Contacts of the helix formed by residues 224 - 233 (chain A) in PDB entry 1KC2
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 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PHE* 3.7 15.9 - - - +
222A PHE* 3.3 9.7 - - - +
223A SER* 1.3 84.4 + - - +
225A LEU* 1.3 64.2 + - - +
226A GLN* 3.0 35.4 - - - +
227A GLN* 3.2 17.9 + - - +
228A LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 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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150A TRP* 3.8 19.5 - - + -
151A TYR* 4.6 7.0 - - + -
176A VAL* 4.3 11.4 - - + -
186A TYR* 4.1 37.9 - - + +
206A ILE* 3.9 39.9 - - + -
214A PHE* 4.1 22.3 - - + -
224A SER* 1.3 75.3 - - - +
226A GLN* 1.3 65.6 + - - +
228A LEU* 3.2 6.5 + - + +
229A VAL* 2.8 33.0 + - + +
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Residues in contact with GLN 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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147A ALA* 3.0 33.2 - - + +
150A TRP* 3.8 17.4 - - + -
224A SER* 3.0 36.2 - - - +
225A LEU* 1.3 87.4 - - - +
227A GLN* 1.3 58.0 + - + +
229A VAL* 3.8 2.4 - - - +
230A ALA* 3.0 28.8 + - - +
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Residues in contact with GLN 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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222A PHE* 3.6 18.8 - - + +
223A SER* 3.1 27.8 + - - +
224A SER* 3.2 18.6 + - - +
225A LEU 3.3 0.2 - - - -
226A GLN* 1.3 74.6 - - + +
228A LEU* 1.3 65.9 + - - +
230A ALA* 3.4 4.9 + - - +
231A TYR* 3.0 24.4 + - - +
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Residues in contact with LEU 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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188A LEU* 4.6 10.3 - - + -
206A ILE* 3.7 46.0 - - + -
214A PHE* 4.6 6.1 - - + -
215A TYR* 4.7 2.9 - - - +
216A ILE* 4.1 19.5 - - + -
222A PHE* 3.5 36.5 - - + -
224A SER 3.1 12.5 + - - +
225A LEU* 3.2 11.9 + - + +
227A GLN* 1.3 75.9 - - - +
229A VAL* 1.3 72.5 + - + +
231A TYR* 3.3 2.1 + - - +
232A TYR* 3.1 44.1 + - + -
243A LEU* 5.3 0.2 - - + -
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Residues in contact with VAL 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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150A TRP* 3.8 43.1 - - + +
174A PHE* 3.9 24.9 - - + -
176A VAL* 4.1 17.3 - - + -
225A LEU 2.8 20.5 + - - +
226A GLN 3.8 4.9 - - - +
227A GLN 3.3 0.2 - - - -
228A LEU* 1.3 81.2 - - + +
230A ALA* 1.3 61.5 + - - +
232A TYR 3.6 0.7 + - - -
233A SER* 2.6 38.0 + - - +
243A LEU* 4.0 8.2 - - + +
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Residues in contact with ALA 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 GLN 3.0 18.9 + - - +
227A GLN* 3.9 6.7 - - - +
228A LEU 3.3 0.2 - - - -
229A VAL* 1.3 77.2 - - - +
231A TYR* 1.3 65.0 + - - +
233A SER* 3.4 16.4 + - - -
234A LYS* 3.6 8.3 + - - +
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Residues in contact with TYR 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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220A THR* 3.7 18.8 + - + +
222A PHE* 3.2 39.3 - + + -
227A GLN 3.0 10.2 + - - +
228A LEU 3.5 2.0 - - - +
230A ALA* 1.3 76.5 - - - +
232A TYR* 1.3 71.3 + + - +
234A LYS* 2.9 22.4 + - - +
235A HIS* 3.2 23.9 + - + +
237A ASP* 2.6 42.6 + - + +
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Residues in contact with TYR 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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188A LEU* 5.0 0.2 - - + -
216A ILE* 4.1 17.1 - - + +
217A THR* 4.5 1.2 - - - +
220A THR* 3.9 19.6 + - - -
222A PHE* 3.7 22.6 - + - -
228A LEU* 3.1 37.0 + - + -
231A TYR* 1.3 91.6 - + - +
233A SER* 1.3 57.2 + - - +
234A LYS 3.2 2.2 - - - -
235A HIS 3.3 13.0 - - - +
236A ALA 3.1 28.0 + - - -
237A ASP* 3.9 9.9 + - + -
239A LEU* 3.5 20.6 - - + -
242A ARG* 3.6 7.6 - - - +
243A LEU* 3.0 42.0 + - + -
307B ILE* 3.4 21.2 - - + +
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Residues in contact with SER 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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174A PHE* 4.9 2.9 - - - -
229A VAL* 2.6 29.2 + - - +
230A ALA* 3.5 9.6 - - - -
231A TYR 3.1 1.0 - - - -
232A TYR* 1.3 78.1 - - - +
234A LYS* 1.3 55.3 + - - +
242A ARG* 2.8 32.5 + - - -
243A LEU* 3.4 23.9 + - - +
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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