Contacts of the helix formed by residues 228 - 236 (chain B) in PDB entry 1D1T
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 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.8 17.6 - - + +
201B GLY* 4.3 5.9 - - - -
205B LEU* 4.9 1.4 - - - +
223B ASP* 3.9 14.8 - - - +
225B ASN* 2.9 29.7 + - + +
227B ASP* 1.3 79.3 - - + +
229B PHE* 1.3 63.1 + - - +
230B GLU 3.5 0.4 - - - -
231B LYS* 3.6 8.3 + - - +
232B ALA* 3.3 20.4 + - - +
362B LEU* 5.9 0.8 + - - +
365B GLY* 3.8 23.4 + - - -
366B GLN 5.5 0.7 - - - -
367B SER 3.7 24.2 + - - -
368B ILE* 3.7 21.1 - - + -
2377B NAD 2.7 38.8 + - - -
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 4.0 4.3 - - + -
223B ASP* 3.6 27.6 - - + -
225B ASN 3.9 4.0 - - - -
226B LYS* 3.5 50.5 - - + +
227B ASP 3.3 1.0 - - - -
228B LYS* 1.3 78.9 - - - +
230B GLU* 1.3 68.1 + - - +
232B ALA* 2.9 3.6 + - - +
233B MET* 2.9 32.9 + - + +
240B CYS* 3.5 37.2 - - + -
241B ILE* 3.4 35.7 - - - -
242B SER 4.1 0.7 - - - -
245B ASP* 5.4 0.7 - - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LYS 4.8 0.6 + - - -
227B ASP 4.3 8.5 + - - +
228B LYS 3.5 0.6 - - - -
229B PHE* 1.3 79.1 - - - +
231B LYS* 1.3 60.6 + - - +
233B MET* 3.5 7.1 - - - +
234B ALA* 3.2 19.8 + - + +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 3.8 26.2 - - + -
227B ASP 5.1 0.6 + - - +
228B LYS* 3.6 10.2 + - - +
229B PHE 3.2 0.4 - - - -
230B GLU* 1.3 78.4 - - - +
232B ALA* 1.3 67.7 + - - +
234B ALA* 3.2 5.0 + - - +
235B VAL* 2.9 31.0 + - + +
343B ASP 5.1 1.2 + - - -
344B GLN* 2.8 47.3 + - - +
346B ILE 5.3 0.6 + - - -
347B THR* 3.9 21.4 - - - +
368B ILE* 4.2 12.8 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.8 24.0 - - + -
205B LEU* 3.4 16.0 - - + +
208B ILE* 4.2 3.1 - - + +
228B LYS 3.3 11.2 + - - +
229B PHE 2.9 8.4 + - - +
231B LYS* 1.3 76.2 - - - +
233B MET* 1.3 57.6 + - - +
235B VAL* 3.1 5.6 + - - +
236B GLY 2.9 24.9 + - - -
237B ALA* 3.0 14.1 + - + +
240B CYS* 3.6 20.9 - - - -
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B PHE* 2.9 17.1 + - + +
230B GLU* 3.5 12.8 - - - +
232B ALA* 1.3 76.8 - - - +
234B ALA* 1.3 61.6 + - - +
236B GLY* 3.3 9.2 + - - -
237B ALA* 3.4 25.7 - - - +
238B THR 3.9 5.6 - - - +
239B GLU* 3.8 24.0 - - - -
240B CYS* 3.4 36.8 - - + +
81D THR* 4.4 7.5 - - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU 3.2 11.2 + - - +
231B LYS* 3.2 12.7 + - - +
233B MET* 1.3 81.3 - - - +
235B VAL* 1.3 62.6 + - - +
236B GLY* 3.4 0.9 + - - -
344B GLN* 4.7 19.0 - - - +
34D LYS* 5.6 3.8 + - - -
79D GLY 5.2 1.0 - - - +
81D THR* 3.7 36.0 - - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 3.4 25.6 - - + +
208B ILE* 4.2 7.0 - - + +
209B MET* 3.2 42.7 - - + +
212B LYS* 4.5 12.0 - - - +
231B LYS* 2.9 33.4 + - + +
232B ALA* 3.5 5.4 - - - +
234B ALA* 1.3 77.3 - - - +
236B GLY* 1.3 57.0 + - - +
344B GLN* 4.5 23.8 - - + +
345B LEU* 5.5 1.6 - - + -
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Residues in contact with GLY 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ILE* 3.7 12.3 - - - -
212B LYS* 4.3 24.2 + - - +
219B ILE* 3.8 13.6 - - - +
232B ALA 2.9 1.6 + - - -
233B MET 3.3 2.2 + - - -
234B ALA 3.3 4.3 - - - -
235B VAL* 1.3 80.2 - - - +
237B ALA* 1.3 72.4 + - - +
238B THR* 3.6 7.8 + - - +
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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