Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 3K0J
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 LYS 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A LYS 3.6 2.9 + - - +
221A ILE* 1.3 75.4 - - - +
223A LYS* 1.3 68.0 + - - +
224A ASP* 4.2 7.0 - - + +
225A GLU* 3.0 24.7 + - + +
226A LEU* 2.8 24.3 + - - +
247A ARG* 3.6 10.3 - - - +
17E C 3.7 11.9 - - - +
18E C 2.7 31.7 + - - +
19E C 5.5 1.0 + - - -
70E A 3.3 35.9 + - - -
71E U 3.6 26.2 - - - +
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Residues in contact with LYS 223 (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 ILE 3.8 1.0 + - - -
222A LYS* 1.3 72.1 - - - +
224A ASP* 1.3 60.2 + - + +
226A LEU* 3.2 3.4 - - - +
227A LYS* 2.9 38.0 + - - +
245A VAL* 3.9 28.4 - - + +
247A ARG* 4.2 18.1 - - + +
17E C 4.6 7.4 + - - +
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Residues in contact with ASP 224 (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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222A LYS* 3.1 5.2 - - + +
223A LYS* 1.3 79.5 - - - +
225A GLU* 1.3 64.8 + - - +
227A LYS* 3.9 11.2 - - - +
228A LYS* 2.9 43.3 + - - +
62E U 2.9 44.3 - - - +
63E C 4.6 4.3 - - - -
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 3.9 15.0 - - + -
222A LYS* 3.0 29.2 + - + +
224A ASP* 1.3 78.4 - - - +
226A LEU* 1.3 58.0 + - - +
228A LYS* 3.5 18.8 + - - -
229A SER* 2.6 40.5 + - - -
278A TYR* 4.2 6.1 - - - +
416C ASN* 4.2 3.1 - - - +
483C ARG* 2.2 37.6 + - - +
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Residues in contact with LEU 226 (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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217A LEU* 3.3 35.2 - - + -
218A ASN 4.7 5.8 - - - +
219A GLU 6.3 0.2 - - - -
221A ILE* 3.3 42.1 - - + +
222A LYS 2.8 7.5 + - - +
223A LYS 3.2 9.2 - - - +
225A GLU* 1.3 73.7 - - - +
227A LYS* 1.3 56.4 + - - +
229A SER* 3.9 3.1 - - - -
230A LEU* 2.6 63.2 + - + +
245A VAL* 3.7 28.0 - - + -
247A ARG* 5.2 3.1 - - - -
253A GLY* 6.0 4.5 - - - +
254A GLN 5.4 0.2 - - - +
277A PHE* 4.4 9.0 - - + -
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Residues in contact with LYS 227 (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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223A LYS* 2.9 24.9 + - - +
224A ASP* 3.9 12.8 - - - +
226A LEU* 1.3 76.3 - - - +
228A LYS* 1.3 56.9 + - - +
231A HIS* 2.9 26.0 + - - +
242A ASP* 4.7 2.0 + - - -
243A ILE* 2.8 51.0 + - + +
244A LEU* 4.1 9.7 - - - +
245A VAL* 3.8 27.1 + - + +
62E U 3.8 50.6 - - + +
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Residues in contact with LYS 228 (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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224A ASP* 2.9 33.0 + - - +
225A GLU* 3.5 22.2 + - - +
227A LYS* 1.3 78.3 - - - +
229A SER* 1.3 63.4 + - - +
231A HIS* 3.1 14.6 + - - +
232A ALA* 3.2 11.3 + - - +
483C ARG* 3.4 33.2 - - - +
62E U 3.5 35.9 - - - +
63E C 3.3 30.5 + - - -
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Residues in contact with SER 229 (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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225A GLU 2.6 20.9 + - - -
226A LEU 3.9 0.9 - - - -
228A LYS* 1.3 74.1 - - - +
230A LEU* 1.3 57.8 + - - +
