Contacts of the helix formed by residues 255 - 269 (chain B) in PDB entry 4PKO
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 GLU 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B LYS* 3.8 16.2 + - - -
228B SER* 3.0 35.0 - - - +
253B ASP* 2.9 23.4 + - - +
254B VAL* 1.3 74.4 - - - +
256B GLY* 1.3 57.9 + - - +
257B GLU* 2.9 29.5 + - - +
258B ALA* 3.0 7.3 + - - +
259B LEU* 2.6 35.1 + - - +
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Residues in contact with GLY 256 (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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304A GLU* 4.1 20.5 - - - +
254B VAL 4.0 0.6 + - - -
255B GLU* 1.3 79.3 + - - +
257B GLU* 1.3 54.4 + - - +
259B LEU* 3.7 12.0 - - - +
260B ALA* 2.6 36.9 + - - +
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Residues in contact with GLU 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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228B SER* 2.7 27.6 - - - +
229B ASN 5.7 0.2 - - - +
231B ARG* 3.0 38.0 + - - +
255B GLU* 2.9 29.6 - - - +
256B GLY* 1.3 73.1 + - - +
258B ALA* 1.3 69.2 + - - +
260B ALA* 3.7 5.3 - - - +
261B THR* 3.2 24.3 + - - +
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Residues in contact with ALA 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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227B ILE* 4.1 13.2 - - + +
231B ARG* 3.3 34.3 - - + +
254B VAL* 4.2 14.0 - - + +
255B GLU 3.0 8.4 + - - +
257B GLU* 1.3 86.6 - - - +
259B LEU* 1.3 62.0 + - - +
261B THR* 2.9 17.1 - - + +
262B LEU* 3.2 12.5 + - - +
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Residues in contact with LEU 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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304A GLU 5.7 0.4 - - - +
200B LEU* 3.4 34.1 - - + +
201B SER* 4.6 17.3 - - - +
204B PHE* 4.8 13.9 - - + -
254B VAL* 3.1 48.7 - - + +
255B GLU 2.6 17.6 + - - +
256B GLY* 3.7 9.4 - - - +
258B ALA* 1.3 71.7 - - - +
260B ALA* 1.3 58.7 + - - +
262B LEU* 3.0 10.0 + - + +
263B VAL* 2.8 34.9 + - + +
275B ALA* 4.8 3.4 - - + +
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Residues in contact with ALA 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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303A GLU 5.0 1.6 - - - +
304A GLU* 2.9 36.3 - - - +
305A ILE* 3.9 11.7 - - - +
306A GLY* 4.6 0.8 + - - -
256B GLY 2.6 19.7 + - - +
257B GLU* 3.7 7.2 - - - +
258B ALA 3.4 0.2 - - - -
259B LEU* 1.3 72.9 - - - +
261B THR* 1.3 62.4 + - - +
263B VAL* 3.2 14.9 + - - +
264B VAL* 3.2 21.5 + - - +
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Residues in contact with THR 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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231B ARG* 3.6 19.5 - - + +
257B GLU 3.2 13.3 + - - +
258B ALA* 2.9 27.8 - - - +
260B ALA* 1.3 79.0 - - - +
262B LEU* 1.3 61.7 + - + +
264B VAL* 4.4 4.6 - - - +
265B ASN* 3.4 23.6 + - - +
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Residues in contact with LEU 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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204B PHE* 3.5 19.3 - - + -
237B LEU* 4.6 17.7 - - + -
249B ILE* 5.7 6.3 - - + -
254B VAL* 5.5 2.0 - - + -
258B ALA 3.4 10.3 - - - +
259B LEU* 3.0 15.6 + - + +
261B THR* 1.3 81.9 - - + +
263B VAL* 1.3 64.1 + - - +
265B ASN* 3.6 7.1 + - + +
266B THR* 3.0 29.3 + - - +
273B VAL* 3.9 27.8 - - + -
275B ALA* 3.3 35.2 - - + +
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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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304A GLU 5.5 2.2 - - - +
305A ILE* 4.3 16.2 - - + -
201B SER* 3.2 29.2 - - - +
203B TYR* 4.0 15.5 - - + -
204B PHE* 3.9 12.8 - - + -
259B LEU* 2.8 19.3 + - + +
260B ALA* 3.2 11.2 + - - +
262B LEU* 1.3 76.6 - - - +
264B VAL* 1.3 58.2 + - + +
266B THR* 2.4 24.1 + - - +
267B MET* 2.9 46.1 + - + +
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Residues in contact with VAL 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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305A ILE* 4.4 7.6 - - + -
306A GLY* 3.1 45.1 - - - +
260B ALA 3.2 11.7 + - - +
261B THR* 3.9 4.9 + - - +
263B VAL* 1.3 72.8 - - + +
265B ASN* 1.3 60.7 + - - +
267B MET* 2.9 31.0 + - + +
268B ARG* 3.1 10.2 + - + +
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Residues in contact with ASN 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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237B LEU* 5.6 7.7 - - - +
261B THR 3.4 17.1 + - - +
262B LEU* 4.0 8.2 - - + +
263B VAL 3.3 0.6 - - - -
264B VAL* 1.3 78.6 - - - +
266B THR* 1.3 61.8 + - + +
267B MET 3.6 0.2 + - - -
268B ARG* 3.8 8.9 + - - +
269B GLY 3.8 2.9 + - - -
270B ILE* 3.0 32.7 - - - +
271B VAL* 3.6 29.6 + - - +
273B VAL* 5.0 3.8 - - - +
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Residues in contact with THR 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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203B TYR 5.4 1.9 + - - -
204B PHE* 4.1 9.0 - - + -
262B LEU 3.0 16.7 + - - +
263B VAL* 2.4 25.8 + - - +
265B ASN* 1.3 76.1 - - + +
267B MET* 1.3 67.0 + - - +
268B ARG 3.4 0.4 + - - -
269B GLY* 3.7 8.9 + - - -
271B VAL 3.7 9.1 - - - +
272B LYS* 4.6 9.5 - - - +
273B VAL* 3.1 56.3 - - + +
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Residues in contact with MET 267 (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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305A ILE* 5.1 9.0 - - + -
203B TYR* 3.6 34.8 - - + +
263B VAL* 2.9 43.2 + - + +
264B VAL* 2.9 23.1 + - + +
266B THR* 1.3 82.4 - - - +
268B ARG* 1.3 60.6 + - - +
269B GLY 3.5 0.3 + - - -
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Residues in contact with ARG 268 (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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264B VAL* 3.1 10.5 + - + +
265B ASN* 3.8 5.6 + - - +
266B THR 3.4 0.2 - - - -
267B MET* 1.3 80.4 - - - +
269B GLY* 1.3 57.9 + - - +
270B ILE* 4.5 9.4 - - + +
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Residues in contact with GLY 269 (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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245B LYS* 5.5 4.2 - - - +
265B ASN 3.8 2.4 + - - -
266B THR 3.7 10.3 + - - -
267B MET 3.4 3.4 - - - -
268B ARG* 1.3 79.3 - - - +
270B ILE* 1.3 67.6 + - - +
271B VAL* 3.3 6.0 + - - -
272B LYS* 4.9 10.2 + - - +
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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