Contacts of the helix formed by residues 336 - 357 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D ARG 3.7 7.4 - - - -
333D GLN* 4.1 14.6 - - - -
334D GLU 3.1 3.3 + - - -
335D VAL* 1.3 76.7 - - - +
337D ALA* 1.3 65.5 - - - +
338D VAL* 3.7 21.9 - - - +
339D VAL* 3.0 16.6 + - - +
340D LEU* 3.0 12.7 + - - +
435D TYR* 4.1 5.6 - - - -
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D SER* 1.3 73.8 - - - +
338D VAL* 1.3 58.4 + - - +
340D LEU* 3.2 11.8 + - - +
341D LEU 2.9 23.9 + - - -
435D TYR* 4.5 1.8 + - - -
463D GLY 5.8 3.8 - - - +
465D PRO* 6.0 1.1 - - + -
516D MS7 3.3 34.5 - - + +
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Residues in contact with VAL 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D SER* 3.7 13.4 + - - +
337D ALA* 1.3 80.7 - - - +
339D VAL* 1.3 65.1 + - + +
341D LEU* 3.4 12.6 + - + +
342D TYR* 2.9 25.8 + - - +
497D PHE* 4.3 23.3 - - + +
516D MS7 4.5 8.4 - - + -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLU 3.4 21.5 - - - +
335D VAL* 4.0 15.0 - - + -
336D SER* 3.0 18.6 + - - +
338D VAL* 1.3 83.6 - - + +
340D LEU* 1.3 63.3 + - - +
342D TYR* 3.1 9.6 + - + +
343D MET* 2.9 32.3 + - - +
375D HIS* 3.5 50.0 - - + +
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Residues in contact with LEU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LEU* 3.8 12.1 - - + -
335D VAL* 3.7 24.2 - - + -
336D SER 3.0 15.8 + - - +
337D ALA* 3.5 11.7 - - - +
339D VAL* 1.3 75.8 - - - +
341D LEU* 1.3 63.2 + - - +
343D MET* 3.3 9.1 + - + +
344D ALA* 3.0 24.3 + - - +
432D ILE* 3.6 43.3 - - + +
433D ALA* 4.4 4.5 - - - +
435D TYR* 3.8 28.7 - - + +
516D MS7 3.9 24.7 - - + -
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Residues in contact with LEU 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D ALA 2.9 13.1 + - - +
338D VAL* 3.4 14.8 - - + +
340D LEU* 1.3 74.7 - - - +
342D TYR* 1.3 62.8 + - - +
344D ALA* 3.2 1.9 + - - +
345D THR* 2.8 31.2 + - - +
493D PHE* 3.7 30.3 - - + +
496D MET* 4.0 13.0 - - + +
497D PHE* 3.7 36.6 - - + +
516D MS7 3.5 53.9 - - + +
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Residues in contact with TYR 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D VAL 2.9 14.9 + - - +
339D VAL* 3.1 10.7 + - + +
341D LEU* 1.3 75.3 - - - +
343D MET* 1.4 63.6 + - - +
345D THR* 3.2 6.2 + - + -
346D GLN* 3.0 65.2 + - + +
374D ASN 3.7 15.0 + - - -
375D HIS* 3.4 25.1 - - + -
376D LEU* 4.8 6.2 - - - +
497D PHE* 3.8 39.3 - + + -
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Residues in contact with MET 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D LEU* 3.8 21.5 - - + -
326D TYR* 4.7 13.9 - - - -
327D LEU* 3.9 17.0 - - + -
335D VAL* 4.5 2.9 - - + -
339D VAL* 2.9 23.2 + - + +
340D LEU* 3.7 35.4 - - + +
341D LEU 3.3 0.2 - - - -
342D TYR* 1.4 74.4 - - - +
344D ALA* 1.3 62.2 + - - +
346D GLN* 3.3 10.2 + - - +
