Contacts of the helix formed by residues 364 - 377 (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 VAL 364 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with LEU 365 (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* 3.5 25.5 - - + +
357P LEU* 4.7 6.7 - - + -
360P LEU* 2.9 42.0 + - + +
361P LEU* 3.9 28.9 - - + -
364P VAL* 1.3 84.0 - - + +
366P MET* 1.3 57.2 + - - +
368P THR* 3.3 6.8 + - + +
369P ALA* 2.8 24.4 + - - +
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Residues in contact with MET 366 (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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304P ILE* 6.5 0.9 - - - -
309P THR* 4.4 0.2 + - - -
315P MET* 3.8 26.7 - - + -
318P ARG* 5.5 1.6 + - - -
321P SER* 4.2 7.6 + - - +
324P LEU* 3.9 20.2 - - + +
325P PHE* 3.6 41.3 - - + +
328P LEU* 4.4 17.5 - - + -
361P LEU* 2.8 40.0 + - + +
362P ILE* 4.4 9.2 - - - +
365P LEU* 1.3 68.9 - - - +
367P PRO* 1.3 71.8 - - + +
369P ALA* 3.1 3.1 + - - +
370P GLY* 2.9 20.1 + - - -
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Residues in contact with PRO 367 (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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307P LEU* 3.7 32.5 - - + +
309P THR* 2.7 35.3 + - + +
362P ILE 3.4 24.9 - - - +
363P LEU 3.6 13.5 - - - +
364P VAL* 3.2 15.3 - - - +
366P MET* 1.3 90.3 - - + +
368P THR* 1.3 58.9 + - - +
371P THR* 3.3 12.9 + - - -
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Residues in contact with THR 368 (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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364P VAL* 2.7 30.0 + - - +
365P LEU* 3.5 7.6 - - + -
366P MET 3.1 0.8 - - - -
367P PRO* 1.3 75.4 - - - +
369P ALA* 1.3 65.3 + - - +
370P GLY 3.1 0.2 - - - -
371P THR* 3.2 8.4 + - - +
372P ILE* 3.1 39.5 + - + +
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Residues in contact with ALA 369 (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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320P LEU* 4.3 16.8 - - + -
321P SER* 4.0 12.3 - - - +
324P LEU* 3.4 32.3 - - + -
365P LEU 2.8 7.7 + - - +
366P MET* 3.1 5.1 + - - +
368P THR* 1.3 75.6 - - - +
370P GLY* 1.3 63.6 + - - +
372P ILE* 3.3 10.3 + - - +
373P GLU* 2.9 31.6 + - - +
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Residues in contact with GLY 370 (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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309P THR* 3.3 17.0 - - - -
310P SER* 4.1 12.3 - - - -
318P ARG* 4.9 2.0 - - - -
321P SER* 4.3 2.9 + - - -
366P MET 2.9 12.1 + - - -
368P THR 3.1 0.4 - - - -
369P ALA* 1.3 78.8 - - - +
371P THR* 1.3 56.2 + - - +
373P GLU* 3.5 13.5 + - - +
374P ASN* 3.1 34.5 + - - +
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Residues in contact with THR 371 (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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309P THR* 3.6 12.9 + - - +
367P PRO 3.3 13.0 + - - -
368P THR* 3.2 10.9 + - - -
370P GLY* 1.3 72.3 - - - +
372P ILE* 1.3 68.0 + - + +
374P ASN* 3.1 11.7 + - - +
375P LYS* 3.0 53.2 + - + +
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Residues in contact with ILE 372 (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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320P LEU* 3.7 22.0 - - + -
368P THR* 3.1 35.0 + - + +
369P ALA* 3.7 6.5 - - - +
371P THR* 1.3 77.8 - - + +
373P GLU* 1.3 63.7 + - - +
375P LYS* 3.2 9.4 + - + +
376P LEU* 3.0 33.1 + - + +
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Residues in contact with GLU 373 (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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310P SER* 4.7 0.8 + - - +
312P GLN* 5.7 1.3 - - - +
318P ARG* 3.0 37.1 + - + +
320P LEU* 3.3 25.2 + - + +
321P SER* 2.8 46.6 + - - -
369P ALA 2.9 25.0 + - - +
370P GLY* 3.7 7.8 - - - +
372P ILE* 1.3 72.5 - - - +
374P ASN* 1.3 66.8 + - - +
376P LEU* 3.2 7.8 + - - +
377P LEU* 3.1 28.0 + - + +
20S TYR* 3.3 23.0 - - + +
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Residues in contact with ASN 374 (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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309P THR 2.9 26.1 + - - -
310P SER* 3.5 3.5 + - - -
311P LYS* 2.9 40.9 + - - +
312P GLN* 5.6 1.2 - - - +
370P GLY 3.1 19.8 + - - +
371P THR* 3.1 13.9 + - - +
373P GLU* 1.3 75.4 - - - +
375P LYS* 1.3 69.2 + - + +
377P LEU 3.1 9.7 + - - -
378P LYS 3.1 9.2 + - - -
379P TRP* 3.2 36.2 + - + +
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Residues in contact with LYS 375 (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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371P THR* 3.0 34.1 + - + +
372P ILE* 3.5 11.4 - - + +
374P ASN* 1.3 81.7 - - - +
376P LEU* 1.3 52.0 + - + +
378P LYS* 2.9 10.1 + - - +
379P TRP* 4.2 15.2 + - - +
17S ARG* 2.5 36.0 + - - +
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Residues in contact with LEU 376 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320P LEU* 4.5 6.7 - - + -
372P ILE* 3.0 35.9 + - + +
373P GLU* 3.2 7.6 + - - +
375P LYS* 1.3 71.5 - - + +
377P LEU* 1.3 61.5 + - - +
378P LYS* 4.4 0.5 - - - +
13S LEU* 4.2 11.9 - - + -
16S ILE* 3.3 39.7 - - + -
17S ARG* 2.6 45.6 + - + +
19S TRP* 5.8 2.5 - - + -
20S TYR* 3.7 40.4 - - + -
83S TYR* 5.7 2.4 - - - -
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Residues in contact with LEU 377 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312P GLN* 3.7 34.1 - - - +
373P GLU* 3.1 8.4 + - + +
374P ASN 3.1 4.4 + - - +
376P LEU* 1.3 77.2 - - - +
378P LYS* 1.3 67.9 + - - +
379P TRP* 3.5 28.9 - - + +
20S TYR* 3.6 34.1 - - + +
21S TYR* 4.4 15.5 - - + -
24S ALA* 5.5 0.4 - - + -
26S PHE* 4.0 27.6 - - + -
33S ARG* 3.0 26.5 + - + +
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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
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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