Contacts of the helix formed by residues 315 - 336 (chain N) in PDB entry 5KZ5
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 MET 315 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N PRO* 5.7 10.1 - - - -
311N ALA 3.2 9.4 + - - +
312N GLN* 3.6 37.2 - - + +
313N GLN 3.3 2.0 + - - -
314N GLU* 1.3 75.3 - - - +
316N GLU* 1.4 75.9 + - + +
318N ASP* 3.7 5.1 - - - +
319N HIS* 3.0 42.2 + - + +
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Residues in contact with GLU 316 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314N GLU 3.1 1.6 + - - +
315N MET* 1.4 95.2 - - + +
317N TYR* 1.4 63.1 + - - +
319N HIS* 3.7 13.9 + - - -
320N LYS* 3.2 52.0 + - - +
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Residues in contact with TYR 317 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 5.5 4.7 - - + -
43B ARG* 3.5 26.8 + - - -
314N GLU* 3.1 29.9 + - + +
316N GLU* 1.4 76.7 - - - +
318N ASP* 1.4 63.5 + - - +
320N LYS* 4.0 5.1 - - - +
321N ARG* 3.1 61.0 + - + +
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Residues in contact with ASP 318 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 4.6 10.6 - - - +
46B ILE* 6.2 0.2 - - - +
238N GLY 5.1 5.0 - - - +
239N LYS* 6.0 0.9 - - - -
311N ALA* 4.8 12.0 - - - +
314N GLU* 3.3 19.4 + - + +
315N MET* 3.7 13.0 - - - +
316N GLU 3.4 0.2 - - - -
317N TYR* 1.4 83.1 - - - +
319N HIS* 1.4 63.4 + - - +
321N ARG* 3.9 2.3 - - - +
322N ILE* 3.2 49.9 + - - +
412N ARG* 4.1 18.0 + - - -
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Residues in contact with HIS 319 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239N LYS 5.4 9.0 - - - +
241N PRO* 6.0 5.8 - - + -
315N MET* 3.0 41.2 + - + +
316N GLU* 3.7 13.6 + - - -
318N ASP* 1.4 77.2 - - - +
320N LYS* 1.4 108.8 + - + +
322N ILE* 4.2 4.9 - - - +
323N SER* 3.1 29.3 + - - -
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Residues in contact with LYS 320 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316N GLU* 3.2 49.0 + - + +
317N TYR* 4.0 4.7 - - - +
318N ASP 3.3 0.4 - - - -
319N HIS* 1.4 104.3 + - + +
321N ARG* 1.3 60.9 + - - +
323N SER* 3.1 18.5 + - - -
324N LYS* 3.4 13.5 + - - +
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Residues in contact with ARG 321 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 6.1 0.4 - - - +
317N TYR* 3.1 51.6 + - + +
318N ASP* 3.9 4.5 - - - +
320N LYS* 1.3 75.1 - - - +
322N ILE* 1.3 65.9 + - + +
324N LYS* 3.6 14.8 + - - +
325N LEU* 3.3 48.9 + - + +
412N ARG* 6.3 0.2 - - - +
414N THR 5.6 0.9 - - - +
415N THR* 3.7 14.8 - - - +
416N GLU* 3.5 48.9 + - - +
417N GLU* 4.7 2.6 + - - -
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Residues in contact with ILE 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238N GLY 5.4 0.7 - - - +
239N LYS* 4.1 26.5 - - + +
318N ASP* 3.2 37.1 + - - +
319N HIS* 4.2 4.9 - - - +
320N LYS 3.5 0.2 - - - -
321N ARG* 1.3 78.5 - - + +
323N SER* 1.4 58.7 + - - +
325N LEU* 3.4 7.8 + - - +
326N SER* 3.0 27.2 + - - -
351N PRO* 3.6 28.5 - - + +
412N ARG* 3.6 40.2 - - - +
414N THR* 4.8 14.0 - - + +
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Residues in contact with SER 323 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319N HIS* 3.1 19.0 + - - -
320N LYS* 3.1 13.7 + - - -
322N ILE* 1.4 77.2 - - - +
324N LYS* 1.4 61.6 + - - +
326N SER* 3.2 16.8 + - - -
327N GLU* 3.3 17.7 + - - +
349N HIS* 4.4 9.8 - - - -
351N PRO* 4.9 5.6 - - - +
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Residues in contact with LYS 324 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N LYS 3.4 13.8 + - - +
321N ARG* 3.8 14.9 - - - +
322N ILE 3.4 0.2 - - - -
323N SER* 1.4 80.0 + - - +
325N LEU* 1.3 64.0 + - + +
327N GLU* 3.0 31.1 - - - +
328N ARG* 3.4 38.8 + - - +
416N GLU* 3.7 14.6 + - - -
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Residues in contact with LEU 325 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321N ARG* 3.3 48.0 + - + +
322N ILE* 3.8 6.1 - - - +
323N SER 3.4 0.2 - - - -
324N LYS* 1.3 81.6 - - + +
326N SER* 1.4 63.3 + - - +
328N ARG* 3.5 6.4 + - - +
329N LEU* 3.1 23.6 + - - +
414N THR* 3.5 39.4 - - + +
415N THR* 3.7 11.9 - - - -
416N GLU* 3.3 48.0 - - - +
419N VAL* 3.9 12.3 - - + +
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Residues in contact with SER 326 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322N ILE* 3.0 18.5 + - - -
