Contacts of the helix formed by residues 225 - 237 (chain A) in PDB entry 4K8T
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 ASP 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A LEU* 3.8 2.0 - - - -
223A THR* 3.0 19.7 + - - +
224A ASP* 1.3 79.9 + - - +
226A PHE* 1.3 62.4 + - - +
227A GLU* 3.1 21.3 + - - +
228A GLU* 3.3 24.7 + - + +
229A ALA 3.2 16.6 + - - -
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Residues in contact with PHE 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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214A ARG* 3.3 62.6 - - + +
217A ALA* 4.4 6.1 - - + -
218A LEU* 3.7 16.4 - - + +
224A ASP 3.7 4.6 + - - +
225A ASP* 1.3 72.5 + - - +
227A GLU* 1.3 70.0 + - + +
229A ALA* 3.3 6.1 + - + -
230A LEU* 3.0 61.3 + - + +
242A VAL* 3.9 24.0 - - + -
244A MSE 3.8 32.5 - - + -
259A TYR* 6.3 0.7 - + - -
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Residues in contact with GLU 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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225A ASP* 3.1 11.0 + - - +
226A PHE* 1.3 83.6 - - + +
228A GLU* 1.3 64.6 - - - +
230A LEU* 3.4 13.2 + - - +
231A ASN* 3.1 34.5 + - - +
257A ARG* 3.2 29.7 + - - -
259A TYR* 4.9 3.5 + - - -
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Residues in contact with GLU 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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221A TYR 4.6 1.0 - - - +
223A THR* 3.0 30.3 + - + +
225A ASP* 3.3 27.9 + - - +
226A PHE 3.3 0.2 - - - -
227A GLU* 1.3 78.7 - - - +
229A ALA* 1.3 56.8 + - - +
231A ASN* 3.3 7.5 + - - +
232A ARG* 2.8 65.5 + - + +
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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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217A ALA* 3.9 37.9 - - + +
218A LEU* 4.3 2.7 - - + +
221A TYR* 3.8 13.4 - - - -
223A THR* 4.3 8.9 - - + +
225A ASP 3.2 9.7 + - - +
226A PHE* 3.5 15.3 - - + +
228A GLU* 1.3 79.5 - - - +
230A LEU* 1.3 56.6 + - - +
233A ILE* 2.8 33.3 + - - +
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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 PHE* 3.0 57.3 + - + +
227A GLU* 3.9 10.8 - - - +
228A GLU 3.3 0.2 - - - -
229A ALA* 1.3 71.7 - - - +
231A ASN* 1.3 66.5 + - - +
233A ILE* 3.4 5.8 - - + +
234A ALA* 3.1 25.6 + - - +
242A VAL* 3.9 12.6 - - + -
250A VAL* 3.8 24.0 - - + -
252A LEU* 3.6 21.3 - - + +
257A ARG* 3.6 32.3 - - - +
259A TYR* 4.3 10.1 - - + +
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Residues in contact with ASN 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 GLU* 3.1 27.2 + - - +
228A GLU* 3.8 5.8 - - - +
230A LEU* 1.3 76.5 - - - +
232A ARG* 1.3 62.8 + - + +
234A ALA* 3.5 5.4 + - - +
235A ALA* 3.2 22.2 + - - +
252A LEU* 5.6 0.2 - - - -
257A ARG* 2.8 24.0 + - - +
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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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199A LEU* 5.9 1.6 - - - +
203A ARG* 4.2 14.6 - - - +
221A TYR* 3.3 59.8 + - + +
228A GLU* 2.8 49.2 + - + +
231A ASN* 1.3 78.4 - - + +
233A ILE* 1.3 62.7 + - - +
235A ALA* 3.1 17.2 + - - +
236A ASP* 3.1 17.7 + - - +
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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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185A LEU* 4.7 0.7 - - + -
202A MSE 3.6 24.0 - - + -
210A VAL* 4.5 10.5 - - + +
212A ALA* 4.3 23.3 - - + -
217A ALA* 5.0 7.2 - - + -
220A LEU* 4.3 12.1 - - + -
221A TYR* 3.3 14.2 + - + +
229A ALA 2.8 24.7 + - - +
230A LEU* 3.4 13.9 - - + +
232A ARG* 1.3 72.5 - - - +
234A ALA* 1.3 64.4 + - - +
236A ASP* 3.1 10.7 + - - -
237A CYS* 3.2 17.2 + - - -
240A ALA* 4.0 24.2 - - + -
242A VAL* 4.3 14.8 - - + -
252A LEU* 4.7 3.1 - - + -
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Residues in contact with ALA 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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230A LEU 3.1 19.1 + - - +
231A ASN* 3.7 6.3 - - - +
233A ILE* 1.3 78.1 - - - +
235A ALA* 1.3 58.3 + - - +
237A CYS 3.1 19.4 - - - +
240A ALA* 5.1 2.7 - - - -
252A LEU* 4.0 24.9 - - + -
254A GLY* 3.7 33.0 + - - +
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Residues in contact with ALA 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 ASN 3.2 11.7 + - - +
232A ARG* 3.1 12.7 + - - +
234A ALA* 1.3 78.4 - - - +
236A ASP* 1.3 64.2 + - - +
237A CYS 3.6 0.2 - - - -
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Residues in contact with ASP 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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199A LEU* 3.8 3.3 - - + +
202A MSE 3.2 42.5 - - + +
203A ARG* 2.9 51.9 + - + +
221A TYR* 2.7 34.6 + - - +
232A ARG* 3.1 8.7 + - - +
233A ILE 3.1 4.4 + - - +
235A ALA* 1.3 85.3 - - - +
237A CYS* 1.3 58.8 + - - +
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Residues in contact with CYS 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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202A MSE 3.9 13.7 - - + -
207A VAL 4.7 5.4 - - - +
208A ASP 4.3 3.4 - - - +
210A VAL* 3.7 28.5 - - + -
233A ILE 3.2 17.2 + - - -
234A ALA* 3.1 19.8 - - - +
235A ALA 3.6 0.4 - - - -
236A ASP* 1.3 79.0 - - - +
238A LYS* 1.3 65.3 + - - +
239A ILE* 3.2 29.1 - - - +
240A ALA* 3.8 10.8 - - - -
254A GLY 5.4 0.2 + - - -
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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