Contacts of the helix formed by residues 330 - 349 (chain N) in PDB entry 1PP9
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 330 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302N LYS 4.1 10.4 + - - -
303N LEU* 3.1 34.9 + - - +
326N CYS* 3.9 4.7 - - - -
327N ASP* 3.1 22.3 + - - +
329N MET* 1.3 80.7 + - - +
331N ILE* 1.3 65.6 + - - +
332N ASP 3.4 2.2 - - - -
333N ASP* 3.3 10.3 + - - +
334N MET* 3.0 22.9 + - - +
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Residues in contact with ILE 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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251N ALA* 3.8 15.5 - - + -
253N VAL* 4.1 11.9 - - + -
324N PHE* 4.1 7.7 - - + -
326N CYS* 3.7 21.5 - - - -
327N ASP 3.9 2.0 - - - +
328N HIS* 3.9 14.1 - - - +
330N SER* 1.3 76.3 - - - +
332N ASP* 1.3 62.9 + - - +
334N MET* 3.3 1.7 + - - +
335N MET* 3.0 22.9 + - - +
427N PRO 3.5 24.7 - - - +
428N ILE* 3.8 17.0 - - + -
430N GLN* 3.0 9.4 + - - +
431N LEU* 3.7 39.7 - - + +
432N PRO* 4.3 0.9 - - + -
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Residues in contact with ASP 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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331N ILE* 1.3 73.5 - - - +
333N ASP* 1.3 63.8 + - - +
335N MET* 3.5 2.1 + - - +
336N PHE* 2.9 30.8 + - - +
430N GLN* 2.9 33.5 + - + +
432N PRO* 3.2 29.9 - - - +
436N ARG* 5.7 2.1 + - - -
20P ASP* 4.9 12.1 - - - +
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Residues in contact with ASP 333 (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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303N LEU* 3.8 28.5 - - + +
329N MET 4.6 9.6 - - - +
330N SER* 3.3 9.5 + - - +
332N ASP* 1.3 79.9 - - - +
334N MET* 1.3 66.6 + - - +
336N PHE* 3.1 8.8 + - - +
337N VAL* 2.9 31.3 + - + +
430N GLN* 4.7 0.2 + - - -
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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
----------------------------------------------------------
294N LEU* 4.1 26.2 - - + -
298N ALA* 4.6 1.6 - - - -
303N LEU* 3.4 45.3 - - + +
304N CYS* 3.9 20.6 - - + -
307N PHE* 4.2 10.3 - - + -
324N PHE* 3.7 50.3 - - + -
326N CYS* 4.5 1.1 - - - -
330N SER 3.0 15.0 + - - +
331N ILE 3.6 4.3 - - - +
333N ASP* 1.3 77.9 - - - +
335N MET* 1.3 58.1 + - - +
337N VAL* 3.3 2.2 + - - +
338N LEU* 2.9 34.2 + - + +
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Residues in contact with MET 335 (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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253N VAL* 3.9 27.8 - - + -
255N ILE* 4.0 31.9 - - + -
324N PHE* 4.2 11.2 - - + -
331N ILE 3.0 16.2 + - - +
332N ASP 3.7 3.8 - - - +
334N MET* 1.3 75.7 - - - +
336N PHE* 1.3 63.4 + - - +
338N LEU* 3.8 7.8 - - - +
339N GLN* 3.0 50.5 + - - +
422N VAL* 5.1 0.9 - - + -
431N LEU* 4.1 15.5 - - + -
432N PRO* 4.3 19.7 - - + -
437N ILE* 4.3 16.4 - - + -
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Residues in contact with PHE 336 (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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332N ASP* 2.9 23.0 + - - +
333N ASP* 3.1 9.4 + - - +
335N MET* 1.3 76.8 - - - +
337N VAL* 1.3 72.8 - - + +
339N GLN* 4.1 3.7 - - - +
340N GLY* 3.0 26.6 + - - -
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Residues in contact with VAL 337 (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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294N LEU* 3.5 33.7 - - + -
297N ILE* 4.3 22.4 - - + -
303N LEU* 4.2 17.0 - - + -
333N ASP* 2.9 18.6 + - + +
334N MET 3.9 0.9 - - - +
336N PHE* 1.3 88.1 - - + +
338N LEU* 1.3 65.5 + - - +
340N GLY* 3.3 1.6 + - - +
341N GLN* 3.0 32.9 + - + +
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Residues in contact with LEU 338 (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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255N ILE* 3.8 28.7 - - + -
277N ILE* 4.7 7.0 - - + -
294N LEU* 3.8 30.4 - - + +
309N THR* 5.3 0.2 - - + -
322N ALA* 3.9 20.2 - - + -
324N PHE* 4.4 17.9 - - + -
334N MET* 2.9 20.7 + - + +
335N MET* 3.8 8.3 - - - +
337N VAL* 1.3 76.7 - - - +
339N GLN* 1.3 62.9 + - - +
341N GLN* 3.1 6.5 + - - +
342N TRP* 3.1 51.3 + - + +
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Residues in contact with GLN 339 (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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255N ILE* 4.5 2.0 - - - +
335N MET* 3.0 46.3 + - - +
336N PHE* 4.2 2.9 - - - +
338N LEU* 1.3 73.0 - - + +
340N GLY* 1.3 67.0 + - - +
342N TRP* 3.2 25.2 + - + +
343N MET* 2.9 30.1 + - + +
436N ARG 4.8 0.9 - - - +
437N ILE* 2.8 40.0 + - - +
440N GLY* 3.6 23.4 - - - +
441N MET* 3.2 22.4 - - - -