232A ALA* 2.9 27.2 + - - +
233A ILE* 3.2 12.0 + - - +
277A PHE* 3.9 7.2 - - - -
278A TYR* 3.0 37.2 + - - -
416C ASN* 3.5 5.5 + - - -
481C PRO* 3.6 9.1 - - - +
483C ARG* 3.1 19.0 + - - +
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Residues in contact with LEU 230 (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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214A ILE* 4.5 12.1 - - + -
217A LEU* 4.6 5.6 - - + -
226A LEU* 2.6 40.4 + - + +
227A LYS 3.6 3.4 - - - +
229A SER* 1.3 69.8 - - - +
231A HIS* 1.3 65.9 + - - +
233A ILE* 3.5 1.5 + - + +
234A PHE* 3.1 50.0 + - + +
243A ILE* 3.9 23.0 - - + +
255A ALA* 3.7 30.5 - - + -
257A VAL* 4.6 1.8 - - + -
277A PHE* 3.1 34.5 - - + -
282A MET* 5.2 1.3 - - - -
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Residues in contact with HIS 231 (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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227A LYS 2.9 12.7 + - - +
228A LYS 3.1 10.0 + - - +
230A LEU* 1.3 75.9 - - - +
232A ALA* 1.3 58.6 + - - +
235A SER* 2.6 63.6 + - - -
240A ILE* 3.9 30.1 - - + +
243A ILE* 3.5 12.5 - - + +
473C GLN* 5.8 4.5 - - - -
62E U 4.1 21.7 + - - +
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Residues in contact with ALA 232 (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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228A LYS 3.2 8.5 + - - +
229A SER* 2.9 21.1 + - - +
231A HIS* 1.3 80.0 - - - +
233A ILE* 1.3 63.2 + - - +
235A SER* 4.1 3.9 + - - -
236A ARG* 4.2 2.9 + - - +
473C GLN* 3.1 38.5 - - - +
474C GLY* 3.6 21.3 - - - +
481C PRO* 5.4 0.9 - - + -
482C MET 4.1 7.2 - - - +
483C ARG* 4.3 7.6 - - + -
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Residues in contact with ILE 233 (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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229A SER 3.2 6.3 + - - +
230A LEU 3.5 4.9 + - - +
232A ALA* 1.3 81.5 - - - +
234A PHE* 1.3 93.5 + - + +
236A ARG* 3.5 15.6 + - - +
237A PHE* 3.5 14.2 - - - -
272A MET* 3.4 34.4 - - + +
276A PRO 4.8 5.2 - - - +
277A PHE* 3.2 40.8 - - + -
282A MET* 4.1 6.1 - - + -
473C GLN 4.5 3.6 - - - -
474C GLY 3.6 22.4 - - - +
481C PRO* 4.2 5.8 - - + -
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Residues in contact with PHE 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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212A ILE* 3.7 17.9 - - + -
214A ILE* 3.3 34.3 - - + -
230A LEU* 3.1 30.5 + - + +
233A ILE* 1.3 102.4 - - + +
235A SER* 1.3 66.3 + - - +
236A ARG 3.4 2.0 - - - -
237A PHE* 3.2 18.0 - + - -
240A ILE* 3.9 14.4 - - + -
257A VAL* 4.3 10.1 - - + -
259A PHE* 3.6 17.2 - + + -
268A ALA* 3.8 23.8 - - + -
272A MET* 3.8 20.2 - - + -
282A MET* 4.1 14.4 - - - -
284A ILE* 4.3 8.3 - - + -
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Residues in contact with SER 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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231A HIS* 2.6 52.1 + - - -
232A ALA* 4.7 4.4 - - - -
233A ILE 3.7 1.8 - - - -
234A PHE* 1.3 72.8 - - - +
236A ARG* 1.3 68.6 + - - +
237A PHE 2.7 3.1 + - - -
238A GLY* 2.8 24.4 + - - +
240A ILE* 4.1 8.3 - - - -
473C GLN* 5.4 7.5 + - - +
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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