Contacts of the helix formed by residues 374 - 390 (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 374 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370N ASP* 3.5 27.1 - - - -
371N GLY* 4.5 4.0 - - - -
370O MET 4.8 0.6 + - - -
371O SER 4.7 2.0 + - - -
373O GLU* 1.3 82.3 - - - +
375O SER* 1.3 64.9 + - - +
376O GLU* 3.6 6.3 + - - +
377O GLY* 3.0 21.1 + - - -
378O PHE* 2.9 24.7 + - - +
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Residues in contact with SER 375 (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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370N ASP* 2.9 25.5 + - - -
40O ASN* 5.6 4.9 - - - -
46O ARG* 2.6 37.7 + - - -
209O LEU* 3.4 25.2 - - - +
374O SER* 1.3 71.2 - - - +
376O GLU* 1.3 56.7 + - - +
378O PHE* 3.7 2.2 - - - +
379O LEU* 2.9 32.2 + - - +
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Residues in contact with GLU 376 (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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370N ASP* 3.9 3.6 + - - +
46O ARG* 3.3 36.2 + - - +
95O LYS* 5.0 6.2 + - - -
374O SER* 3.2 6.5 + - - +
375O SER* 1.3 79.8 + - - +
377O GLY* 1.3 66.2 + - - +
379O LEU* 3.5 1.9 + - - +
380O ASP* 3.2 24.4 + - + +
77V ARG* 4.7 18.6 + - - -
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Residues in contact with GLY 377 (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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371O SER 3.2 26.0 - - - +
372O VAL* 4.1 1.7 - - - +
374O SER* 3.0 15.4 + - - -
376O GLU* 1.3 79.5 - - - +
378O PHE* 1.3 60.6 - - - +
380O ASP* 3.8 5.3 - - - +
381O GLU* 3.2 23.0 + - - +
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Residues in contact with PHE 378 (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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24O LEU* 4.3 12.6 - - + -
38O LEU* 3.8 26.7 - - + -
207O ILE* 6.2 0.4 - - + -
209O LEU* 3.5 36.8 - - + -
372O VAL* 3.7 31.9 - - + +
374O SER 2.9 17.3 + - - +
375O SER* 3.7 4.9 - - - +
377O GLY* 1.3 73.5 - - - +
379O LEU* 1.3 65.3 + - - +
381O GLU* 3.2 4.9 + - + +
382O VAL* 3.0 48.3 + - + +
392O TYR* 4.1 19.3 - + - -
395O PRO* 6.6 0.2 - - + -
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Residues in contact with LEU 379 (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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46O ARG* 3.5 39.7 - - + +
48O GLY* 4.0 12.1 - - - +
50O PHE* 3.6 10.6 - - + -
108O THR* 4.0 26.5 - - + -
207O ILE* 3.6 32.4 - - + +
209O LEU* 3.8 23.3 - - + -
375O SER 2.9 17.9 + - - +
376O GLU 3.9 3.6 - - - +
378O PHE* 1.3 79.3 - - - +
380O ASP* 1.3 57.4 + - - +
382O VAL* 3.8 1.4 - - - +
383O GLY* 2.8 29.3 + - - -
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Residues in contact with ASP 380 (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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50O PHE* 3.9 19.1 - - + -
376O GLU* 3.2 15.9 + - + +
377O GLY* 3.8 5.2 - - - +
378O PHE 3.3 0.2 - - - -
379O LEU* 1.3 78.4 - - - +
381O GLU* 1.3 52.0 + - - +
383O GLY* 3.8 0.2 - - - -
384O SER* 2.7 54.3 + - - -
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Residues in contact with GLU 381 (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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368O TYR* 3.1 35.2 + - - +
371O SER* 5.3 1.4 + - - -
372O VAL* 3.7 18.7 - - + +
377O GLY 3.2 11.4 + - - +
378O PHE* 3.2 10.1 + - + +
380O ASP* 1.3 77.7 - - - +
382O VAL* 1.3 62.6 + - + +
384O SER* 3.2 7.3 + - - -
385O GLN* 2.6 64.7 + - - +
392O TYR* 5.6 2.7 - - + -
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Residues in contact with VAL 382 (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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24O LEU* 4.3 13.2 - - + -
26O PHE* 6.0 1.1 - - + -
36O ALA* 4.0 15.5 - - + -
