Contacts of the helix formed by residues 353 - 372 (chain O) 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 353 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O LEU* 1.3 75.1 - - - +
354O ASN* 1.3 65.7 + - - +
355O PRO* 3.6 15.3 - - - -
356O ASP* 2.9 39.2 + - - +
357O VAL* 3.1 13.9 + - - +
407O ASP* 4.3 0.4 - - - -
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Residues in contact with ASN 354 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O LEU 3.8 1.8 + - - -
353O SER* 1.3 72.5 - - - +
355O PRO* 1.3 68.4 - - + +
357O VAL* 3.1 5.5 + - - +
358O GLN* 2.9 38.2 + - - +
361O LYS* 6.2 0.2 - - - +
407O ASP* 3.1 38.2 + - - +
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Residues in contact with PRO 355 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353O SER* 3.4 12.8 - - - -
354O ASN* 1.3 100.0 - - + +
356O ASP* 1.3 56.8 + - - +
358O GLN* 3.2 8.1 + - + +
359O ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 356 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278O VAL* 4.3 10.5 - - + +
352O LEU* 4.1 13.6 - - + +
353O SER* 2.9 35.8 + - - +
355O PRO* 1.3 79.3 - - - +
357O VAL* 1.3 57.7 + - - +
359O ALA* 3.3 8.2 + - - +
360O ALA* 3.0 27.3 + - - +
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Residues in contact with VAL 357 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274O VAL* 4.2 14.1 - - + -
278O VAL* 4.4 5.2 - - + -
352O LEU* 3.5 40.6 - - + -
353O SER 3.1 5.2 + - - +
354O ASN* 3.1 9.7 + - - +
356O ASP* 1.3 76.7 - - - +
358O GLN* 1.3 58.7 + - - +
360O ALA* 3.4 6.7 + - - +
361O LYS* 2.9 48.6 + - + +
405O VAL* 5.2 0.7 - - + +
407O ASP* 3.8 28.9 - - + +
410O VAL* 4.6 7.2 - - + -
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Residues in contact with GLN 358 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354O ASN* 2.9 25.7 + - - +
355O PRO* 3.2 12.7 + - + +
357O VAL* 1.3 77.3 - - - +
359O ALA* 1.3 64.1 + - - +
361O LYS* 3.4 26.2 + - - +
362O ASN* 3.0 44.1 + - - +
365O LYS* 4.9 3.2 - - - +
403O ASP* 4.6 8.1 + - - -
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Residues in contact with ALA 359 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N SER* 4.0 32.2 - - - +
292O THR* 5.8 5.4 - - + -
355O PRO 3.0 12.6 + - - +
356O ASP* 3.6 11.2 - - - +
358O GLN* 1.3 75.8 - - - +
360O ALA* 1.3 63.4 + - - +
362O ASN* 3.1 5.8 + - - +
363O LYS* 2.9 36.5 + - - +
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Residues in contact with ALA 360 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274O VAL* 3.8 10.1 - - + +
277O HIS* 3.6 16.8 - - - +
278O VAL* 3.5 46.2 - - + +
356O ASP 3.0 8.5 + - - +
357O VAL 3.5 7.4 - - - +
359O ALA* 1.3 77.1 - - - +
361O LYS* 1.3 57.3 + - - +
363O LYS* 3.2 7.0 + - - +
364O LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 361 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274O VAL* 4.3 10.8 - - + -
357O VAL* 2.9 35.4 + - + +
358O GLN* 3.7 29.8 + - - +
360O ALA* 1.3 76.5 - - - +
362O ASN* 1.3 58.2 + - - +
364O LEU* 3.8 5.5 - - - +
365O LYS* 2.8 43.1 + - + +
402O ILE* 3.0 37.5 - - + -
403O ASP* 2.9 20.9 + - - +
405O VAL* 2.6 31.7 + - - -
406O ALA* 5.0 0.2 - - - +
407O ASP* 5.1 2.6 + - - -
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Residues in contact with ASN 362 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N SER 2.9 25.3 + - - +
82N MET* 4.1 15.2 - - - +
83N GLY* 4.1 2.4 - - - -
102N LEU* 5.4 5.7 - - + +
104N LYS* 5.9 1.2 + - - -
358O GLN* 3.0 35.4 + - - +
359O ALA* 3.1 8.0 + - - +
361O LYS* 1.3 76.3 - - - +
363O LYS* 1.3 63.6 + - - +
365O LYS* 3.9 12.0 + - - +
366O ALA* 2.9 27.4 + - - +
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Residues in contact with LYS 363 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N GLU* 3.4 28.7 - - - +
81N SER 4.7 0.7 - - - +
83N GLY* 3.8 8.6 - - - +
277O HIS* 3.6 37.6 + - + +
280O GLY* 5.9 2.2 - - - -
284O HIS* 3.7 31.1 + - + +
292O THR* 2.6 45.8 + - - -
293O SER* 5.2 0.8 - - - +
359O ALA* 2.9 26.1 + - - +
360O ALA* 3.5 6.7 - - - +
362O ASN* 1.3 76.6 - - - +
