Contacts of the helix formed by residues 226 - 234 (chain E) in PDB entry 3TKR
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 226 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219E ILE* 4.0 7.2 - - + -
220E ILE 3.4 14.5 + - - +
222E ASP 2.8 22.2 + - - +
223E PRO* 3.5 25.0 + - + +
224E ALA 3.1 0.4 + - - -
225E GLY* 1.3 72.4 - - - +
227E LEU* 1.3 69.6 + - + +
228E LYS 3.2 0.2 - - - -
229E TYR* 3.1 13.3 + - - +
230E PHE* 3.1 33.5 + - + -
83J PHE* 3.7 30.3 + - - +
84J THR 4.7 1.9 + - - +
85J PHE* 3.9 24.5 - - + -
129J GLN 3.6 27.3 + - - -
130J GLY* 4.5 6.3 + - - -
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Residues in contact with LEU 227 (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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223E PRO 4.0 8.5 - - - +
224E ALA* 3.5 18.8 - - + +
225E GLY 3.1 1.2 - - - -
226E LYS* 1.3 88.6 - - + +
228E LYS* 1.3 61.0 + - - +
230E PHE* 3.8 2.7 - - + +
231E ASP* 2.8 41.7 + - + +
128J ARG 3.9 5.2 - - - +
129J GLN* 3.9 40.6 - - + +
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Residues in contact with LYS 228 (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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220E ILE* 4.1 24.9 - - + +
224E ALA 4.6 2.8 + - - -
225E GLY* 3.7 19.7 - - - +
226E LYS 3.2 0.6 - - - -
227E LEU* 1.3 78.6 - - - +
229E TYR* 1.3 61.5 + - - +
231E ASP* 4.6 1.5 - - - +
232E LYS* 3.1 27.1 + - - +
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Residues in contact with TYR 229 (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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209E PRO* 3.8 24.5 - - + +
217E GLU* 4.0 26.2 - - + -
218E THR 3.6 25.4 - - - +
219E ILE* 3.6 20.0 - - + -
220E ILE 5.4 0.4 - - - +
225E GLY 4.5 0.8 + - - +
226E LYS 3.1 9.1 + - - +
228E LYS* 1.3 78.9 - - - +
230E PHE* 1.3 91.5 + + - +
232E LYS* 3.3 5.8 + - - +
233E LEU* 3.0 62.3 + - + +
89J THR* 3.6 25.6 - - + +
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Residues in contact with PHE 230 (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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219E ILE* 4.2 5.2 - - + -
226E LYS* 3.1 49.0 + - + +
227E LEU* 4.4 1.6 - - - +
229E TYR* 1.3 103.2 - + - +
231E ASP* 1.3 61.5 + - - +
233E LEU* 5.8 0.7 - - + -
234E ASN* 2.7 36.9 + - - +
84J THR 4.3 2.9 - - - -
85J PHE* 3.6 23.1 - - - -
88J PRO* 3.6 24.0 - - + -
89J THR* 4.2 5.6 - - + -
92J ILE* 5.8 4.7 - - + -
127J ARG* 3.4 20.6 - - + +
128J ARG* 3.4 13.4 - - - +
129J GLN 4.6 0.4 - - - -
130J GLY* 3.6 20.6 - - - +
131J GLY 5.6 0.9 - - - -
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Residues in contact with ASP 231 (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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227E LEU* 2.8 28.5 + - + +
228E LYS* 4.6 0.9 - - - +
230E PHE* 1.3 72.4 - - - +
232E LYS* 1.3 59.3 + - - +
234E ASN 2.7 28.4 - - - +
128J ARG* 2.9 58.4 + - - +
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Residues in contact with LYS 232 (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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217E GLU* 3.4 38.2 + - + +
228E LYS 3.1 20.2 + - - +
229E TYR* 3.3 4.7 + - - +
231E ASP* 1.3 81.0 - - - +
233E LEU* 1.3 62.6 + - - +
234E ASN 3.6 3.5 - - - +
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Residues in contact with LEU 233 (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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217E GLU* 5.8 3.4 - - + -
229E TYR* 3.0 55.7 + - + +
230E PHE* 5.8 0.4 - - + -
232E LYS* 1.3 78.3 - - - +
234E ASN* 1.3 90.0 + - - +
92J ILE* 6.2 7.0 - - + -
127J ARG* 6.2 1.1 - - - +
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Residues in contact with ASN 234 (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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230E PHE* 2.7 32.5 + - - +
231E ASP 2.7 19.2 - - - +
232E LYS 3.2 5.1 - - - +
233E LEU* 1.3 107.0 - - - +
92J ILE* 6.2 0.6 - - - +
127J ARG* 3.6 43.7 + - + +
128J ARG* 2.9 51.8 + - + +
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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