347D ILE* 3.1 31.5 + - + +
371D VAL* 5.3 0.9 - - - -
375D HIS* 4.3 11.9 - - + +
377D VAL* 3.7 22.5 - - + +
432D ILE* 4.4 10.5 - - + -
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D LEU 3.0 17.2 + - - +
341D LEU 3.6 4.3 - - - +
343D MET* 1.3 76.3 - - - +
345D THR* 1.3 63.6 + - - +
347D ILE* 3.4 5.1 + - - +
348D SER* 3.0 24.4 + - - -
425D PHE* 3.9 5.9 - - + -
429D LEU* 3.7 29.8 - - + -
432D ILE* 4.2 12.7 - - + +
493D PHE* 3.9 16.3 - - + -
516D MS7 4.2 3.6 - - + -
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LEU* 2.8 25.5 + - - +
342D TYR* 3.5 11.9 - - + -
344D ALA* 1.3 77.3 - - - +
346D GLN* 1.3 61.2 + - + +
348D SER* 3.0 9.4 + - - -
349D SER* 2.9 27.5 + - - -
490D HIS* 3.5 21.0 + - + +
493D PHE* 3.4 23.1 - - + +
494D GLU* 4.4 11.4 - - + +
497D PHE* 3.9 19.0 - - + +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ASN* 3.1 41.3 + - - +
342D TYR* 3.0 54.5 + - + +
343D MET* 3.5 13.9 - - - +
345D THR* 1.3 78.7 - - + +
347D ILE* 1.3 62.9 - - - +
349D SER* 3.3 4.0 + - - -
350D ALA 3.2 16.5 + - - -
375D HIS 2.9 24.4 + - - -
376D LEU* 3.4 9.5 - - - +
377D VAL* 2.8 30.7 + - + +
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Residues in contact with ILE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ASN* 5.4 0.4 - - - -
323D LEU* 3.9 20.0 - - + -
343D MET* 3.1 18.4 + - + +
344D ALA* 3.4 4.5 + - - +
345D THR 3.3 0.2 - - - -
346D GLN* 1.3 75.8 - - - +
348D SER* 1.3 57.6 + - - +
350D ALA* 3.2 4.0 + - - +
351D MET* 3.0 27.4 + - + +
364D LEU* 4.4 5.2 - - + -
369D CYS* 4.2 7.4 - - - -
377D VAL* 3.7 18.8 - - + -
379D VAL* 3.9 25.1 - - + -
425D PHE* 3.7 21.3 - - + -
428D LEU* 3.9 18.4 - - + -
432D ILE* 3.8 25.8 - - + -
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Residues in contact with SER 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ALA 3.0 15.5 + - - -
345D THR* 3.0 17.8 + - - -
347D ILE* 1.3 75.8 - - - +
349D SER* 1.3 53.0 + - - +
351D MET* 3.3 6.0 + - - +
352D GLU* 2.8 35.3 + - - +
425D PHE* 3.9 11.9 - - - -
486D PHE* 4.4 5.4 - - - +
489D ILE* 3.8 27.4 - - - -
490D HIS* 3.3 24.1 + - - +
493D PHE* 3.8 3.0 - - - -
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Residues in contact with SER 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D HIS* 3.2 28.3 + - - -
297D ASN* 4.2 5.4 + - - -
345D THR 2.9 14.2 + - - -
346D GLN* 3.4 11.4 - - - -
347D ILE 3.2 0.2 - - - -
348D SER* 1.3 77.4 + - - +
350D ALA* 1.3 61.2 + - - +
352D GLU* 3.4 5.9 + - - +
353D TYR 3.1 17.7 + - - -
490D HIS* 3.5 24.2 + - - -
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D HIS* 3.7 14.5 - - - -
297D ASN* 3.3 35.7 - - + +
298D LEU* 4.0 6.6 - - + +
346D GLN 3.2 5.8 + - - +
347D ILE 3.5 8.3 - - - +
349D SER* 1.3 74.2 - - - +
351D MET* 1.3 60.7 + - - +
353D TYR* 3.4 6.4 + - - +
354D LEU* 3.0 29.7 + - - +
379D VAL* 3.7 19.1 - - + -