364O LEU* 1.3 53.7 + - - +
366O ALA* 3.8 0.7 - - - +
367O GLY* 2.7 35.3 + - - -
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Residues in contact with LEU 364 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O ASN* 5.0 1.3 - - - +
273O SER* 4.1 27.8 - - - -
274O VAL* 4.2 13.7 - - + -
277O HIS* 3.5 34.6 - - + +
360O ALA 2.9 16.5 + - - +
361O LYS* 3.8 4.3 - - - +
363O LYS* 1.3 75.3 - - - +
365O LYS* 1.3 58.0 + - - +
367O GLY* 3.8 0.8 - - - -
368O TYR* 2.9 33.0 + - + +
402O ILE* 3.5 40.6 - - + -
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Residues in contact with LYS 365 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N LEU* 4.9 6.5 - - + -
104N LYS* 6.1 0.6 - - - +
358O GLN* 4.9 5.7 - - - +
361O LYS* 2.8 28.4 + - + +
362O ASN* 3.9 13.7 + - - +
364O LEU* 1.3 74.1 - - - +
366O ALA* 1.3 61.8 + - - +
368O TYR* 3.4 2.5 + - - +
369O LEU* 3.2 28.7 + - + +
399O LEU* 3.3 38.3 - - + +
402O ILE* 3.7 28.0 - - + -
403O ASP* 2.7 38.3 + - - +
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Residues in contact with ALA 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 4.6 0.2 - - - +
82N MET 4.5 1.6 - - - +
83N GLY* 3.4 26.7 - - - +
102N LEU* 3.7 32.6 - - + +
362O ASN 2.9 17.6 + - - +
363O LYS 3.9 0.4 - - - +
365O LYS* 1.3 73.2 - - - +
367O GLY* 1.3 66.6 + - - +
369O LEU* 3.4 2.0 + - - +
370O MET* 2.9 37.2 + - + +
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Residues in contact with GLY 367 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N GLY 5.0 0.4 + - - -
85N HIS* 5.5 7.0 - - - -
277O HIS* 5.8 2.5 - - - -
363O LYS 2.7 21.8 + - - -
364O LEU* 3.8 1.1 - - - -
366O ALA* 1.3 73.7 - - - +
368O TYR* 1.3 62.0 + - - +
370O MET* 3.4 9.4 + - - +
371O SER* 3.0 23.0 + - - -
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Residues in contact with TYR 368 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364O LEU* 2.9 20.3 + - + +
365O LYS* 3.7 6.1 - - - +
367O GLY* 1.3 75.9 - - - +
369O LEU* 1.3 76.5 + - + +
371O SER* 2.6 31.0 + - - -
372O VAL* 3.3 14.3 + - + +
381O GLU* 3.1 46.5 + - + +
385O GLN* 3.6 8.7 + - - -
392O TYR* 6.0 0.2 - - - -
393O THR 4.5 2.3 + - - -
395O PRO* 4.4 18.3 - - + +
398O VAL* 3.8 40.7 - - + +
399O LEU* 5.1 3.6 - - + -
402O ILE* 5.1 6.1 - - + -
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Residues in contact with LEU 369 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PRO* 4.1 32.3 - - + +
34N THR* 3.5 18.4 + - + +
102N LEU* 3.8 24.7 - - + -
365O LYS* 3.2 13.7 + - + +
366O ALA 3.4 1.5 + - - +
368O TYR* 1.3 87.4 - - + +
370O MET* 1.3 60.5 + - - +
372O VAL* 3.3 21.3 + - + +
373O GLU* 3.5 10.4 + - - +
395O PRO* 3.6 33.0 - - + -
399O LEU* 4.1 24.9 - - + -
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Residues in contact with MET 370 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 4.1 9.0 - - + -
35N CYS 6.1 0.2 - - - +
83N GLY 3.9 15.3 - - - +
85N HIS* 3.7 23.3 - - + -
100N LYS* 3.3 56.9 + - + +
101N ALA* 3.6 16.4 - - - +
366O ALA* 2.9 28.2 + - + +
367O GLY* 3.7 6.5 - - - +
369O LEU* 1.3 75.5 - - - +
371O SER* 1.3 61.2 + - - +
372O VAL 3.3 0.5 + - - -
373O GLU* 3.4 37.0 + - - +
374O SER* 4.8 0.7 + - - -
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Residues in contact with SER 371 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367O GLY 3.0 12.3 + - - -
368O TYR* 2.6 29.3 + - - -
370O MET* 1.3 78.5 - - - +
372O VAL* 1.3 63.8 + - - +
373O GLU 3.5 0.4 + - - -
374O SER* 4.7 2.3 + - - -
377O GLY* 3.2 24.3 - - - +
381O GLU* 5.3 1.7 + - - -
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Residues in contact with VAL 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N GLN* 5.2 0.7 + - - -
368O TYR* 3.8 20.9 - - + +
369O LEU* 3.4 21.8 - - + +
370O MET 3.2 0.2 - - - -
371O SER* 1.3 89.4 + - - +
373O GLU* 1.3 60.5 + - - +
374O SER 3.3 4.2 + - - -
377O GLY 4.1 2.5 - - - +
378O PHE* 3.7 35.5 - - + +
381O GLU* 3.7 37.2 - - + -
395O PRO* 5.2 8.5 - - + -
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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