Contacts of the helix formed by residues 255 - 269 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C LYS* 5.8 4.7 - - - +
228C SER* 3.0 40.9 - - - +
253C ASP* 3.2 22.8 - - - +
254C VAL* 1.3 83.9 + - - +
256C GLY* 1.3 65.4 + - - +
257C GLU* 3.0 7.7 + - + +
258C ALA* 3.2 4.5 + - - +
259C LEU* 3.0 18.2 + - - +
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Residues in contact with GLY 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C GLU* 1.3 72.2 - - - +
257C GLU* 1.3 54.0 + - - +
259C LEU* 3.7 14.2 - - - +
260C ALA* 2.4 42.9 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C SER 3.9 9.3 - - - +
229C ASN* 3.8 17.7 - - - +
230C ILE 5.0 1.1 - - - +
231C ARG* 3.5 33.6 + - - +
255C GLU* 3.0 4.9 + - + +
256C GLY* 1.3 78.3 - - - +
258C ALA* 1.3 78.3 + - - +
260C ALA* 4.1 3.1 - - - +
261C THR* 3.1 23.7 + - - +
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Residues in contact with ALA 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ILE* 4.5 9.0 - - + +
228C SER 4.2 10.2 + - - +
231C ARG* 3.5 30.8 - - + +
233C MET* 6.3 1.6 - - + -
254C VAL* 3.9 20.4 - - + -
255C GLU 3.2 3.1 + - - +
257C GLU* 1.3 85.6 + - - +
259C LEU* 1.3 58.2 + - - +
261C THR* 3.1 4.7 - - - +
262C LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU* 3.3 34.5 - - + +
201C SER* 3.9 20.9 - - - +
204C PHE* 4.5 3.4 - - + -
254C VAL* 3.0 45.1 - - + +
255C GLU 3.0 14.4 + - - +
256C GLY* 3.6 8.5 - - - +
258C ALA* 1.3 75.4 - - - +
260C ALA* 1.3 54.0 + - - +
262C LEU* 2.8 22.4 + - + +
263C VAL* 2.4 42.7 + - + +
275C ALA* 4.8 3.6 - - + -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLU 5.8 0.2 - - - +
304B GLU* 3.3 30.4 - - - +
305B ILE* 4.8 3.1 - - - -
256C GLY* 2.4 33.5 + - - +
257C GLU* 4.1 4.5 - - - +
259C LEU* 1.3 67.8 - - - +
261C THR* 1.3 58.0 + - - +
263C VAL* 3.0 8.7 + - - +
264C VAL* 2.9 34.8 + - - +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ARG* 3.1 35.2 + - - +
257C GLU* 3.1 13.4 + - - +
258C ALA 3.1 18.4 - - - +
260C ALA* 1.3 79.7 - - - +
262C LEU* 1.3 53.5 + - - +
264C VAL* 3.9 8.8 - - - +
265C ASN* 2.8 45.9 + - - +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PHE* 3.4 30.1 - - + -
233C MET* 5.1 15.5 - - + -
237C LEU* 5.2 7.9 - - + -
249C ILE* 5.9 1.1 - - + -
254C VAL* 5.4 1.8 - - + -
258C ALA 2.9 21.2 + - - +
259C LEU* 2.8 23.9 + - + +
261C THR* 1.3 77.7 - - - +
263C VAL* 1.3 63.0 + - - +
265C ASN* 3.3 9.5 + - + +
266C THR* 3.1 28.6 + - - +
273C VAL* 3.8 32.8 - - + -
275C ALA* 4.1 16.4 - - + +
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Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE* 3.3 24.0 - - + -
201C SER* 3.9 27.8 - - - +
203C TYR* 3.2 36.3 - - + -
204C PHE* 4.7 3.8 - - + -
259C LEU* 2.4 30.5 + - + +
260C ALA* 3.0 8.9 + - - +
262C LEU* 1.3 73.2 - - - +
264C VAL* 1.3 57.6 + - - +
266C THR* 2.7 22.1 + - - -
267C MET* 2.9 31.0 + - + +
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE* 3.9 7.0 - - + -
306B GLY* 3.0 43.5 - - - +
260C ALA 2.9 22.7 + - - +
261C THR* 4.0 7.9 - - - +
263C VAL* 1.3 75.8 - - - +
265C ASN* 1.3 57.3 + - - +
267C MET* 3.6 8.9 - - + +
268C ARG* 2.9 32.9 + - + +
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Residues in contact with ASN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU* 5.3 13.6 - - - +
261C THR* 2.8 34.8 + - - +
262C LEU* 3.5 15.0 - - + +
263C VAL 3.2 0.2 - - - -
264C VAL* 1.3 79.6 - - - +
266C THR* 1.3 61.0 + - + +
268C ARG* 4.2 3.9 - - - +
269C GLY 3.4 15.6 + - - -
270C ILE* 3.9 14.7 + - - +
271C VAL* 3.6 19.2 + - + +
273C VAL* 6.1 1.3 - - + -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C TYR 5.1 3.3 + - - -
204C PHE* 4.0 12.6 - - + -
262C LEU* 3.1 14.1 + - + +
263C VAL* 2.7 24.4 + - - +
265C ASN* 1.3 74.6 - - + +
267C MET* 1.3 69.6 + - - +
269C GLY* 3.7 9.6 + - - -
271C VAL 3.8 9.4 - - - +
272C LYS* 4.2 12.2 - - - +
273C VAL* 3.2 48.9 - - + +
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Residues in contact with MET 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE* 5.1 7.2 - - + -
203C TYR* 3.3 51.6 - - + +
263C VAL* 2.9 31.0 + - + +
264C VAL* 3.3 9.8 + - + +
266C THR* 1.3 81.1 - - - +
268C ARG* 1.3 64.2 + - - +
269C GLY* 3.5 1.2 + - - -
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Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C VAL* 2.9 19.9 + - + +
265C ASN* 4.2 6.7 - - - +
267C MET* 1.3 77.9 - - - +
269C GLY* 1.3 59.6 + - - +
270C ILE* 4.6 17.0 - - + +
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Residues in contact with GLY 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ASN 3.4 5.8 + - - -
266C THR* 3.7 11.0 + - - -
267C MET 3.3 2.3 - - - -
268C ARG* 1.3 80.7 - - - +
270C ILE* 1.3 67.3 + - - +
271C VAL* 3.3 6.2 - - - -
272C LYS* 5.0 6.1 + - - +
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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