Contacts of the helix formed by residues 221 - 232 (chain B) in PDB entry 3KSA
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 GLY 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B ILE* 4.2 2.2 + - - +
220B GLN* 1.3 75.7 - - - +
222B ARG* 1.3 69.2 + - - +
223B ASP 3.0 3.7 + - - -
224B GLU* 3.3 8.2 + - - +
225B ILE* 3.0 30.2 + - - +
236B VAL* 4.3 6.1 - - - +
237B VAL* 5.1 0.4 - - - -
483B GLU 4.4 3.8 - - - -
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Residues in contact with ARG 222 (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 MET* 4.6 3.9 - - - +
221B GLY* 1.3 75.6 - - - +
223B ASP* 1.3 63.7 + - - +
225B ILE* 3.1 19.1 + - - +
226B LYS* 3.2 13.7 + - - +
483B GLU 5.1 9.5 + - - +
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Residues in contact with ASP 223 (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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221B GLY* 3.0 1.4 + - - -
222B ARG* 1.3 79.8 - - - +
224B GLU* 1.3 63.1 + - - +
226B LYS* 3.3 8.4 + - - +
227B LYS* 3.3 15.6 + - - +
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Residues in contact with GLU 224 (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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221B GLY* 3.3 8.4 + - - +
223B ASP* 1.3 76.2 - - - +
225B ILE* 1.3 59.6 + - - +
227B LYS* 3.1 12.9 + - + +
228B ALA* 2.9 27.5 + - - +
234B GLY* 4.3 3.7 - - - -
235B ARG 3.0 35.0 - - - +
236B VAL* 4.8 2.0 - - - -
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Residues in contact with ILE 225 (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 MET* 4.2 7.9 - - + -
209B PRO 4.4 6.3 - - - +
210B GLY* 4.1 11.7 - - - -
211B PRO* 4.0 21.5 - - + -
219B ILE* 4.2 18.8 - - + -
221B GLY 3.0 24.5 + - - +
222B ARG* 3.1 12.3 + - - +
224B GLU* 1.3 71.8 - - - +
226B LYS* 1.3 62.3 + - - +
228B ALA* 3.2 7.4 + - - +
229B TYR* 2.9 54.4 + - + -
236B VAL* 3.4 17.9 - - + +
327B PHE* 5.1 2.9 - - + -
482B LEU* 5.7 3.4 - - + -
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Residues in contact with LYS 226 (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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201B ILE* 4.5 8.2 - - + +
202B ASP* 5.9 2.2 - - - +
205B MET* 3.5 24.6 - - + +
222B ARG 3.2 6.7 + - - +
223B ASP* 3.4 11.0 - - - +
225B ILE* 1.3 76.9 - - - +
227B LYS* 1.3 66.5 + - - +
229B TYR* 2.9 5.5 + - - +
230B GLU* 2.8 25.2 + - - +
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Residues in contact with LYS 227 (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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223B ASP 3.3 4.8 + - - +
224B GLU* 3.1 20.9 + - + +
226B LYS* 1.3 77.3 - - - +
228B ALA* 1.3 52.8 + - - +
230B GLU* 4.7 2.7 - - - +
231B THR* 2.7 51.1 + - + +
233B LYS 3.7 6.7 - - - +
234B GLY* 5.1 2.2 - - - -
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Residues in contact with ALA 228 (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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224B GLU 2.9 12.6 + - - +
225B ILE* 3.3 9.9 - - - +
227B LYS* 1.3 76.7 - - - +
229B TYR* 1.3 61.2 + - - +
232B GLY* 2.7 29.8 + - - -
233B LYS 3.4 13.4 + - - +
234B GLY* 4.1 4.3 - - - -
327B PHE* 3.4 45.8 - - + -
329B MET* 5.9 0.2 - - - +
341B GLY* 4.4 2.1 - - - -
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Residues in contact with TYR 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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163B LEU* 5.5 0.7 - - + -
181B HIS* 2.8 36.7 + + - -
201B ILE* 3.3 19.5 - - + +
205B MET* 3.3 24.2 - - + -
208B LEU* 3.5 21.5 + - - +
210B GLY* 2.8 31.5 + - - -
211B PRO 3.5 0.5 - - - -
225B ILE* 2.9 20.5 + - + +
226B LYS* 3.7 5.6 - - - +
228B ALA* 1.3 79.1 - - + +
230B GLU* 1.3 58.9 + - - +
327B PHE* 4.2 16.4 - + - -
341B GLY* 3.1 4.5 - - - -
342B ILE* 2.8 62.2 + - + +
343B VAL 4.5 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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201B ILE* 3.2 20.0 - - + +
226B LYS 2.8 18.9 + - - +
227B LYS* 3.9 3.1 - - - +
229B TYR* 1.3 76.1 - - - +
231B THR* 1.3 67.9 + - + +
341B GLY* 3.8 9.2 + - - -
344B PRO* 5.8 0.9 - - - +
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Residues in contact with THR 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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227B LYS* 2.7 34.3 + - + +
230B GLU* 1.3 80.4 - - + +
232B GLY* 1.3 63.2 + - - +
233B LYS* 2.8 22.0 + - - +
339B GLN* 3.3 26.2 - - - +
340B VAL 4.5 1.7 - - - -
341B GLY 4.6 1.3 + - - -
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Residues in contact with GLY 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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228B ALA* 2.7 23.9 + - - -
230B GLU 3.6 0.4 - - - -
231B THR* 1.3 73.7 + - - +
233B LYS* 1.3 61.0 + - - +
327B PHE* 3.4 7.7 - - - +
328B ASN* 3.4 0.9 - - - -
329B MET* 2.8 30.3 + - - +
339B GLN* 4.0 8.1 - - - -
340B VAL 3.6 20.9 - - - -
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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