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Residues in contact with MET 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D ILE* 3.0 23.4 + - + +
348D SER* 3.7 3.4 - - - +
350D ALA* 1.3 78.2 - - - +
352D GLU* 1.3 60.5 + - - +
354D LEU* 3.8 22.1 - - + +
355D GLU* 2.9 30.1 + - - +
361D HIS* 3.9 14.1 - - + -
364D LEU* 3.9 29.2 - - + -
379D VAL* 4.4 9.2 - - - -
418D ILE* 4.5 5.1 - - + +
421D ASP* 3.8 26.5 - - + +
486D PHE* 3.4 50.1 - - + +
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Residues in contact with GLU 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D SER 2.8 20.7 + - - +
349D SER* 3.6 7.1 + - - +
351D MET* 1.3 72.4 - - - +
353D TYR* 1.3 56.9 + - - +
355D GLU* 3.3 4.9 - - - +
356D LYS* 2.8 30.8 + - + +
486D PHE* 3.6 18.7 - - - +
487D ALA* 3.7 31.6 - - + +
490D HIS* 3.3 31.9 - - - +
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Residues in contact with TYR 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D GLU 3.7 2.6 + - - -
293D ILE* 3.5 13.9 - - + -
294D LYS* 2.9 39.1 + - - +
295D HIS* 3.4 31.2 - + + -
298D LEU* 3.5 30.5 - - + -
349D SER 3.1 6.5 + - - +
350D ALA 3.4 6.1 - - - +
352D GLU* 1.3 74.1 - - - +
354D LEU* 1.4 69.7 + - + +
356D LYS* 3.1 17.6 + - + +
357D LYS* 2.9 65.1 + - + +
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D STI 5.3 7.0 - - + -
293D ILE* 4.4 13.7 - - + -
298D LEU* 3.9 32.3 - - + -
350D ALA 3.0 18.6 + - - +
351D MET* 3.3 36.8 + - + +
353D TYR* 1.4 76.3 - - + +
355D GLU* 1.3 63.6 + - - +
357D LYS* 3.2 3.5 + - - -
358D ASN 2.9 18.0 + - - -
359D PHE* 3.0 47.0 + - + +
360D ILE 5.5 0.2 - - - +
361D HIS* 4.4 22.4 - - + +
418D ILE* 4.9 0.4 - - + -
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Residues in contact with GLU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D MET 2.9 18.1 + - - +
352D GLU* 3.3 5.4 - - - +
354D LEU* 1.3 76.1 - - - +
356D LYS* 1.3 63.8 + - - +
358D ASN* 3.0 18.2 + - - +
359D PHE 4.5 0.9 - - - -
418D ILE* 3.7 35.9 - - + +
419D LYS* 5.3 0.5 + - - -
422D VAL* 5.0 0.9 - - - +
485D SER* 3.6 17.4 - - - -
486D PHE* 2.9 32.2 + - - +
487D ALA* 3.1 30.3 + - - +
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Residues in contact with LYS 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLU* 2.8 23.0 + - + +
353D TYR* 3.5 19.8 - - + +
355D GLU* 1.3 73.7 - - - +
357D LYS* 1.3 67.0 + - + +
358D ASN* 3.4 12.1 + - - +
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Residues in contact with LYS 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D GLU* 4.3 13.2 + - - +
353D TYR* 2.9 60.8 + - + +
354D LEU* 3.2 1.5 + - - +
356D LYS* 1.3 82.1 - - + +
358D ASN* 1.3 74.4 + - - +
359D PHE* 3.3 32.1 + - + -
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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
------------------------------------------------------------
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