Contacts of the helix formed by residues 203 - 212 (chain E) in PDB entry 1KXT
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 TRP 203 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140E LYS* 5.5 1.0 - - + +
154E PRO* 4.5 5.4 - - + -
155E TYR* 3.8 58.1 - + - -
158E ARG* 3.4 43.8 - - + +
159E ASP* 3.0 26.8 + - - -
202E MET* 1.3 73.1 - - - +
204E PRO* 1.3 75.9 - - + +
205E GLY* 3.1 6.8 + - - +
206E ASP* 3.1 35.1 + - - +
207E ILE* 3.0 16.4 + - - +
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Residues in contact with PRO 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E ARG* 3.9 16.6 - - - +
202E MET 3.6 4.7 - - - +
203E TRP* 1.3 89.1 - - + +
205E GLY* 1.3 57.0 + - - +
207E ILE* 3.3 5.2 + - + +
208E LYS* 3.0 26.2 + - - +
246E GLU* 3.4 35.7 - - + +
247E TYR* 3.7 21.8 - - + -
250E ASN* 3.3 20.7 + - - +
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Residues in contact with GLY 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ARG* 4.9 0.7 + - - -
203E TRP* 3.0 4.4 - - - +
204E PRO* 1.3 79.2 - - - +
206E ASP* 1.3 66.5 + - - +
208E LYS* 3.4 8.6 + - - +
209E ALA* 3.1 19.8 + - - +
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Residues in contact with ASP 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 3.2 45.8 - - + +
171E GLU* 3.5 12.1 + - - +
176E ARG* 3.1 22.4 + - - +
202E MET* 5.7 1.1 - - + -
203E TRP* 3.1 34.3 + - + +
205E GLY* 1.3 73.5 - - - +
207E ILE* 1.3 70.6 + - + +
209E ALA* 3.0 13.0 + - - +
210E VAL* 3.2 16.8 + - - +
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Residues in contact with ILE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ILE* 5.2 6.1 - - + -
170E LEU* 5.9 0.9 - - + -
196E ILE* 4.3 16.2 - - + -
199E SER* 4.7 4.5 - - - +
202E MET* 3.3 52.0 - - + +
203E TRP 3.0 18.5 + - - +
204E PRO* 3.4 10.8 - - + +
206E ASP* 1.3 76.8 - - - +
208E LYS* 1.3 64.3 + - - +
210E VAL* 3.1 9.9 + - + +
211E LEU* 3.0 44.1 + - + +
232E GLN* 4.1 13.0 - - - +
247E TYR* 4.8 3.6 - - + -
250E ASN* 3.9 9.9 - - - +
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Residues in contact with LYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E GLN* 6.6 0.4 - - - -
204E PRO 3.0 10.5 + - - +
205E GLY* 3.4 12.8 - - - +
206E ASP 3.1 0.2 - - - -
207E ILE* 1.3 77.7 - - - +
209E ALA* 1.3 63.1 + - - +
211E LEU* 3.1 6.5 + - + +
212E ASP* 2.8 63.3 + - - +
249E GLY* 3.8 18.6 - - - +
250E ASN* 2.7 28.7 + - + +
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Residues in contact with ALA 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ARG* 3.3 45.1 - - - +
205E GLY 3.1 7.7 + - - +
206E ASP 3.0 9.5 + - - +
208E LYS* 1.3 78.9 - - - +
210E VAL* 1.3 62.8 + - - +
212E ASP* 3.6 11.8 + - - +
213E LYS* 3.5 20.9 + - - +
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Residues in contact with VAL 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ILE* 4.9 6.5 - - + -
170E LEU* 4.1 15.9 - - + -
176E ARG* 3.5 32.1 - - + +
179E ILE* 4.0 15.9 - - + -
180E ALA* 4.2 10.8 - - + -
183E LEU* 3.7 29.8 - - + -
206E ASP 3.7 7.9 - - - +
207E ILE* 3.1 8.8 + - + +
209E ALA* 1.3 72.9 - - - +
211E LEU* 1.3 62.1 + - + +
213E LYS* 2.7 40.0 + - - +
214E LEU* 3.7 4.0 + - - +
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E GLN* 5.0 9.9 + - + +
183E LEU* 5.2 2.5 - - + -
196E ILE* 4.7 11.0 - - + -
207E ILE* 3.0 25.3 + - + +
208E LYS* 3.5 9.9 - - + +
210E VAL* 1.3 85.3 - - + +
212E ASP* 1.3 62.9 + - - +
213E LYS 3.0 5.2 + - - -
214E LEU* 3.0 34.3 + - + +
227E ARG* 4.6 6.4 + - - -
230E ILE* 4.0 31.9 - - + -
250E ASN* 3.4 48.0 - - + +
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Residues in contact with ASP 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E LYS* 2.8 67.3 + - - +
209E ALA* 3.9 9.5 + - - +
210E VAL 3.0 0.6 + - - -
211E LEU* 1.3 78.4 - - - +
213E LYS* 1.3 60.4 + - - +
214E LEU 3.3 2.7 - - - +
227E ARG* 6.0 1.6 - - - +
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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