Contacts of the helix formed by residues 346 - 364 (chain P) 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 PRO 346 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345P HIS* 1.3 106.3 - - + +
347P TYR* 1.3 69.0 + - + +
348P ILE 3.2 2.7 - - - -
349P THR* 3.1 11.7 + - - +
350P ILE* 3.0 25.1 + - + +
61T TRP* 3.9 25.4 - - + -
62T GLY* 3.7 28.9 - - - +
65T GLU* 3.8 11.9 - - + -
66T PHE* 4.1 14.4 - - + +
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Residues in contact with TYR 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282P ARG* 6.2 0.4 - - - +
337P TRP* 3.5 25.8 - + - -
338P ILE* 3.9 34.9 - - + +
341P GLN* 3.5 42.8 + - + -
342P PRO* 3.7 21.3 - - + +
344P GLU 3.0 9.9 + - - +
346P PRO* 1.3 80.2 - - + +
348P ILE* 1.3 58.1 + - - +
350P ILE* 4.3 3.6 - - + -
351P GLY* 2.9 27.4 + - - -
62T GLY 3.9 12.8 - - - -
63T THR* 3.7 16.6 + - - +
66T PHE* 3.5 49.8 - + + +
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Residues in contact with ILE 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E LYS* 6.0 4.5 - - - +
282P ARG 6.1 0.2 - - - +
283P SER* 4.9 3.6 + - - -
343P VAL* 3.6 37.5 - - + +
344P GLU* 3.1 26.6 + - - +
345P HIS* 4.3 4.9 - - + +
346P PRO 3.2 0.6 - - - -
347P TYR* 1.3 75.6 - - - +
349P THR* 1.3 59.4 + - - +
351P GLY* 4.1 0.9 - - - -
352P GLN* 3.2 46.0 + - - +
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Residues in contact with THR 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345P HIS* 5.8 3.7 - - - +
346P PRO* 3.1 13.0 + - - +
348P ILE* 1.3 77.9 - - - +
350P ILE* 1.3 65.8 + - + +
352P GLN* 3.2 13.7 + - + +
353P LEU* 3.0 41.0 + - + +
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Residues in contact with ILE 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P THR* 4.0 8.5 - - + -
337P TRP* 4.0 16.8 - - + -
338P ILE* 3.8 17.9 - - + -
346P PRO* 3.0 21.3 + - + +
347P TYR* 4.0 6.1 - - + +
349P THR* 1.3 77.2 - - + +
351P GLY* 1.3 59.6 + - - +
353P LEU* 3.3 10.3 + - + +
354P ALA* 2.9 27.5 + - - +
58T VAL* 3.9 26.0 - - + -
61T TRP* 4.2 17.7 - - + -
62T GLY* 4.0 25.8 - - - -
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Residues in contact with GLY 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283P SER* 3.4 10.9 + - - -
335P LEU* 3.9 3.3 - - - +
338P ILE* 3.9 22.8 - - - +
347P TYR 2.9 17.0 + - - -
348P ILE 4.1 0.7 - - - -
350P ILE* 1.3 78.5 - - - +
352P GLN* 1.3 56.3 + - - +
354P ALA* 3.8 5.1 - - - +
355P SER* 2.8 34.0 + - - -
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Residues in contact with GLN 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283P SER* 3.3 37.8 + - - +
285P PRO* 4.9 7.1 - - - +
348P ILE* 3.2 35.6 + - - +
349P THR* 3.2 18.2 + - + +
351P GLY* 1.3 73.2 - - - +
353P LEU* 1.3 63.4 + - + +
355P SER* 3.4 2.6 + - - -
356P VAL* 3.0 34.1 + - + +
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Residues in contact with LEU 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349P THR* 3.0 37.4 + - + +
350P ILE* 3.6 8.3 - - + +
352P GLN* 1.3 79.1 - - + +
354P ALA* 1.3 52.0 + - - +
356P VAL* 3.2 8.3 + - + +
357P LEU* 2.7 37.5 + - - +
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Residues in contact with ALA 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331P ASP* 2.7 41.8 - - - +
334P THR* 3.9 18.6 - - + -
335P LEU* 3.6 24.6 - - + +
350P ILE 2.9 17.5 + - - +
351P GLY* 3.8 2.0 - - - +
353P LEU* 1.3 76.0 - - - +
355P SER* 1.3 58.2 + - - +
357P LEU* 4.2 2.2 - - - -
358P TYR* 3.0 13.5 + - - +
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Residues in contact with SER 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ILE* 3.4 38.3 - - - -
283P SER* 3.5 8.5 + - - -
284P ILE* 6.2 2.5 - - - -
335P LEU* 3.5 9.1 - - - +
351P GLY 2.8 23.8 + - - -
352P GLN* 3.7 6.7 - - - -
353P LEU 3.2 0.2 - - - -
354P ALA* 1.3 74.3 - - - +
356P VAL* 1.3 64.4 + - - +
358P TYR* 3.4 10.8 + - - +
