Contacts of the helix formed by residues 219 - 229 (chain A) in PDB entry 7KAC
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 HIS 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ASP 3.9 1.8 + - - -
218A VAL* 1.3 76.2 - - - +
220A PRO* 1.4 82.5 - - + +
221A ASP* 3.2 46.9 + - + +
222A ARG* 3.0 23.4 + - + +
223A VAL* 3.0 10.2 + - - +
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A HIS* 1.4 100.6 - - + +
221A ASP* 1.3 66.5 + - - +
223A VAL* 3.3 1.8 + - + -
224A LEU* 3.2 22.7 + - - +
174B GLY 5.4 2.0 - - - +
175B THR* 5.6 0.4 - - - -
176B PRO* 3.4 36.6 - - + +
177B TYR* 3.4 21.1 - - + +
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Residues in contact with ASP 221 (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 HIS* 3.2 25.1 + - + +
220A PRO* 1.3 80.8 - - - +
222A ARG* 1.3 60.0 + - - +
224A LEU* 3.5 13.2 + - - +
225A GLU* 2.6 34.7 + - - +
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Residues in contact with ARG 222 (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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218A VAL* 3.7 15.3 - - + -
219A HIS* 3.0 19.6 + - + +
221A ASP* 1.3 79.2 - - - +
223A VAL* 1.4 56.0 + - - +
225A GLU* 3.5 8.2 + - - +
226A LEU* 3.1 34.3 + - + +
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Residues in contact with VAL 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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215A LEU* 3.9 16.4 - - + +
218A VAL* 3.7 20.4 - - + -
219A HIS 3.0 13.4 + - - +
220A PRO 3.3 7.2 + - - +
222A ARG* 1.4 75.2 - - - +
224A LEU* 1.3 63.2 + - - +
226A LEU* 3.4 6.8 + - - +
227A MET* 3.1 52.3 + - + +
176B PRO* 4.1 15.0 - - + -
177B TYR* 3.6 31.6 - - + -
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Residues in contact with LEU 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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220A PRO 3.2 16.2 + - - +
221A ASP* 3.7 11.7 - - - +
222A ARG 3.4 0.2 - - - -
223A VAL* 1.3 75.3 - - - +
225A GLU* 1.3 68.3 + - - +
227A MET* 3.6 4.8 + - - +
228A THR* 2.8 33.1 + - - -
173B ILE* 6.2 0.7 - - + -
176B PRO* 3.6 11.9 - - + -
179B MET* 3.4 33.4 - - + -
184B ALA* 4.4 14.3 - - + +
187B ALA* 4.8 7.4 - - + -
188B LEU* 4.3 25.4 - - + +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASP* 2.6 28.9 + - - +
222A ARG* 3.7 10.1 - - - +
223A VAL 3.3 0.4 - - - -
224A LEU* 1.3 80.7 - - - +
226A LEU* 1.3 65.8 + - + +
228A THR* 3.3 2.4 + - - -
229A LYS* 3.0 23.4 + - - +
188B LEU* 4.0 27.3 - - + +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.6 20.2 - - + -
218A VAL* 4.3 21.8 - - + -
222A ARG* 3.1 24.0 + - + +
223A VAL* 3.4 7.4 + - - +
225A GLU* 1.3 74.6 - - + +
227A MET* 1.3 62.3 + - - +
229A LYS* 3.2 21.6 + - + +
232A TYR* 3.4 26.1 - - + +
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Residues in contact with MET 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A TRP* 5.5 4.3 - - + +
203A ILE* 6.0 1.8 - - + -
214A PRO 6.0 0.9 - - - +
215A LEU* 4.8 4.9 - - + -
223A VAL* 3.1 34.9 + - + +
224A LEU 4.0 3.4 - - - +
226A LEU* 1.3 75.8 - - + +
228A THR* 1.3 60.1 + - - +
229A LYS 3.9 1.0 - - - +
232A TYR* 3.7 49.9 - - + +
257A LYS* 6.0 0.5 - - - +
176B PRO* 3.6 24.0 - - - +
177B TYR* 4.0 12.3 - - - +
179B MET 3.6 22.9 - - - +
180B ALA 4.9 1.8 - - - +
181B PRO* 4.0 22.1 - - + +
184B ALA* 4.0 21.1 - - + -
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Residues in contact with THR 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 LEU 2.8 19.5 + - - -
225A GLU* 3.9 4.3 - - - -
227A MET* 1.3 73.2 - - - +
229A LYS* 1.3 66.6 + - - +
230A SER* 3.7 0.9 + - - -
181B PRO 5.5 2.7 - - - -
184B ALA* 4.0 3.5 - - - +
185B ALA* 3.9 28.0 + - + +
188B LEU* 3.8 16.4 - - + +
189B LYS* 3.8 41.9 + - + +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLU 3.0 13.2 + - - +
226A LEU* 3.2 18.2 + - + +
227A MET 3.9 1.2 - - - +
228A THR* 1.3 79.0 - - - +
230A SER* 1.3 68.3 + - - +
231A GLY 3.4 4.3 - - - +
232A TYR* 3.3 18.3 + - - +
257A LYS* 5.3 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