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Residues in contact with GLY 340 (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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336N PHE* 3.0 20.3 + - - -
337N VAL* 3.7 2.7 - - - -
338N LEU 3.2 0.2 - - - -
339N GLN* 1.3 76.7 - - - +
341N GLN* 1.3 61.4 + - - +
343N MET* 3.4 7.4 + - - +
344N ARG* 2.8 28.8 + - - +
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Residues in contact with GLN 341 (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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277N ILE* 4.1 21.0 - - + +
293N PRO* 3.6 28.5 - - + +
294N LEU* 4.3 20.0 - - + +
297N ILE* 6.1 0.2 - - - +
337N VAL* 3.0 26.8 + - + +
338N LEU* 3.5 9.4 - - - +
339N GLN 3.1 0.2 - - - -
340N GLY* 1.3 76.5 - - - +
342N TRP* 1.3 65.9 + - - +
344N ARG* 3.1 42.9 + - - +
345N LEU* 3.0 27.2 + - - +
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Residues in contact with TRP 342 (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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255N ILE* 3.8 47.6 - - + -
256N ALA* 5.2 1.6 - - - -
257N VAL* 5.6 0.7 - - + -
274N ASN* 5.2 3.2 + - - -
277N ILE* 3.4 27.7 - - + +
309N THR* 5.2 3.6 - - - +
321N GLY* 3.9 20.5 - - - -
322N ALA* 4.4 0.2 - - + -
338N LEU* 3.1 34.7 + - + +
339N GLN* 3.2 27.3 + - + +
341N GLN* 1.3 75.2 - - - +
343N MET* 1.3 74.3 + - + +
345N LEU* 3.1 8.7 + - + +
346N CYS* 3.0 25.0 + - - -
411N CYS* 5.1 1.0 - - - +
415N PHE* 3.4 54.1 - + + -
441N MET* 4.1 20.2 - - + -
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Residues in contact with MET 343 (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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339N GLN 2.9 19.3 + - - +
340N GLY* 3.6 8.1 - - - +
342N TRP* 1.3 89.3 - - + +
344N ARG* 1.3 61.1 + - - +
346N CYS* 3.2 15.8 + - - +
347N THR* 3.2 28.1 + - + +
415N PHE* 4.3 14.4 - - + +
416N TYR* 3.9 14.1 - - - -
440N GLY 3.6 11.9 - - - +
441N MET* 3.4 44.6 - - - +
442N PHE* 3.6 10.8 - - - +
443N TRP 4.6 5.2 - - - +
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Residues in contact with ARG 344 (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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276N ILE* 4.4 5.5 - - - +
277N ILE* 6.1 1.0 - - - +
293N PRO* 4.2 14.1 - - - +
340N GLY 2.8 21.0 + - - +
341N GLN* 3.1 35.0 + - - +
342N TRP 3.2 0.4 - - - -
343N MET* 1.3 72.7 - - - +
345N LEU* 1.3 70.5 + - - +
347N THR* 4.2 4.7 - - - -
348N SER* 2.6 54.7 + - - +
349N ALA* 3.4 1.7 + - - +
350N THR* 5.0 3.6 - - - +
353N GLU* 2.7 45.2 + - - -
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Residues in contact with LEU 345 (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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273N ALA* 3.7 39.9 - - + +
276N ILE* 4.1 13.9 - - + -
277N ILE* 4.1 22.7 - - + -
341N GLN 3.0 15.1 + - - +
342N TRP* 3.1 8.9 + - + +
344N ARG* 1.3 102.4 - - - +
346N CYS* 1.3 61.8 + - - +
347N THR 3.4 0.3 + - - -
349N ALA* 3.5 22.9 + - + +
353N GLU* 3.8 18.6 - - - +
407N VAL* 4.7 1.8 - - + -
408N ARG* 3.5 15.9 + - - +
411N CYS* 4.1 13.5 - - - -
415N PHE* 6.4 0.4 - - + -
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Residues in contact with CYS 346 (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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342N TRP 3.0 19.3 + - - -
343N MET* 3.2 14.1 + - - +
345N LEU* 1.3 76.8 - - - +
347N THR* 1.3 64.7 + - + +
408N ARG* 3.3 24.0 - - - +
411N CYS* 3.5 33.7 - - - -
412N SER* 3.2 28.6 + - - +
415N PHE* 3.9 13.7 - - - -
416N TYR* 4.1 14.8 - - + -
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Residues in contact with THR 347 (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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343N MET* 3.2 16.3 + - + +
344N ARG* 3.9 2.9 + - - -
346N CYS* 1.3 85.4 - - + +
348N SER* 1.3 72.0 + - - +
349N ALA 4.0 0.4 - - - -
408N ARG* 3.4 20.8 + - - +
412N SER* 5.7 0.2 - - - +
416N TYR* 5.0 14.1 - - + -
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Residues in contact with SER 348 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344N ARG* 2.6 37.0 + - - +
347N THR* 1.3 89.5 + - - +
349N ALA* 1.3 69.0 + - - +
350N THR* 3.2 12.6 + - - +
353N GLU* 3.9 2.0 - - - +
408N ARG* 3.6 11.6 + - - +
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Residues in contact with ALA 349 (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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344N ARG 3.4 4.2 + - - -
345N LEU* 3.5 26.0 + - + +
348N SER* 1.3 76.0 - - - +
350N THR* 1.3 59.7 + - - +
353N GLU* 3.1 11.4 - - - +
354N VAL* 4.0 11.4 - - + -
404N ALA* 3.5 10.2 - - - +
407N VAL* 3.9 22.4 - - + -
408N ARG* 3.1 31.4 + - + +
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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