359P PHE* 3.2 25.8 - - - -
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Residues in contact with VAL 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352P GLN* 3.0 21.7 + - + +
353P LEU* 3.7 9.0 - - + +
355P SER* 1.3 77.0 - - - +
357P LEU* 1.3 65.8 + - - +
358P TYR 3.2 0.3 + - - -
359P PHE* 3.3 7.3 + - - +
360P LEU* 3.0 33.3 + - + +
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Residues in contact with LEU 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327P ALA* 5.1 5.6 - - + +
331P ASP* 3.6 22.0 - - + +
353P LEU 2.7 21.9 + - - +
354P ALA* 3.8 5.4 - - - +
355P SER 3.3 0.2 - - - -
356P VAL* 1.3 75.5 - - - +
358P TYR* 1.3 55.9 + - - +
360P LEU* 4.2 12.1 - - + -
361P LEU* 2.9 54.7 + - + +
365P LEU* 4.7 11.2 - - + -
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Residues in contact with TYR 358 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276P PHE* 4.9 2.0 - + - -
280P ILE* 4.1 10.1 - - + -
297P SER* 2.7 36.6 + - - -
300P ILE* 4.0 7.8 - - + +
301P LEU* 5.6 1.0 - - - +
328P LEU* 3.5 29.5 - - + +
331P ASP* 3.3 15.2 + - - +
332P LEU* 3.6 32.8 - - + -
335P LEU* 4.4 6.1 - - + -
354P ALA 3.0 8.7 + - - +
355P SER* 3.5 10.1 - - - +
356P VAL 3.2 0.4 - - - -
357P LEU* 1.3 79.1 - - - +
359P PHE* 1.3 93.3 + + - +
361P LEU* 3.5 2.5 + - - +
362P ILE* 3.4 40.1 + - + +
3007P PEE 4.2 17.1 - - + +
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Residues in contact with PHE 359 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280P ILE* 4.2 17.0 - - + -
293P ALA* 3.7 28.7 - - + -
296P PHE* 3.4 36.8 - + + -
297P SER* 3.9 15.7 - - - -
300P ILE* 3.8 14.1 - - + -
355P SER* 3.2 24.2 - - - -
356P VAL* 3.3 7.4 + - - +
358P TYR* 1.3 97.3 - + - +
360P LEU* 1.3 60.7 + - - +
362P ILE* 4.7 2.5 - - - +
363P LEU* 2.9 43.7 + - + +
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Residues in contact with LEU 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356P VAL* 3.0 28.9 + - + +
357P LEU* 3.7 14.1 - - + +
359P PHE* 1.3 76.8 - - - +
361P LEU* 1.3 59.7 + - - +
364P VAL* 2.9 39.5 + - + +
365P LEU* 2.9 44.4 + - + -
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Residues in contact with LEU 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324P LEU* 3.8 42.4 - - + +
327P ALA* 4.0 11.9 - - + +
328P LEU* 3.6 41.3 - - + +
331P ASP* 4.6 2.2 - - + -
357P LEU* 2.9 44.5 + - + +
358P TYR 3.8 3.8 - - - +
359P PHE 3.4 0.2 - - - -
360P LEU* 1.3 77.3 - - - +
362P ILE* 1.3 58.7 + - - +
365P LEU* 3.9 15.7 - - + -
366P MET* 2.8 41.3 + - + +
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Residues in contact with ILE 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P ILE* 3.8 31.0 - - + -
301P LEU* 6.3 2.5 - - + -
304P ILE* 3.3 33.9 - - + +
307P LEU* 3.6 11.9 - - + +
328P LEU* 4.1 22.4 - - + -
358P TYR* 3.4 52.5 + - + +
359P PHE 4.1 1.8 - - - +
360P LEU 3.3 0.4 - - - -
361P LEU* 1.3 77.7 - - - +
363P LEU* 1.3 60.9 + - - +
366P MET* 4.4 9.2 - - - +
367P PRO* 3.4 17.2 - - - +
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Residues in contact with LEU 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296P PHE* 4.2 21.5 - - + -
300P ILE* 3.8 21.8 - - + -
303P LEU* 4.3 14.8 - - + -
307P LEU* 3.8 28.4 - - + +
359P PHE* 2.9 31.5 + - + +
362P ILE* 1.3 73.4 - - - +
364P VAL* 1.3 69.5 + - + +
367P PRO* 3.6 13.0 - - - +
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Residues in contact with VAL 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360P LEU* 2.9 30.0 + - + +
362P ILE 3.5 0.6 - - - -
363P LEU* 1.3 91.8 - - + +
365P LEU* 1.3 75.6 + - + +
367P PRO* 3.2 5.2 - - - +
368P THR* 2.7 36.2 + - - +
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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) + - + + + + + -
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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