - - -
297A ASN* 4.1 5.5 + - - -
345A THR 2.9 13.9 + - - -
346A GLN* 3.4 11.0 - - - -
347A ILE 3.1 0.4 - - - -
348A SER* 1.3 74.6 + - - +
350A ALA* 1.3 65.3 + - - +
352A GLU* 3.4 5.1 + - - +
353A TYR 3.0 18.0 + - - -
490A HIS* 3.7 26.1 + - - -
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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
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295A HIS* 3.7 13.3 - - - -
297A ASN* 3.3 35.2 - - + +
298A LEU* 3.9 10.7 - - + +
346A GLN 3.2 6.0 + - - +
347A ILE 3.6 7.9 - - - +
349A SER* 1.3 76.0 - - - +
351A MET* 1.3 58.8 + - + +
353A TYR* 3.2 5.4 + - - +
354A LEU* 2.9 30.7 + - - +
379A VAL* 3.7 16.2 - - + -
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Residues in contact with MET 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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347A ILE* 3.0 26.0 + - + +
348A SER* 3.9 1.3 - - - +
350A ALA* 1.3 73.9 - - - +
352A GLU* 1.3 61.0 + - - +
354A LEU* 3.8 27.2 - - + +
355A GLU* 2.9 30.5 + - - +
361A HIS* 4.1 8.3 - - + -
364A LEU* 3.8 33.9 - - + -
379A VAL* 4.5 8.3 - - + -
418A ILE* 4.3 6.7 - - + +
421A ASP* 3.7 23.1 - - + +
486A PHE* 3.4 50.7 - - + -
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Residues in contact with GLU 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 SER 2.8 20.9 + - - +
349A SER* 3.4 6.5 + - - +
351A MET* 1.3 71.6 - - - +
353A TYR* 1.3 58.5 + - - +
355A GLU* 3.3 4.6 + - - +
356A LYS* 3.0 62.6 + - + +
486A PHE* 3.5 18.9 - - - +
487A ALA* 3.8 32.4 - - + +
490A HIS* 2.9 31.6 - - - -
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Residues in contact with TYR 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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292A GLU 3.7 2.1 + - - -
293A ILE* 3.4 23.0 - - + -
294A LYS* 2.8 39.0 + - - +
295A HIS* 3.5 27.8 - + + -
298A LEU* 3.5 28.5 - - + -
349A SER 3.0 7.0 + - - +
350A ALA 3.4 7.2 - - - +
352A GLU* 1.3 75.1 - - - +
354A LEU* 1.3 70.9 + - + +
356A LYS* 3.3 11.5 + - + +
357A LYS* 2.9 50.6 + - + +
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Residues in contact with LEU 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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1A STI 5.2 7.2 - - - -
293A ILE* 4.1 27.6 - - + -
298A LEU* 3.8 33.7 - - + -
350A ALA 2.9 19.0 + - - +
351A MET* 3.4 38.1 + - + +
353A TYR* 1.3 74.3 - - + +
355A GLU* 1.3 63.3 + - - +
357A LYS* 3.2 3.9 + - - +
358A ASN 3.1 4.5 + - - -
359A PHE* 3.0 49.5 + - + +
361A HIS* 4.4 23.8 - - + +
418A ILE* 4.9 0.2 - - + -
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Residues in contact with GLU 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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351A MET 2.9 18.1 + - - +
352A GLU* 3.3 6.4 - - - +
354A LEU* 1.3 77.7 - - - +
356A LYS* 1.3 64.5 - - + +
358A ASN* 3.0 19.9 + - - +
359A PHE 4.5 1.3 - - - -
418A ILE* 3.8 37.0 - - + +
419A LYS* 5.3 0.9 + - - -
422A VAL* 4.9 1.0 - - - +
485A SER* 3.6 15.7 - - - -
486A PHE* 2.8 31.4 + - - +
487A ALA* 3.1 29.8 + - - +
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Residues in contact with LYS 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 GLU* 3.0 48.6 + - + +
353A TYR* 3.5 13.7 - - + +
355A GLU* 1.3 78.2 - - + +
357A LYS* 1.3 64.0 + - + +
358A ASN* 3.3 11.4 + - - -
487A ALA* 5.8 2.2 - - + -
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Residues in contact with LYS 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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292A GLU* 4.1 16.3 + - - +
353A TYR* 2.9 59.8 + - + +
354A LEU 3.8 0.9 - - - +
355A GLU 3.1 0.4 - - - -
356A LYS* 1.3 81.4 - - + +
358A ASN* 1.3 72.7 + - - +
359A PHE* 3.4 34.1 + - + -
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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