207O ILE* 3.7 30.5 - - + -
378O PHE* 3.0 52.8 + - + +
379O LEU 3.8 3.6 - - - +
381O GLU* 1.3 75.0 - - + +
383O GLY* 1.3 57.7 + - - +
385O GLN* 3.1 6.9 + - - +
386O ALA* 2.7 30.2 + - + +
391O SER 5.2 0.2 - - - +
392O TYR* 4.2 20.2 - - + -
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Residues in contact with GLY 383 (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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50O PHE* 3.8 20.6 - - - +
207O ILE* 3.7 23.9 - - - +
379O LEU 2.8 21.1 + - - -
382O VAL* 1.3 74.4 - - - +
384O SER* 1.3 60.8 + - - +
386O ALA* 3.4 3.0 + - - +
387O LEU* 3.2 27.4 + - - +
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Residues in contact with SER 384 (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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50O PHE* 4.2 3.7 - - - -
104O ASN* 4.9 13.9 + - - +
380O ASP* 2.7 41.3 + - - -
381O GLU* 3.7 7.4 - - - -
383O GLY* 1.3 70.4 - - - +
385O GLN* 1.3 66.1 + - - +
387O LEU* 3.5 2.0 + - - +
388O ALA* 3.0 27.9 + - - +
3013O GOL 4.7 16.7 + - - -
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Residues in contact with GLN 385 (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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368O TYR* 3.6 6.9 + - - -
381O GLU* 2.6 49.1 + - - +
382O VAL* 3.6 4.5 - - - +
384O SER* 1.3 76.5 - - - +
386O ALA* 1.3 58.9 + - - +
388O ALA* 4.6 3.6 - - - +
389O ALA* 2.9 31.9 + - + +
390O GLY 3.3 4.2 + - - -
391O SER 3.5 12.2 - - - +
392O TYR* 3.4 13.3 - - + -
393O THR* 2.6 52.8 + - - -
398O VAL* 5.1 2.0 - - - +
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Residues in contact with ALA 386 (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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26O PHE* 4.6 5.6 - - + -
28O ARG* 4.9 0.3 + - - -
34O VAL* 4.1 22.6 - - + +
205O ALA* 3.6 22.2 - - + -
207O ILE* 4.1 7.9 - - + -
382O VAL* 2.7 17.9 + - + +
383O GLY 3.5 7.2 - - - +
385O GLN* 1.3 76.5 - - - +
387O LEU* 1.3 58.4 + - - +
390O GLY* 3.1 24.4 + - - +
391O SER 3.9 9.3 + - - +
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Residues in contact with LEU 387 (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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50O PHE* 3.8 13.0 - - + +
51O ILE 3.7 27.1 - - - +
52O LYS* 3.1 39.3 + - + +
104O ASN* 3.6 36.6 - - - +
202O ALA 6.0 0.2 - - - +
203O ARG* 3.6 22.0 - - - +
204O MET 3.7 23.8 - - - +
205O ALA* 3.8 3.8 - - + -
383O GLY 3.2 13.8 + - - +
384O SER 4.2 2.0 - - - +
385O GLN 3.2 0.2 - - - -
386O ALA* 1.3 79.6 - - - +
388O ALA* 1.3 65.1 + - - +
390O GLY 4.6 1.2 + - - -
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Residues in contact with ALA 388 (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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52O LYS* 5.3 0.4 - - - +
264O ILE* 4.6 21.8 - - + -
317O SER* 6.1 6.3 - - - -
384O SER 3.0 18.8 + - - +
385O GLN* 4.3 2.7 - - - +
387O LEU* 1.3 78.3 - - - +
389O ALA* 1.3 63.2 + - + +
3013O GOL 5.3 8.1 - - - +
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Residues in contact with ALA 389 (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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385O GLN* 2.9 12.4 + - + +
388O ALA* 1.3 79.4 - - + +
390O GLY* 1.3 68.9 + - - +
391O SER* 3.0 19.1 + - - +
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Residues in contact with GLY 390 (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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26O PHE* 3.2 20.4 - - - -
28O ARG* 3.5 31.0 + - - -
385O GLN 3.3 0.2 + - - -
386O ALA 3.1 23.5 + - - -
387O LEU 4.4 1.8 + - - -
388O ALA 3.9 0.2 - - - -
389O ALA* 1.3 76.3 - - - +
391O SER* 1.3 58.9 + - - +
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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