Contacts of the helix formed by residues 222 - 232 (chain A) in PDB entry 1KR2
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 SER 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A HIS* 6.2 0.2 - - - -
220A ASP 3.1 12.4 + - - -
221A ILE* 1.3 72.8 - - - +
223A SER* 1.3 63.9 + - - +
224A THR* 3.5 10.2 + - - -
225A LYS* 3.0 42.2 + - - +
226A ILE* 3.1 15.2 + - - +
809A TAD 5.3 11.4 - - - -
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Residues in contact with SER 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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16A SER* 5.9 0.9 - - - -
18A ASN* 3.6 25.7 + - - -
19A PRO* 2.7 25.1 + - - +
21A THR* 4.4 2.7 - - - +
24A HIS* 3.4 16.1 + - - -
221A ILE 3.8 1.8 + - - -
222A SER* 1.3 72.5 - - - +
224A THR* 1.3 63.0 + - - +
226A ILE* 3.1 9.4 + - - +
227A ARG* 3.0 33.2 + - - +
809A TAD 4.1 12.6 + - - -
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Residues in contact with THR 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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57A LYS* 5.8 2.4 + - - -
222A SER* 3.0 9.7 + - - +
223A SER* 1.3 79.9 - - - +
225A LYS* 1.3 58.8 + - + +
227A ARG* 3.4 29.7 + - - +
228A ARG* 3.0 46.6 + - - +
231A ARG* 5.1 0.7 + - - -
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Residues in contact with LYS 225 (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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220A ASP* 4.5 14.4 + - - +
222A SER* 3.0 23.6 + - - +
224A THR* 1.3 74.4 - - + +
226A ILE* 1.3 60.6 + - - +
228A ARG* 3.7 20.7 - - - +
229A ALA* 2.8 29.3 + - - +
216B TRP* 2.9 30.1 + - - +
217B ILE* 3.9 25.8 - - + +
218B ALA* 5.3 1.6 - - - +
198E TYR* 3.5 24.7 + - - +
199E GLU* 6.1 0.9 - - - -
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Residues in contact with ILE 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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19A PRO* 3.9 18.2 - - + -
21A THR* 3.8 20.0 - - + -
221A ILE* 4.0 12.3 - - + -
222A SER 3.4 13.2 - - - +
223A SER* 3.1 9.8 + - - +
225A LYS* 1.3 74.0 - - - +
227A ARG* 1.3 66.4 + - - +
229A ALA* 3.0 6.1 + - - +
230A LEU* 2.8 39.8 + - + +
236A ILE* 3.9 22.4 - - + -
239A LEU* 3.9 33.4 - - + -
240A VAL* 4.2 5.8 - - + -
217B ILE* 4.4 5.6 - - + -
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Residues in contact with ARG 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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18A ASN* 3.0 46.5 + - - +
19A PRO* 4.1 3.1 - - + -
57A LYS* 5.7 9.9 - - - +
58A LYS 5.0 5.7 + - - -
59A GLY 4.4 2.6 + - - -
223A SER* 3.0 32.6 + - - +
224A THR* 3.4 32.5 + - - +
226A ILE* 1.3 74.8 - - - +
228A ARG* 1.3 64.6 + - - +
230A LEU* 3.2 10.6 + - - +
231A ARG* 2.9 31.5 + - + +
254A TYR* 3.4 35.3 - - + +
259A GLU* 2.9 44.0 + - - +
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Residues in contact with ARG 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 THR* 3.0 35.8 + - - +
225A LYS* 3.7 24.5 - - - +
227A ARG* 1.3 79.0 - - - +
229A ALA* 1.3 63.4 + - - +
231A ARG* 3.3 29.6 + - - +
232A ARG* 3.2 65.5 + - - +
198E TYR* 3.2 41.1 + - + +
199E GLU* 4.0 25.6 + - - +
201E ASP* 4.2 0.4 - - - -
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Residues in contact with ALA 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 LYS 2.8 15.7 + - - +
226A ILE* 3.3 8.5 - - - +
228A ARG* 1.3 78.0 - - - +
230A LEU* 1.3 61.1 + - - +
232A ARG* 3.1 6.9 + - - -
234A GLN* 2.9 53.9 + - + +
235A SER 4.7 1.8 - - - +
236A ILE* 3.7 20.0 - - + -
26B ARG* 6.2 0.4 - - - +
217B ILE* 4.6 11.7 - - + -
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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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226A ILE* 2.8 37.1 + - + +
227A ARG 3.2 6.3 + - - +
229A ALA* 1.3 70.1 - - - +
231A ARG* 1.3 67.4 + - - +
233A GLY* 2.8 15.8 + - - +
234A GLN 4.7 4.9 - - - +
236A ILE* 3.9 23.3 - - + -
248A ILE* 3.6 27.1 - - + -
249A GLU* 3.3 30.1 - - - +
254A TYR* 3.7 34.2 - - + +
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Residues in contact with ARG 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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224A THR 5.1 0.8 + - - -
227A ARG* 2.9 26.2 + - - +
228A ARG* 3.5 37.0 - - - +
230A LEU* 1.3 76.7 - - - +
232A ARG* 1.3 61.5 + - + +
233A GLY 3.5 0.5 + - - -
254A TYR* 4.5 4.7 + - + -
255A SER* 3.5 44.2 - - - +
256A SER* 3.5 13.0 - - - +
259A GLU* 3.2 37.2 + - - +
201E ASP* 2.8 44.0 + - - +
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Residues in contact with ARG 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 ARG* 3.2 31.3 + - - +
229A ALA 3.1 7.9 + - - +
230A LEU 3.0 1.2 - - - -
231A ARG* 1.3 82.3 - - + +
233A GLY* 1.3 62.1 + - - +
234A GLN* 3.2 21.6 + - + +
198E TYR* 2.8 46.9 + - - -
199E GLU 4.2 0.2 - - - -
200E SER 3.6 4.4 + - - -
201E ASP* 2.9 44.8 + - - +
204E TRP* 3.4 48.6 + - + +
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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