Contacts of the helix formed by residues 255 - 269 (chain G) in PDB entry 4PKN
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226G LYS* 3.7 22.3 + - - +
227G ILE 4.6 1.0 - - - -
228G SER* 3.1 35.7 - - - +
253G ASP* 3.2 20.7 - - - +
254G VAL* 1.3 78.1 - - - +
256G GLY* 1.3 69.2 + - - +
257G GLU* 3.4 23.6 - - - +
258G ALA* 3.5 4.0 + - - +
259G LEU* 3.0 19.1 + - - +
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Residues in contact with GLY 256 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255G GLU* 1.3 75.8 - - - +
257G GLU* 1.3 57.2 + - - +
259G LEU* 2.7 30.8 + - - +
260G ALA* 2.8 16.7 + - - +
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Residues in contact with GLU 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ILE 4.1 2.6 - - - +
228G SER* 2.8 26.1 - - - +
231G ARG* 3.6 44.6 - - + +
232G GLU* 4.3 4.3 - - - +
255G GLU* 3.4 19.4 - - - +
256G GLY* 1.3 75.5 + - - +
258G ALA* 1.3 58.5 + - - +
260G ALA* 3.6 6.6 + - - +
261G THR* 3.0 35.8 + - - +
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Residues in contact with ALA 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ILE* 4.0 22.2 - - + +
231G ARG* 3.9 23.6 - - - +
232G GLU* 4.6 4.9 - - - +
235G PRO* 5.9 1.6 - - + -
254G VAL* 4.2 8.1 - - + -
255G GLU 3.5 7.6 + - - +
256G GLY 3.1 0.4 - - - -
257G GLU* 1.3 78.1 - - - +
259G LEU* 1.3 65.3 - - - +
261G THR* 2.3 27.9 + - - +
262G LEU* 2.9 18.5 + - + +
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Residues in contact with LEU 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G LEU* 4.3 24.7 - - + +
201G SER* 3.9 31.0 - - - +
204G PHE* 4.8 1.3 - - + -
254G VAL* 3.2 44.6 - - + +
255G GLU 3.0 9.9 + - - +
256G GLY* 2.7 17.5 + - - +
258G ALA* 1.3 72.2 - - - +
260G ALA* 1.3 56.7 + - - +
262G LEU* 2.9 15.4 + - + +
263G VAL* 2.8 33.6 + - + +
275G ALA* 4.8 7.0 - - + -
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Residues in contact with ALA 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256G GLY 2.8 19.1 + - - +
257G GLU* 3.8 7.4 - - - +
259G LEU* 1.3 71.7 - - - +
261G THR* 1.3 64.1 + - + +
263G VAL* 3.2 8.2 + - - +
264G VAL* 3.0 34.3 + - + +
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Residues in contact with THR 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232G GLU* 3.6 38.5 - - + +
235G PRO* 5.8 0.9 - - - +
257G GLU* 3.0 21.7 + - + +
258G ALA* 2.3 34.0 + - - +
260G ALA* 1.3 76.5 - - + +
262G LEU* 1.3 53.5 + - - +
264G VAL* 3.1 13.0 - - - +
265G ASN* 2.2 38.2 + - - -
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Residues in contact with LEU 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G PHE* 4.1 17.9 - - + -
227G ILE* 6.5 0.4 - - + -
235G PRO* 5.5 15.0 - - + -
249G ILE* 5.4 8.1 - - + -
254G VAL* 4.5 14.4 - - + -
258G ALA* 2.9 23.2 + - + +
259G LEU* 2.9 16.7 + - + +
261G THR* 1.3 77.8 + - - +
263G VAL* 1.3 59.5 + - - +
265G ASN* 3.2 8.5 + - + +
266G THR* 3.0 33.0 + - - +
273G VAL* 4.0 28.9 - - + -
275G ALA* 4.9 7.6 - - + -
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Residues in contact with VAL 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G SER* 3.9 29.8 - - - +
203G TYR* 3.5 47.6 - - + -
204G PHE* 4.5 2.5 - - + -
259G LEU 2.8 23.5 + - - +
260G ALA* 3.6 9.9 - - - +
262G LEU* 1.3 70.7 - - - +
264G VAL* 1.3 70.5 + - + +
266G THR* 2.9 9.2 + - - -
267G MET* 2.9 29.6 + - + +
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Residues in contact with VAL 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G ALA* 3.0 17.2 + - + +
261G THR* 3.1 24.5 - - - +
263G VAL* 1.3 78.8 - - + +
265G ASN* 1.3 63.8 + - - +
267G MET* 3.8 8.2 - - - +
268G ARG* 2.9 33.6 + - - +
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Residues in contact with ASN 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G THR* 2.2 36.7 + - - +
262G LEU* 3.4 10.5 - - + +
263G VAL 3.1 0.6 - - - -
264G VAL* 1.3 91.5 - - - +
266G THR* 1.3 58.4 + - + +
269G GLY 3.0 5.0 + - - -
270G ILE* 2.9 65.5 + - + +
271G VAL* 3.8 12.5 - - + +
273G VAL* 5.7 1.3 - - + -
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Residues in contact with THR 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G TYR* 4.9 5.5 + - - +
204G PHE* 3.7 20.9 - - + -
262G LEU 3.0 13.0 + - - +
263G VAL* 2.9 19.8 + - - +
265G ASN* 1.3 75.3 - - - +
267G MET* 1.3 64.3 + - - +
269G GLY* 3.5 9.6 + - - -
271G VAL 3.4 11.6 - - - +
272G LYS* 5.0 4.8 - - - +
273G VAL* 3.3 44.6 - - + +
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Residues in contact with MET 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G TYR* 5.8 7.2 - - + -
263G VAL* 2.9 25.7 + - + +
264G VAL* 3.8 8.1 - - - +
266G THR* 1.3 77.3 + - - +
268G ARG* 1.3 65.6 + - - +
269G GLY* 3.0 1.8 + - - -
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Residues in contact with ARG 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264G VAL 2.9 17.7 + - - +
265G ASN* 4.4 2.0 - - - +
267G MET* 1.3 78.3 - - - +
269G GLY* 1.3 60.0 + - - +
270G ILE* 4.2 28.9 - - + +
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Residues in contact with GLY 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G ASN 3.0 7.1 + - - -
266G THR* 3.7 11.0 - - - -
267G MET 3.0 4.3 - - - -
268G ARG* 1.3 81.2 - - - +
270G ILE* 1.3 66.1 + - - +
271G VAL* 3.5 3.8 - - - -
272G LYS* 6.3 2.2 - - - -
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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