Contacts of the strand formed by residues 307 - 315 (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 PHE 307 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296O TYR* 3.7 45.6 + + - -
299O VAL* 3.4 31.9 - - + -
300O ALA* 3.5 23.3 - - + -
303O VAL* 3.3 29.4 - - + -
305O GLN 3.5 9.4 + - - +
306O PRO* 1.3 77.4 - - + +
308O ASP* 1.3 84.9 + - - +
309O VAL* 4.0 15.7 - - + -
327O ILE 3.2 15.3 - - - +
328O SER* 4.3 9.6 - - - -
336O VAL* 4.6 7.0 - - + -
52V ARG* 3.9 15.4 - - + +
55V LEU* 3.7 15.4 - - - +
56V ARG 5.0 0.2 + - - -
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Residues in contact with ASP 308 (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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296O TYR* 3.5 3.5 - - - -
307O PHE* 1.3 86.0 - - - +
309O VAL* 1.3 65.7 + - - +
326O THR* 3.4 2.6 - - - -
327O ILE* 2.9 38.3 + - + +
336O VAL* 4.9 0.7 - - - +
55V LEU* 3.0 25.6 - - + +
56V ARG* 2.7 39.7 + - - -
57V GLY 2.9 21.7 + - - -
59V ALA* 3.1 23.3 + - + +
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Residues in contact with VAL 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O SER* 5.2 1.4 + - - -
295O LEU* 3.9 24.4 - - + +
296O TYR* 3.6 37.7 - - + +
299O VAL* 4.1 6.5 - - + -
307O PHE* 4.0 12.3 - - + -
308O ASP* 1.3 80.3 + - - +
310O SER* 1.3 66.2 + - - +
324O PHE* 4.6 1.6 - - + -
325O TYR 3.2 14.4 - - - +
326O THR* 3.7 17.9 - - + -
336O VAL* 5.1 0.4 - - + -
340O ALA* 4.2 12.6 - - + -
56V ARG* 2.9 23.6 + - - -
59V ALA* 4.1 1.8 - - - -
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Residues in contact with SER 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280O GLY 3.6 11.4 + - - -
281O ALA* 3.7 12.1 - - - -
282O GLY* 4.0 4.4 + - - -
295O LEU* 4.1 7.0 - - - -
309O VAL* 1.3 79.7 - - - +
311O ALA* 1.3 72.8 + - - +
324O PHE* 3.2 2.3 - - - +
325O TYR* 2.7 37.2 + - - +
56V ARG* 4.3 7.0 - - - -
59V ALA* 3.6 22.3 + - - -
60V ALA 3.7 7.9 + - - -
61V GLY* 4.3 3.6 - - - -
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Residues in contact with ALA 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O GLN* 3.5 38.7 + - + +
279O LEU* 3.8 19.3 - - + -
280O GLY 2.7 20.5 + - - +
281O ALA* 4.6 0.3 - - - -
295O LEU* 4.0 5.1 - - - +
310O SER* 1.3 86.9 + - - +
312O PHE* 1.3 57.9 + - - +
313O ASN 4.3 0.2 - - - -
322O PHE* 4.5 2.2 - - + -
323O GLY 3.4 10.3 - - - +
324O PHE* 4.1 1.3 - - - +
60V ALA 3.9 0.2 - - - +
61V GLY* 3.6 9.9 - - - -
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Residues in contact with PHE 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O ILE* 3.6 29.6 - - + -
163O LEU* 4.1 17.5 - - + -
164O HIS* 4.5 10.3 - + - -
256O ALA* 5.8 1.6 - - + -
258O VAL* 3.9 17.9 - - + -
311O ALA* 1.3 73.7 - - - +
313O ASN* 1.3 61.7 + - - +
314O ALA* 3.9 28.9 - - + -
321O LEU* 4.1 11.0 - - + -
322O PHE* 3.3 9.5 - - - -
323O GLY 2.8 41.4 + - - +
324O PHE* 4.2 11.4 - - - +
325O TYR* 4.4 4.0 - + + +
60V ALA* 4.0 10.5 - - + +
61V GLY* 3.7 18.8 - - - -
62V ARG 3.5 25.1 - - - -
63V PRO 4.5 0.4 - - - -
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Residues in contact with ASN 313 (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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261O SER* 4.7 3.5 + - - -
269O ALA 5.0 0.8 + - - -
272O PHE* 3.8 16.3 - - - +
273O SER* 3.7 23.4 + - - +
276O GLN* 3.6 27.5 + - - +
312O PHE* 1.3 77.6 - - - +
314O ALA* 1.3 64.1 + - - +
315O SER* 4.4 12.0 + - - +
321O LEU 3.6 1.8 - - - +
322O PHE* 3.3 26.2 - - + +
61V GLY 3.0 17.3 + - - +
62V ARG* 3.6 4.7 - - - +
63V PRO* 3.5 12.2 - - - +
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Residues in contact with ALA 314 (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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164O HIS* 4.7 1.3 - - - +
261O SER* 4.2 1.7 + - - -
312O PHE* 3.9 19.9 - - + -
313O ASN* 1.3 75.2 - - - +
315O SER* 1.3 60.0 + - - +
316O TYR* 3.7 29.1 - - + +
320O GLY* 3.2 3.5 - - - -
321O LEU* 2.8 43.9 + - + +
63V PRO* 3.7 18.4 - - + -
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Residues in contact with SER 315 (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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262O ALA 3.1 10.9 + - - -
263O ALA 3.4 0.7 + - - -
264O ILE* 2.8 48.5 + - - +
269O ALA* 4.3 7.0 - - - +
313O ASN* 4.2 10.9 - - - +
314O ALA* 1.3 74.1 - - - +
316O TYR* 1.3 62.6 + - - +
319O SER 4.0 2.0 - - - -
320O GLY* 4.3 1.1 - - - -
3013O GOL 3.2 33.2 - - - -
63V PRO* 4.9 0.6 - - - +
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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