Contacts of the helix formed by residues 224 - 231 (chain B) in PDB entry 1SMN
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 ASP 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B LEU 4.3 2.4 - - - +
223B PRO* 1.3 71.3 - - - +
225B ASP* 1.3 59.4 + - - +
227B GLN* 3.2 16.1 + - - +
228B ALA* 2.9 30.0 + - - +
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Residues in contact with ASP 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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136A ARG* 2.9 40.0 + - - -
240A LEU* 5.4 0.7 - - - +
223B PRO* 3.7 15.9 - - - +
224B ASP* 1.3 79.0 - - - +
226B VAL* 1.3 60.7 + - - +
228B ALA* 3.3 6.2 + - - +
229B SER* 3.0 31.7 + - - -
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Residues in contact with VAL 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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136A ARG* 3.8 24.2 - - - +
240A LEU* 4.6 6.7 - - + -
181B ALA* 3.9 24.5 - - + -
222B LEU* 3.9 21.8 - - + -
223B PRO* 3.1 24.5 + - + +
225B ASP* 1.3 77.2 - - - +
227B GLN* 1.3 61.7 + - - +
229B SER* 3.5 5.5 + - - -
230B LEU* 2.9 53.3 + - + +
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Residues in contact with GLN 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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217B ILE* 3.8 13.0 - - - +
219B TRP 3.9 6.8 - - - +
220B ALA* 3.9 13.3 - - - +
222B LEU* 2.9 35.1 - - + +
223B PRO 3.1 13.7 + - - +
224B ASP* 3.5 16.2 - - - +
226B VAL* 1.3 77.0 - - - +
228B ALA* 1.3 63.5 + - - +
231B LYS* 2.7 73.4 + - + +
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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 ASP 2.9 17.1 + - - +
225B ASP* 3.7 6.7 - - - +
227B GLN* 1.3 78.6 - - - +
229B SER* 1.3 62.0 + - - +
231B LYS* 4.1 3.6 + - - +
232B SER* 4.3 11.8 + - - -
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Residues in contact with SER 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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239A GLU* 3.3 45.6 + - - +
240A LEU* 3.8 16.8 - - - +
243A CYS 5.4 1.1 - - - -
225B ASP* 3.0 17.6 + - - -
226B VAL 3.5 3.3 + - - -
228B ALA* 1.3 80.2 - - - +
230B LEU* 1.3 65.4 + - - +
232B SER* 4.0 6.8 + - - -
233B LYS* 4.0 4.5 + - - +
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Residues in contact with LEU 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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184A HIS* 4.0 7.0 - - - +
236A VAL* 4.4 13.5 - - + +
239A GLU* 4.1 22.9 - - + -
240A LEU* 4.3 15.5 - - + -
180B PRO* 3.1 31.9 - - + +
181B ALA* 4.1 2.2 - - - -
185B TYR* 3.3 31.5 + - + +
207B VAL* 5.5 0.3 - - - +
219B TRP* 5.3 7.4 - - + -
222B LEU* 6.3 0.7 - - + -
226B VAL* 2.9 35.1 + - + +
229B SER* 1.3 77.2 - - - +
231B LYS* 1.3 65.8 + - + +
232B SER 3.1 2.7 - - - -
233B LYS* 3.1 23.4 + - - +
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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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206B THR* 3.3 8.5 - - - -
207B VAL* 3.3 20.6 + - + -
208B ASP* 2.9 36.9 + - + +
211B GLU* 2.7 31.9 + - - +
217B ILE* 3.6 3.8 - - - +
218B ILE 2.6 31.0 + - - -
219B TRP* 4.3 20.2 - - + -
227B GLN* 2.7 63.8 + - + +
228B ALA 4.9 0.7 - - - +
230B LEU* 1.3 77.5 - - + +
232B SER* 1.3 58.0 + - - +
233B LYS 3.4 0.2 - - - -
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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