Contacts of the helix formed by residues 233 - 244 (chain A) 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 MET 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.9 28.3 - - + -
227A ILE* 4.7 25.1 - - + -
230A ILE 4.8 3.8 - - - +
231A ARG 2.8 16.5 + - - +
232A GLU* 1.3 72.2 - - - +
234A LEU* 1.3 63.1 + - - +
235A PRO* 3.0 14.8 - - - +
236A VAL* 3.2 14.5 + - + +
237A LEU* 3.7 27.3 + - + +
247A LEU* 5.2 3.1 - - - -
249A ILE* 4.3 21.1 - - + -
262A LEU* 6.1 6.7 - - + -
310A GLU* 3.7 17.8 - - - +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 3.3 37.7 - - + +
233A MET* 1.3 76.7 - - - +
235A PRO* 1.3 74.0 - - + +
236A VAL 3.1 0.2 - - - -
237A LEU* 2.7 23.6 + - + +
238A GLU* 2.3 64.7 + - + +
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Residues in contact with PRO 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 5.0 5.4 - - + +
233A MET* 3.0 6.7 - - - +
234A LEU* 1.3 109.3 - - + +
236A VAL* 1.3 62.7 + - + +
238A GLU* 4.2 4.0 - - + +
239A ALA* 3.6 17.8 + - - +
310A GLU* 3.8 20.4 - - + +
311A LYS* 4.9 6.7 - - + -
312A ALA 4.9 4.5 - - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 5.1 11.0 - - + -
233A MET* 3.2 10.7 + - + +
234A LEU 3.1 0.4 - - - -
235A PRO* 1.3 74.9 - - + +
237A LEU* 1.3 62.1 + - - +
239A ALA* 3.4 7.4 + - + +
240A VAL* 3.0 30.0 + - + +
247A LEU* 5.6 1.6 - - + -
310A GLU 4.4 3.8 - - - +
312A ALA* 2.9 55.9 - - + +
313A THR 4.7 4.5 - - - +
314A LEU* 5.1 1.3 - - - +
317A LEU* 3.6 40.8 - - + -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ARG 6.0 0.4 - - - +
233A MET* 3.7 20.1 + - + +
234A LEU* 2.7 27.9 + - + +
236A VAL* 1.3 78.3 - - - +
238A GLU* 1.3 63.5 + - - +
240A VAL* 3.2 7.6 + - + +
241A ALA* 3.1 21.8 + - - +
247A LEU* 3.5 28.5 - - + -
262A LEU* 5.2 15.5 - - + -
265A ASN* 6.1 6.3 - - - +
271A VAL* 5.3 8.8 - - + +
273A VAL* 4.3 15.3 - - + -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 2.3 51.7 + - + +
235A PRO* 4.2 5.3 - - + +
237A LEU* 1.3 68.8 - - - +
239A ALA* 1.3 60.1 + - - +
241A ALA* 3.4 19.6 - - + +
242A LYS* 3.5 25.2 + - + +
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A PRO 3.6 12.0 + - - +
236A VAL* 3.4 11.8 + - + +
238A GLU* 1.3 77.8 - - - +
240A VAL* 1.3 63.2 + - + +
242A LYS* 3.4 20.2 + - - +
243A ALA* 3.4 12.1 + - - +
314A LEU* 5.2 21.5 - - + +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.8 22.4 - - + -
236A VAL 3.0 18.6 + - - +
237A LEU* 3.2 8.0 + - + +
239A ALA* 1.3 75.0 - - + +
241A ALA* 1.3 63.4 + - - +
243A ALA* 3.4 6.4 + - - +
244A GLY* 3.4 16.6 + - - -
245A LYS 3.2 24.5 - - - +
246A PRO* 4.5 0.4 - - + -
247A LEU* 4.0 29.8 - - + +
273A VAL* 5.2 4.0 - - + -
314A LEU* 6.5 0.2 - - + -
317A LEU* 4.0 25.8 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU 3.1 10.9 + - - +
238A GLU* 3.4 15.5 - - + +
239A ALA 3.2 0.2 - - - -
240A VAL* 1.3 80.5 - - - +
242A LYS* 1.3 62.2 + - + +
243A ALA 3.4 0.5 + - - -
244A GLY* 3.6 10.0 + - - -
270A ILE* 5.6 3.0 - - + +
271A VAL* 3.0 41.5 - - + +
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 3.5 25.3 + - + +
239A ALA* 3.4 13.4 + - - +
240A VAL 3.3 0.4 - - - -
241A ALA* 1.3 74.9 - - + +
243A ALA* 1.3 63.8 + - - +
244A GLY* 4.7 0.2 - - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 4.5 19.1 - - + -
239A ALA 3.4 9.6 + - - +
240A VAL* 3.4 12.5 + - - +
241A ALA 3.2 0.8 - - - -
242A LYS* 1.3 81.3 - - - +
244A GLY* 1.3 58.3 + - - +
245A LYS* 3.6 6.9 - - + +
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Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL 3.4 6.2 + - - -
241A ALA 3.6 7.7 + - - -
242A LYS 3.5 1.4 - - - -
243A ALA* 1.3 78.8 - - - +
245A LYS* 1.3 74.2 - - - +
272A LYS* 4.6 6.6 + - - -
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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