Contacts of the helix formed by residues 256 - 268 (chain A) in PDB entry 3PEJ
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 ASN 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LYS* 3.6 20.1 + - - +
252A THR 5.0 1.0 - - - +
253A ASN* 3.3 40.7 + - - +
255A LEU* 1.3 80.6 - - - +
257A ASP* 1.3 65.2 + - - +
258A LYS* 3.6 2.2 - - + +
259A LYS* 3.5 10.6 + - + +
260A LEU* 3.1 27.7 + - - +
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Residues in contact with ASP 257 (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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139A LYS* 4.7 6.7 - - - +
255A LEU 3.9 2.4 + - - -
256A ASN* 1.3 72.5 - - - +
258A LYS* 1.3 67.7 + - + +
260A LEU* 3.5 5.2 + - - +
261A MET* 3.1 48.4 + - - +
277A LEU* 4.3 1.8 - - - +
279A HIS* 3.1 38.9 + - - +
280A GLU* 3.6 19.8 + - - +
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Residues in contact with LYS 258 (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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256A ASN* 3.6 2.3 - - + +
257A ASP* 1.3 80.3 - - + +
259A LYS* 1.4 59.8 + - - +
261A MET* 3.6 7.7 + - - +
262A ASP* 3.1 25.6 + - - +
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Residues in contact with LYS 259 (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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97A GLU* 3.1 43.7 + - - +
253A ASN* 3.4 47.3 - - + +
254A LEU* 4.3 12.1 - - + -
256A ASN* 3.5 9.4 + - + +
257A ASP 3.3 0.6 - - - -
258A LYS* 1.4 73.8 - - - +
260A LEU* 1.4 59.7 + - - +
262A ASP* 3.3 7.5 + - - +
263A LEU* 2.9 46.3 + - + +
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Residues in contact with LEU 260 (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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100A LEU* 4.5 16.4 - - + -
135A ILE* 4.0 13.9 - - + -
137A ALA* 4.2 13.9 - - + +
144A LEU* 3.7 27.8 - - + -
254A LEU* 3.4 29.2 - - + +
255A LEU 4.5 4.3 - - - +
256A ASN 3.1 16.1 + - - +
257A ASP* 3.9 4.5 - - - +
259A LYS* 1.4 74.7 - - - +
261A MET* 1.3 52.4 + - - +
263A LEU* 3.7 8.4 - - + +
264A ILE* 2.8 42.5 + - + +
277A LEU* 4.0 26.0 - - + -
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Residues in contact with MET 261 (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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257A ASP* 3.1 38.8 + - - +
258A LYS* 3.8 6.7 - - - +
260A LEU* 1.3 75.5 - - - +
262A ASP* 1.3 57.0 + - - +
265A SER* 3.0 31.9 + - - -
277A LEU* 3.6 15.0 - - + -
279A HIS* 3.4 34.1 - - + +
327A THR* 5.8 1.3 - - + -
329A MET* 3.6 28.7 - - + +
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Residues in contact with ASP 262 (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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258A LYS 3.1 16.1 + - - +
259A LYS* 3.4 7.6 - - - +
261A MET* 1.3 79.3 - - - +
263A LEU* 1.4 69.4 + - - +
265A SER* 3.4 5.0 + - - -
266A LYS* 3.1 35.7 + - - +
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Residues in contact with LEU 263 (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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97A GLU* 3.7 36.6 - - + +
100A LEU* 3.8 21.1 - - + -
254A LEU* 3.6 31.4 - - + -
259A LYS* 2.9 33.0 + - + +
260A LEU* 3.8 7.0 - - + +
262A ASP* 1.4 80.0 + - - +
264A ILE* 1.4 59.3 + - - +
266A LYS* 3.4 12.6 + - + +
267A TYR* 3.0 50.0 + - + +
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Residues in contact with ILE 264 (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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100A LEU* 3.9 12.1 - - + -
104A ILE* 4.8 5.8 - - + +
135A ILE* 3.7 31.9 - - + -
260A LEU* 2.8 29.0 + - + +
261A MET 4.1 2.5 - - - +
263A LEU* 1.4 68.3 - - - +
265A SER* 1.4 57.8 + - - +
267A TYR 3.3 1.2 + - - -
268A SER* 2.6 42.9 + - - +
275A ILE* 3.7 26.0 - - + -
277A LEU* 3.8 37.2 - - + -
329A MET* 3.7 22.9 - - + -
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Residues in contact with SER 265 (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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261A MET 3.0 19.2 + - - -
262A ASP* 3.6 6.3 - - - -
264A ILE* 1.4 76.4 - - - +
266A LYS* 1.3 63.1 + - - +
268A SER* 3.5 12.9 + - - -
269A GLN* 4.6 3.8 + - - +
329A MET* 4.8 10.9 - - - +
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Residues in contact with LYS 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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262A ASP* 3.1 25.8 + - - +
263A LEU* 3.5 13.3 - - + +
265A SER* 1.3 80.3 - - - +
267A TYR* 1.4 88.9 + - + +
268A SER 3.7 0.7 + - - -
269A GLN* 4.2 12.8 + - - +
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Residues in contact with TYR 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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97A GLU* 3.0 42.4 + - - +
98A VAL* 3.7 13.4 - - - +
100A LEU* 3.9 11.2 - - + -
101A ARG* 3.5 69.6 - - + +
104A ILE* 4.1 18.5 - - + +
263A LEU* 3.0 30.6 + - + +
264A ILE 3.3 0.6 + - - -
266A LYS* 1.4 106.0 + - + +
268A SER* 1.3 56.6 + - - +
269A GLN* 3.4 6.1 + - - -
271A ILE* 4.0 10.6 - - - +
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Residues in contact with SER 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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104A ILE* 5.4 0.2 - - - -
264A ILE* 2.6 26.8 + - - +
265A SER* 3.5 10.9 + - - -
266A LYS 3.5 1.6 - - - -
267A TYR* 1.3 77.7 - - - +
269A GLN* 1.3 64.7 + - - +
270A PHE 3.7 1.6 - - - -
271A ILE* 3.6 20.1 + - - +
275A ILE* 3.5 29.4 - - - -
329A MET 4.8 2.1 + - - -
330A ASN* 4.4 19.0 + - - +
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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