Contacts of the helix formed by residues 216 - 226 (chain A) in PDB entry 1DXK
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A LEU* 3.9 23.8 - - + -
201A ARG* 3.9 27.4 - - - +
203A ILE* 4.9 18.6 + - + +
206A VAL* 3.8 4.6 - - - +
215A ASP* 1.3 77.3 - - + +
217A GLY* 1.3 56.4 + - - +
219A LEU* 3.0 36.0 + - + +
220A LEU* 3.3 27.0 + - + +
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Residues in contact with GLY 217 (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 ASP* 2.8 16.8 + - - -
216A LYS* 1.3 79.0 - - - +
218A LEU* 1.3 50.6 - - - -
220A LEU* 3.3 15.3 + - - +
221A HIS* 2.7 34.6 + - - +
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Residues in contact with LEU 218 (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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170A VAL* 3.5 15.0 - - + -
171A LYS 3.6 6.5 - - - +
172A SER* 3.8 0.9 - - - -
173A THR* 3.5 41.7 - - - +
206A VAL* 3.7 16.8 - - + +
208A PRO* 4.0 16.4 - - + -
212A GLU 3.9 12.6 - - - +
214A GLY* 3.6 33.0 - - - +
215A ASP* 2.9 12.6 + - - +
217A GLY* 1.3 76.1 - - - +
219A LEU* 1.3 61.5 + - - +
221A HIS* 3.5 6.9 - - + +
222A THR* 2.8 32.8 + - - -
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Residues in contact with LEU 219 (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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164A LEU* 4.2 10.5 - - + -
170A VAL* 3.4 32.1 - - + -
193A ILE* 3.6 25.3 - - + +
196A VAL* 4.4 17.3 - - + -
197A LEU* 3.5 33.0 - - + -
203A ILE* 4.0 23.3 - - + -
206A VAL* 4.5 5.2 - - + -
216A LYS* 3.0 17.5 + - - +
218A LEU* 1.3 76.2 - - - +
220A LEU* 1.3 60.4 + - - +
222A THR* 3.3 6.5 + - - -
223A LEU* 3.0 31.2 + - - +
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Residues in contact with LEU 220 (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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197A LEU* 4.2 22.7 - - + -
216A LYS* 3.6 35.7 - - + +
217A GLY* 3.3 14.1 + - - +
219A LEU* 1.3 74.7 - - - +
221A HIS* 1.3 64.2 + - - +
223A LEU* 3.3 16.0 + - + +
224A ASP* 3.1 22.0 + - - +
227A LYS* 5.6 0.3 + - - -
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Residues in contact with HIS 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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171A LYS 3.6 9.4 - - - -
172A SER 2.9 29.6 + - - -
173A THR* 3.5 17.7 + - + +
175A ALA 2.7 28.8 + - - -
176A LYS* 4.9 6.3 - - + -
217A GLY 2.7 18.1 + - - +
218A LEU* 3.5 9.4 - - + +
220A LEU* 1.3 76.3 - - - +
222A THR* 1.3 55.3 + - - +
224A ASP* 3.2 11.3 + - - +
225A LEU* 3.0 49.0 + - + +
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Residues in contact with THR 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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169A LEU 3.5 20.2 - - - +
170A VAL* 3.8 3.5 - - - +
171A LYS* 3.0 34.1 + - + +
178A LEU* 4.9 1.6 - - + -
189A TRP* 3.6 19.1 - - + +
193A ILE* 4.0 11.0 - - + -
218A LEU 2.8 21.7 + - - -
219A LEU 3.6 5.2 - - - -
220A LEU 3.3 0.2 - - - -
221A HIS* 1.3 73.5 - - - +
223A LEU* 1.3 65.9 + - - +
225A LEU* 3.1 11.1 + - - +
226A LEU* 3.1 27.4 + - + +
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Residues in contact with LEU 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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190A SER* 3.6 46.0 + - - +
193A ILE* 3.6 18.8 - - + -
194A GLU* 3.3 24.2 - - + +
197A LEU* 4.1 11.7 - - + -
219A LEU 3.0 18.3 + - - +
220A LEU* 3.5 19.7 - - + +
222A THR* 1.3 76.6 - - - +
224A ASP* 1.3 62.8 + - - +
226A LEU* 3.3 18.6 + - - +
227A LYS* 3.6 23.6 + - - +
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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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220A LEU 3.1 13.1 + - - +
221A HIS* 3.4 13.8 + - - +
222A THR 3.1 0.2 - - - -
223A LEU* 1.3 71.6 - - - +
225A LEU* 1.3 63.0 + - + +
226A LEU 3.0 4.3 - - - -
227A LYS* 3.0 49.3 + - - +
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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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171A LYS* 3.9 22.0 - - + -
175A ALA 3.4 20.6 - - - +
176A LYS* 3.6 28.7 - - - +
177A ASP* 3.7 20.4 - - - +
178A LEU* 3.7 26.4 - - + +
221A HIS* 3.0 32.0 + - + +
222A THR* 3.1 9.2 + - - +
224A ASP* 1.3 80.0 - - - +
226A LEU* 1.3 58.4 + - - +
227A LYS* 3.5 5.4 + - - +
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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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178A LEU* 3.8 21.8 - - + -
186A VAL* 3.9 20.0 - - + +
189A TRP* 3.7 49.6 - - + +
190A SER* 3.4 40.3 + - - +
193A ILE* 4.7 0.2 - - + -
222A THR* 3.1 24.8 + - + +
223A LEU* 3.5 13.0 - - + +
224A ASP 3.0 0.6 - - - -
225A LEU* 1.3 76.7 - - - +
227A LYS* 1.3 61.5 + - - +
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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