323N SER* 3.2 6.8 + - - -
325N LEU* 1.4 74.3 - - - +
327N GLU* 1.4 62.6 + - - +
329N LEU* 3.5 16.0 + - - +
330N ILE* 3.3 23.8 + - - +
349N HIS* 3.0 31.4 - - - -
351N PRO* 3.8 26.2 - - - +
354N ILE* 4.8 4.9 - - - +
414N THR* 4.8 6.7 - - - +
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Residues in contact with GLU 327 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323N SER 3.3 17.5 - - - +
324N LYS* 3.0 24.6 - - - +
326N SER* 1.4 76.5 + - - +
328N ARG* 1.4 79.9 + - - +
330N ILE* 3.4 9.8 + - - +
331N GLN* 3.1 44.6 + - + +
346N PRO* 4.1 12.0 - - - +
347N LYS* 5.9 0.7 - - + -
349N HIS* 4.0 15.5 + - - +
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Residues in contact with ARG 328 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N LYS* 3.4 39.8 + - - +
325N LEU* 3.5 7.6 - - - +
326N SER 3.3 0.2 - - - -
327N GLU* 1.4 84.7 + - - +
329N LEU* 1.3 63.6 + - - +
331N GLN* 3.4 13.4 + - - +
332N ASN* 3.2 33.9 + - - +
416N GLU* 3.4 30.5 + - - -
419N VAL* 3.8 17.0 - - + +
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Residues in contact with LEU 329 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325N LEU 3.1 10.9 + - - +
326N SER* 3.5 13.5 - - - +
328N ARG* 1.3 78.5 - - - +
330N ILE* 1.4 58.5 + - - +
332N ASN* 3.3 9.8 + - - +
333N ILE* 3.2 38.8 + - + +
354N ILE* 4.2 21.5 - - + -
410N ILE* 5.2 14.1 - - + -
414N THR* 5.9 6.1 - - + -
418N GLU* 4.7 4.0 - - + +
419N VAL* 4.7 15.4 - - + +
422N THR* 3.1 39.9 - - + +
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Residues in contact with ILE 330 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326N SER* 3.3 17.7 - - - +
327N GLU* 3.6 7.6 - - - +
328N ARG 3.4 0.4 - - - -
329N LEU* 1.4 71.1 - - - +
331N GLN* 1.4 66.7 + - + +
333N ILE* 3.5 9.3 + - - +
334N MET* 3.1 27.5 + - + +
342N MET* 3.7 44.6 - - + -
346N PRO* 4.3 13.9 - - + +
349N HIS* 3.8 31.0 - - + -
354N ILE* 3.7 27.8 - - + -
356N LEU* 6.3 1.1 - - + -
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Residues in contact with GLN 331 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327N GLU* 3.1 44.9 + - + +
328N ARG* 3.4 13.7 + - + +
330N ILE* 1.4 77.7 - - + +
332N ASN* 1.4 64.5 + - - +
334N MET* 3.4 4.5 + - - +
335N LYS* 3.2 60.8 + - - +
346N PRO* 6.4 1.8 - - + -
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Residues in contact with ASN 332 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328N ARG* 3.2 19.1 + - - +
329N LEU* 3.3 8.8 + - - +
331N GLN* 1.4 78.0 - - - +
333N ILE* 1.4 60.7 + - - +
335N LYS* 4.4 3.1 - - - +
336N SER* 3.2 27.4 + - - -
419N VAL* 3.3 43.4 + - - +
422N THR* 4.5 8.9 - - + -
423N VAL* 3.5 22.1 - - + +
426N CYS* 4.5 2.4 - - - -
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Residues in contact with ILE 333 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329N LEU* 3.2 34.5 + - + +
330N ILE* 3.8 9.2 - - - +
332N ASN* 1.4 74.7 - - - +
334N MET* 1.4 63.6 + - - +
337N LEU* 3.4 44.3 + - + +
340N VAL* 4.0 6.4 - - + +
354N ILE* 5.8 5.8 - - + -
356N LEU* 4.0 28.7 - - + -
371N LYS* 5.8 2.7 - - + +
408N PHE* 5.9 4.3 - - + -
422N THR* 3.6 20.4 - - + -
426N CYS* 4.6 7.4 - - - -
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Residues in contact with MET 334 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330N ILE* 3.1 21.9 + - + +
331N GLN* 3.6 7.4 - - - +
333N ILE* 1.4 77.1 - - - +
335N LYS* 1.3 67.9 - - + +
337N LEU 3.2 19.2 - - - +
340N VAL* 3.3 42.9 - - + +
341N VAL* 4.6 0.2 - - - -
342N MET* 3.9 31.2 - - + +
356N LEU* 5.7 0.9 - - + -
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Residues in contact with LYS 335 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331N GLN* 3.2 48.1 + - + +
332N ASN* 4.5 2.9 - - - +
334N MET* 1.3 86.6 - - + +
336N SER* 1.4 59.9 + - - +
337N LEU 3.4 1.5 + - - +
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Residues in contact with SER 336 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332N ASN 3.2 19.6 + - - -
333N ILE 4.2 0.7 - - - -
334N MET 3.3 0.8 - - - -
335N LYS* 1.4 79.0 - - - +
337N LEU* 1.3 62.0 + - - +
338N PRO* 4.2 4.4 - - - +
423N VAL* 5.1 4.4 + - - +
426N CYS* 3.2 33.1 - - - +
427N ILE* 5.1 6.4 - - - +
430N VAL* 5.5 5.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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