Contacts of the helix formed by residues 224 - 231 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU 4.3 4.1 - - - +
223A PRO* 1.3 73.0 - - - +
225A ASP* 1.3 58.2 + - - +
227A GLN* 3.2 13.0 + - - +
228A ALA* 2.9 29.9 + - - +
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Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO* 3.5 17.2 - - - +
224A ASP* 1.3 79.5 - - - +
226A VAL* 1.3 67.7 + - - +
228A ALA* 3.3 6.4 + - - +
229A SER* 3.0 26.3 + - - -
136B ARG* 2.9 37.6 + - - -
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 4.0 24.0 - - + -
222A LEU* 4.0 20.0 - - + -
223A PRO* 3.1 25.9 + - + +
225A ASP* 1.3 83.5 - - - +
227A GLN* 1.3 59.3 + - - +
229A SER* 3.3 5.6 + - - -
230A LEU* 2.9 52.2 + - + +
136B ARG* 3.9 22.7 - - - +
138B ASP* 6.0 0.2 - - - +
240B LEU* 4.7 8.3 - - + -
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Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 3.8 13.9 - - - +
219A TRP 3.9 6.0 - - - +
220A ALA 3.8 13.0 - - - +
222A LEU* 2.8 36.5 - - + +
223A PRO 3.1 11.2 + - - +
224A ASP* 3.5 15.4 - - - +
226A VAL* 1.3 80.0 - - - +
228A ALA* 1.3 63.4 + - - +
230A LEU* 5.5 0.2 - - - -
231A LYS* 2.8 71.2 + - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ASP 2.9 17.1 + - - +
225A ASP* 3.8 7.9 - - - +
226A VAL 3.3 0.2 - - - -
227A GLN* 1.3 79.3 - - - +
229A SER* 1.3 61.9 + - - +
231A LYS* 4.2 1.4 + - - +
232A SER* 3.5 15.2 + - - -
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASP 3.0 17.7 + - - -
226A VAL 3.4 2.9 + - - -
228A ALA* 1.3 80.1 - - - +
230A LEU* 1.3 65.4 + - - +
232A SER* 3.5 11.4 + - - -
233A LYS* 4.0 2.4 - - - +
239B GLU* 3.3 47.4 + - - +
240B LEU* 3.8 15.8 - - - +
243B CYS 5.3 1.6 - - - -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO* 3.1 34.8 - - + +
181A ALA* 3.9 4.0 - - - +
185A TYR* 3.2 41.0 + - + +
207A VAL* 5.6 0.3 - - - +
219A TRP* 5.3 8.0 - - + -
222A LEU* 6.0 1.1 - - + -
226A VAL* 2.9 32.0 + - + +
227A GLN* 5.5 0.2 - - - -
229A SER* 1.3 76.4 - - - +
231A LYS* 1.3 64.1 + - + +
232A SER 3.2 2.9 - - - -
233A LYS* 3.2 14.1 + - - +
184B HIS* 3.9 7.2 - - - +
236B VAL* 4.5 12.6 - - + +
239B GLU* 4.0 22.2 - - + -
240B LEU* 4.3 16.4 - - + -
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Residues in contact with LYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A THR* 3.3 2.4 - - - -
207A VAL* 3.2 27.1 + - + -
208A ASP* 2.8 38.2 + - + +
211A GLU* 2.7 30.4 + - - +
217A ILE* 3.6 4.0 - - - +
218A ILE 2.6 31.3 + - - -
219A TRP* 4.3 20.2 - - + -
227A GLN* 2.8 62.6 + - + +
228A ALA 5.1 0.4 - - - +
229A SER 3.5 0.2 - - - -
230A LEU* 1.3 76.5 - - + +
232A SER* 1.3 57.8 + - - +
233A LYS 3.4 0.4 - - - -
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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