Contacts of the helix formed by residues 265 - 273 (chain A) in PDB entry 1PJR
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 GLN 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.0 19.5 + - - +
264A ILE* 1.3 93.3 - - - +
266A ASN* 1.3 58.3 + - - +
268A LEU* 3.7 17.6 - - + +
269A SER* 2.8 38.8 + - - +
305A ASN* 3.0 30.0 + - - +
595A ASP* 5.5 2.8 - - - +
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Residues in contact with ASN 266 (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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225A TYR* 3.7 11.8 + - + -
228A THR* 3.1 40.6 - - + +
229A ASN 4.0 3.6 - - - +
230A ARG* 3.6 24.0 - - - +
233A TYR* 3.4 34.5 - - + +
263A ASP* 3.7 21.9 + - - +
264A ILE 3.0 1.2 + - - -
265A GLN* 1.3 75.1 - - - +
267A ILE* 1.4 64.4 + - - +
269A SER* 3.1 15.8 + - - -
270A PHE* 3.6 7.3 + - - -
273A ASP* 4.8 2.3 - - - +
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Residues in contact with ILE 267 (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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28A LEU* 4.0 26.1 - - + +
30A MET* 4.3 13.4 - - - +
225A TYR* 3.6 24.8 + - + -
226A GLN* 4.0 26.9 - - + +
250A GLY* 3.7 38.1 - - - +
251A ASP 4.0 2.9 - - - +
252A ALA* 3.9 23.6 - - + +
263A ASP 4.7 0.2 + - - -
264A ILE* 3.3 14.8 + - + +
266A ASN* 1.4 75.2 - - - +
268A LEU* 1.3 65.4 + - + +
269A SER 3.3 0.5 + - - -
270A PHE* 3.4 15.8 + - - +
271A GLU* 5.7 0.2 - - - +
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Residues in contact with LEU 268 (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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30A MET* 5.8 2.2 - - - -
252A ALA* 3.6 28.7 - - + -
264A ILE* 3.5 20.4 + - + +
265A GLN* 3.8 29.2 - - + +
266A ASN 3.2 0.6 - - - -
267A ILE* 1.3 85.7 - - + +
269A SER* 1.3 60.2 + - - +
270A PHE 3.4 1.0 + - - -
271A GLU* 4.3 12.0 - - - +
272A ARG* 4.2 12.5 + - - +
305A ASN* 4.0 29.2 - - + +
306A ARG 4.5 2.2 - - - +
307A LYS* 4.3 38.4 + - + +
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Residues in contact with SER 269 (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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233A TYR* 5.5 1.8 - - - -
265A GLN* 2.8 27.1 + - - +
266A ASN* 3.1 7.5 + - - -
268A LEU* 1.3 77.0 - - - +
270A PHE* 1.3 63.4 + - - +
271A GLU 3.4 2.2 - - - -
272A ARG* 2.8 41.7 + - - +
273A ASP* 3.0 23.8 + - - -
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Residues in contact with PHE 270 (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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26A PRO* 4.2 4.0 - - + -
27A LEU 3.9 18.4 - - - -
28A LEU* 3.7 39.3 - - + -
225A TYR* 4.1 20.9 - + - -
246A ILE* 4.2 19.3 - - + -
248A ALA* 3.8 19.5 - - + -
266A ASN 3.6 4.2 + - - +
267A ILE* 3.4 17.4 + - - +
268A LEU 3.4 1.0 - - - -
269A SER* 1.3 75.7 - - - +
271A GLU* 1.3 59.7 + - + +
272A ARG 3.0 0.7 + - - -
273A ASP* 3.2 5.8 + - - +
274A TYR* 2.9 59.3 + + - -
277A ALA* 3.6 26.9 - - + -
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Residues in contact with GLU 271 (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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28A LEU* 5.2 5.1 - - + +
267A ILE 5.7 0.3 - - - +
268A LEU 4.3 7.3 - - - +
269A SER 3.4 0.8 - - - -
270A PHE* 1.3 78.3 + - + +
272A ARG* 1.3 55.3 + - - +
274A TYR 4.0 9.4 - - - -
275A PRO* 3.1 26.1 - - + +
277A ALA* 4.4 9.2 - - + +
279A VAL* 4.0 29.9 - - + +
307A LYS* 3.4 33.8 + - - -
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Residues in contact with ARG 272 (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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268A LEU* 4.2 13.5 + - - +
269A SER* 2.8 30.3 + - - +
271A GLU* 1.3 79.3 - - - +
273A ASP* 1.3 62.5 + - - +
274A TYR* 3.4 0.4 - - - -
275A PRO* 4.3 8.1 - - - +
307A LYS* 5.1 7.1 - - - +
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Residues in contact with ASP 273 (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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225A TYR* 4.7 3.6 + - - -
233A TYR* 2.9 39.1 + - - -
237A LYS* 3.6 22.0 + - - +
244A GLN* 5.3 1.4 - - - +
266A ASN 4.8 1.0 - - - +
269A SER* 3.0 25.7 + - - +
270A PHE* 3.8 5.0 - - - +
272A ARG* 1.3 77.4 - - - +
274A TYR* 1.3 87.3 + - + +
275A PRO* 3.6 5.8 - - - +
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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