Contacts of the helix formed by residues 275 - 282 (chain A) in PDB entry 1PFY
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.9 10.0 + - - +
274A SER* 1.3 92.0 - - - +
276A SER* 1.3 70.8 + - - +
277A PHE 3.4 3.2 + - - -
278A ASP* 3.5 8.8 + - - +
279A GLU* 2.9 46.7 + - + +
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 5.3 0.5 + - - -
44A GLU* 4.8 4.7 + - - -
264A PHE* 4.1 3.4 - - - -
268A CYS* 3.9 11.4 - - - -
271A ARG* 6.3 0.4 - - - -
273A ASP* 2.7 33.0 + - - -
274A SER 3.9 0.2 - - - -
275A VAL* 1.3 77.9 - - - +
277A PHE* 1.3 66.7 + - - +
279A GLU* 3.2 16.1 + - - -
280A TYR* 3.0 45.0 + - - -
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.1 18.6 - - + -
261A MET* 3.4 45.5 - - + -
264A PHE* 3.9 10.8 - + - -
265A LYS* 3.7 33.7 - - + -
268A CYS* 3.7 15.0 - - + +
273A ASP 6.0 0.2 - - - +
274A SER 5.4 1.7 - - - +
275A VAL 3.4 1.6 - - - +
276A SER* 1.3 76.5 - - - +
278A ASP* 1.3 73.3 + - - +
280A TYR 3.2 0.2 + - - -
281A TRP* 2.9 62.8 + + + +
314A PHE* 4.5 10.1 - + - -
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A SER 5.0 7.0 - - - +
275A VAL* 3.5 8.7 + - - +
277A PHE* 1.3 95.0 - - - +
279A GLU* 1.3 61.3 + - + +
281A TRP* 5.2 0.2 - - - -
282A LYS* 2.8 48.2 + - + +
314A PHE* 6.0 1.0 - - - -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 2.7 35.6 + - + +
275A VAL* 2.9 42.3 + - + +
276A SER* 3.2 19.4 + - - +
278A ASP* 1.3 76.5 - - + +
280A TYR* 1.3 55.4 + - + +
282A LYS* 3.9 17.9 - - - +
285A SER* 2.6 32.9 + - - -
286A THR 4.4 1.2 + - - -
287A ALA* 4.2 4.1 + - - +
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 3.5 22.1 - - + +
7A ILE 3.9 23.9 + - - -
8A LEU* 3.8 22.7 - - + -
44A GLU* 2.7 37.1 + - - +
46A ASN* 2.9 19.1 + - - -
264A PHE* 3.6 25.6 - + + -
276A SER* 3.0 36.4 + - - +
277A PHE 3.9 0.7 - - - +
279A GLU* 1.3 83.2 - - + +
281A TRP* 1.3 68.6 + - + +
285A SER* 3.7 4.5 - - - -
287A ALA* 3.7 19.5 - - + -
288A GLU 4.8 1.1 - - - -
289A LEU* 5.6 0.3 - - - +
315A ARG* 2.9 31.3 + - - +
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Residues in contact with TRP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 21.5 - - + +
260A TYR* 4.5 10.5 - - + -
261A MET* 3.5 49.1 - - + -
264A PHE* 3.5 20.3 - + - +
277A PHE* 2.9 49.9 + + + +
278A ASP* 5.2 0.4 - - - -
280A TYR* 1.3 86.3 - - + +
282A LYS* 1.3 67.5 + - - +
289A LEU* 3.6 33.0 - - + -
291A HIS* 4.8 0.7 - - - -
305A TRP* 4.2 17.0 - + - -
309A LEU* 4.3 11.0 - - + -
314A PHE* 3.5 21.9 - - + -
315A ARG* 3.0 33.5 + - - -
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ASP* 2.8 38.0 + - + +
279A GLU* 3.9 22.6 - - - +
281A TRP* 1.3 81.0 - - - +
283A LYS* 1.3 63.9 + - - +
284A ASP* 3.4 36.0 + - - +
285A SER* 3.1 29.1 + - - +
286A THR 5.5 0.7 - - - +
313A ASN 5.1 3.1 - - - -
314A PHE* 5.1 2.2 - - - -
315A ARG* 3.4 4.4 - - - +
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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