Contacts of the helix formed by residues 256 - 266 (chain B) in PDB entry 2PKG
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 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ASP* 3.1 30.9 + - - +
221B ARG* 3.9 3.1 - - - -
254B ASP* 2.8 18.5 + - - -
255B LYS* 1.3 71.4 - - - +
257B TRP* 1.3 70.0 + - - +
258B ARG* 3.4 21.1 + - - +
259B VAL* 2.8 26.5 + - - +
260B ARG* 3.1 12.3 + - - +
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Residues in contact with TRP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LYS 3.4 1.8 + - - -
256B SER* 1.3 72.8 - - - +
258B ARG* 1.3 106.6 + - + +
260B ARG* 3.3 26.4 - - - +
261B TYR* 2.5 52.9 + + + +
295B GLU* 3.4 40.6 + - + -
297B GLU* 3.3 43.3 - - + -
298B VAL* 3.9 13.4 - - + +
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Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASP* 4.1 20.1 + - + +
219B SER* 6.6 0.4 - - - +
222B LEU* 4.3 22.8 - - + +
256B SER* 3.4 11.4 + - - +
257B TRP* 1.3 124.7 - - + +
259B VAL* 1.3 65.9 + - + +
261B TYR* 3.1 7.7 - - - +
262B MET* 3.0 21.3 + - - +
150D LEU* 5.5 12.9 - - - +
151D ASP* 4.4 16.9 + - - -
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASP* 4.4 4.3 - - + -
221B ARG* 4.3 8.3 - - + +
222B LEU* 4.0 29.8 - - + +
225B VAL* 3.8 22.9 - - + -
251B ALA* 4.0 8.3 - - - +
254B ASP* 3.4 42.0 - - + +
256B SER* 2.8 18.1 + - - +
258B ARG* 1.3 74.2 - - - +
260B ARG* 1.3 68.1 + - - +
262B MET* 2.6 18.6 + - - +
263B VAL* 3.1 10.6 + - + +
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ALA 4.1 2.2 - - - +
252B ALA 3.1 27.8 - - - +
253B GLU* 4.2 3.1 - - - +
254B ASP 2.8 38.4 + - - +
255B LYS* 2.9 23.2 + - - +
256B SER 3.1 1.7 + - - +
257B TRP* 3.3 29.1 - - - +
259B VAL* 1.3 77.9 - - - +
261B TYR* 1.3 52.3 + - - +
263B VAL* 3.0 14.6 + - - +
264B ALA* 2.8 34.3 + - - +
290B LEU* 4.0 9.0 - - + +
293B ASP* 2.5 45.3 + - - +
294B CYS* 4.2 14.5 - - - +
295B GLU* 4.3 4.6 - - - +
298B VAL* 4.5 5.6 - - + -
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TRP* 2.5 32.0 + + + +
258B ARG* 3.1 12.1 - - - +
259B VAL 2.8 0.4 + - - -
260B ARG* 1.3 72.4 - - - +
262B MET* 1.3 67.6 + - + +
264B ALA* 2.9 7.8 + - - +
265B ASP* 2.7 62.6 + - + +
297B GLU* 4.1 32.5 - - + -
298B VAL* 4.3 5.4 - - + +
301B ALA* 3.8 25.9 - - + +
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 3.3 42.0 - - + +
225B VAL* 3.6 20.9 - - + -
226B GLU* 4.3 12.8 - - + +
258B ARG 3.0 6.2 + - - +
259B VAL 2.6 13.7 + - - +
261B TYR* 1.3 89.4 - - + +
263B VAL* 1.3 52.7 + - - +
265B ASP* 3.1 4.2 + - + +
266B LYS* 2.7 78.8 + - + +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 3.8 19.3 - - + +
248B LEU* 4.2 12.3 - - + -
251B ALA* 4.0 5.8 - - + -
252B ALA* 3.9 37.2 - - + +
259B VAL 3.1 18.4 - - - +
260B ARG* 3.2 15.0 - - - +
262B MET* 1.3 73.1 - - - +
264B ALA* 1.3 58.4 + - - +
266B LYS 3.3 1.3 + - - +
267B PHE* 2.8 40.2 + - + +
270B LEU* 3.9 20.3 - - + +
290B LEU* 4.7 4.5 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ARG 2.8 12.0 + - - +
261B TYR 3.2 8.3 - - - +
263B VAL* 1.3 75.6 - - - +
265B ASP* 1.3 57.0 + - - +
267B PHE* 2.8 31.0 + - - +
290B LEU* 4.0 21.0 - - + +
298B VAL* 4.1 10.8 - - + +
301B ALA* 3.6 22.7 - - + -
302B ALA* 4.1 11.2 - - + +
305B LYS* 3.9 10.7 - - - +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 2.7 51.7 + - + +
262B MET* 3.7 7.6 - - + +
264B ALA* 1.3 73.3 - - - +
266B LYS* 1.3 78.7 + - + +
267B PHE 3.4 0.4 - - - -
269B GLU* 4.5 1.0 - - - +
301B ALA* 4.4 9.6 - - - +
305B LYS* 3.1 28.1 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 4.8 5.8 - - + -
226B GLU* 3.2 38.8 - - - +
229B VAL* 4.5 15.3 - - + -
262B MET* 2.7 45.4 + - + +
263B VAL 3.5 2.5 - - - +
265B ASP* 1.3 91.1 + - - +
267B PHE* 1.3 65.6 + - - +
268B THR 3.5 2.0 - - - -
269B GLU* 3.0 38.6 + - + +
270B LEU* 2.8 25.3 + - + +
305B LYS* 4.8 0.2 - - - +
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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