Contacts of the helix formed by residues 281 - 296 (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 PHE 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280C GLY* 1.3 73.1 - - - -
282C GLY* 1.3 74.2 + - - +
283C ASP* 3.5 8.1 - - + -
284C ARG* 3.0 41.7 + - - +
285C ARG* 2.5 34.3 + - - +
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Residues in contact with GLY 282 (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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252C GLU* 5.4 2.7 + - - -
281C PHE* 1.3 85.0 - - - +
283C ASP* 1.3 63.1 + - - +
285C ARG* 3.0 43.5 + - - +
286C LYS* 3.5 10.3 + - - +
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Residues in contact with ASP 283 (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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281C PHE* 3.5 7.0 - - + -
282C GLY* 1.3 75.9 - - - +
284C ARG* 1.3 73.8 + - + +
286C LYS* 3.6 15.8 + - - +
287C ALA* 3.5 17.2 + - - +
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Residues in contact with ARG 284 (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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280C GLY* 5.0 1.8 - - - -
281C PHE* 3.0 47.0 + - - +
283C ASP* 1.3 83.6 - - + +
285C ARG* 1.3 61.0 + - - +
287C ALA* 3.1 18.0 + - - +
288C MET* 3.2 15.6 + - - +
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Residues in contact with ARG 285 (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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223C ALA 4.2 1.8 + - - -
224C ASP* 2.6 37.5 + - - +
225C LYS* 5.4 2.2 - - - +
252C GLU* 2.8 30.8 + - - +
278C ALA* 4.9 13.5 - - + -
279C PRO* 5.8 0.4 - - - -
280C GLY* 3.3 37.5 - - - +
281C PHE 2.5 24.9 + - - +
282C GLY* 3.0 28.2 + - - +
284C ARG* 1.3 70.2 - - - +
286C LYS* 1.3 74.6 + - - +
288C MET* 2.7 8.0 + - - +
289C LEU* 2.5 69.3 + - + +
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Residues in contact with LYS 286 (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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224C ASP* 2.9 33.1 + - - +
225C LYS* 5.8 0.6 - - - +
282C GLY 3.5 16.1 + - - +
283C ASP* 3.9 14.1 + - - +
284C ARG 3.3 0.8 - - - -
285C ARG* 1.3 87.5 - - - +
287C ALA* 1.3 60.3 + - - +
289C LEU* 3.5 21.4 + - + +
290C GLN* 3.8 11.3 + - - +
304C GLU* 3.3 31.8 + - - +
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Residues in contact with ALA 287 (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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283C ASP 3.5 8.4 + - - +
284C ARG* 3.1 13.2 + - - +
285C ARG 3.0 0.2 - - - -
286C LYS* 1.3 82.0 - - - +
288C MET* 1.3 52.5 + - + +
290C GLN* 3.5 17.7 + - - +
291C ASP* 2.7 29.9 - - - +
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Residues in contact with MET 288 (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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193C MET* 4.5 22.0 - - + -
195C PHE* 5.1 5.2 - - + -
279C PRO* 4.3 27.6 - - + -
280C GLY* 5.6 3.4 - - - -
284C ARG 3.2 14.3 + - - +
285C ARG* 2.7 12.0 + - - +
287C ALA* 1.3 75.3 - - + +
289C LEU* 1.3 62.4 + - - +
290C GLN 3.5 0.2 - - - -
291C ASP* 3.2 16.5 - - + +
292C ILE* 3.1 29.7 + - - +
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Residues in contact with LEU 289 (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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222C LEU* 2.9 37.5 - - + +
223C ALA 3.9 24.5 - - - +
224C ASP* 4.4 5.2 - - - +
250C ILE* 4.1 15.3 - - + +
278C ALA* 3.8 27.1 - - + -
279C PRO* 4.3 7.9 - - + -
285C ARG* 2.5 53.7 + - + +
286C LYS* 3.7 10.8 - - + +
287C ALA 3.3 1.0 - - - -
288C MET* 1.3 70.9 - - - +
290C GLN* 1.3 66.7 + - - +
291C ASP 3.1 1.1 - - - -
292C ILE* 3.1 3.6 + - + -
293C ALA 3.1 7.1 + - - -
300C VAL* 4.1 10.8 - - + -
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Residues in contact with GLN 290 (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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286C LYS 3.8 8.6 + - - +
287C ALA* 3.5 21.4 + - - +
289C LEU* 1.3 79.5 - - - +
291C ASP* 1.3 67.5 + - - +
293C ALA* 3.7 0.6 - - - +
294C THR* 2.9 36.1 + - + +
300C VAL* 3.6 20.5 - - + +
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Residues in contact with ASP 291 (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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193C MET* 6.0 2.5 - - + -
287C ALA 2.7 23.3 - - - +
288C MET* 3.2 23.7 - - + +
290C GLN* 1.3 90.2 + - - +
292C ILE* 1.3 61.6 + - + +
294C THR* 3.4 13.9 + - - -
295C LEU* 3.5 13.9 + - - +
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Residues in contact with ILE 292 (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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193C MET* 3.8 25.4 - - + -
195C PHE* 3.8 20.6 - - + -
220C ILE* 4.4 9.6 - - + -
222C LEU* 4.1 2.2 - - + -
250C ILE* 3.6 30.5 - - + -
279C PRO* 3.6 35.7 - - + -
288C MET* 3.1 16.6 - - + +
289C LEU* 3.1 9.1 + - + +
291C ASP* 1.3 75.5 - - + +
293C ALA* 1.3 64.2 + - - +
295C LEU* 3.4 7.8 + - + +
296C THR* 3.3 23.8 + - + +
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Residues in contact with ALA 293 (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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220C ILE* 4.7 0.2 - - - -
222C LEU* 3.5 21.1 - - + +
289C LEU 3.1 4.8 + - - +
290C GLN 3.7 3.8 - - - +
291C ASP 3.3 0.4 - - - -
292C ILE* 1.3 78.0 - - - +
294C THR* 1.3 57.3 + - + +
296C THR* 3.4 5.4 + - - -
297C GLY 2.8 8.1 + - - -
298C GLY 2.6 44.9 + - - +
300C VAL* 3.4 33.0 - - + -
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Residues in contact with THR 294 (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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290C GLN* 2.9 20.5 + - + +
291C ASP* 3.4 9.5 + - - -
293C ALA* 1.3 75.5 - - + +
295C LEU* 1.3 66.7 + - - +
297C GLY* 3.4 12.0 + - - +
298C GLY 4.5 4.7 - - - +
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Residues in contact with LEU 295 (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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193C MET* 3.5 41.7 - - + -
291C ASP 3.5 11.8 + - - +
292C ILE* 3.4 12.1 + - + +
293C ALA 3.2 0.6 - - - -
294C THR* 1.3 83.2 + - - +
296C THR* 1.3 65.3 + - + +
297C GLY 3.3 0.6 + - - -
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Residues in contact with THR 296 (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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220C ILE* 3.2 52.1 - - + +
292C ILE* 3.3 16.6 + - + +
293C ALA 3.4 5.0 + - - -
295C LEU* 1.3 84.9 - - + +
297C GLY* 1.3 60.9 + - - +
298C GLY 3.5 2.1 + - - -
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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