Contacts of the helix formed by residues 227 - 240 (chain A) in PDB entry 3SM9
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 ILE 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ARG 3.4 23.8 + - - +
228A ARG* 1.4 63.1 + - - +
229A LYS* 4.5 6.1 - - + +
230A SER* 3.4 27.5 + - - +
231A TYR* 3.2 28.2 - - - -
258A GLU* 5.7 0.7 - - - -
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Residues in contact with ARG 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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227A ILE* 1.4 71.6 - - - +
229A LYS* 1.3 59.5 + - - +
231A TYR* 3.7 12.7 + - - +
232A ASP* 3.1 17.5 + - - +
258A GLU* 4.9 9.2 - - - +
265A ARG* 3.3 22.9 + - - +
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Residues in contact with LYS 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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227A ILE* 3.3 4.2 - - + +
228A ARG* 1.3 75.6 - - - +
230A SER* 1.4 64.9 + - - +
232A ASP* 3.0 22.5 + - - +
233A SER* 3.1 17.6 + - - +
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Residues in contact with SER 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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222A VAL* 5.6 9.0 - - - -
223A GLY 5.9 3.6 - - - -
224A ARG 5.5 0.3 + - - -
227A ILE* 3.4 31.3 + - - +
229A LYS* 1.4 77.3 - - - +
231A TYR* 1.3 66.0 + - - +
233A SER* 3.5 10.0 + - - -
234A VAL* 3.3 26.3 + - - +
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Residues in contact with TYR 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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222A VAL* 3.5 31.7 - - + +
223A GLY 5.0 0.9 + - - -
227A ILE 3.2 36.6 - - - -
228A ARG* 4.0 8.3 - - - +
229A LYS 3.3 0.8 - - - -
230A SER* 1.3 75.1 - - - +
232A ASP* 1.4 54.8 + - - +
234A VAL* 3.2 5.8 + - - +
235A ILE* 2.8 36.7 + - - +
251A MET* 4.2 0.9 - - + -
254A ASP 4.7 0.2 - - - -
255A ASP* 3.0 46.9 + - - -
258A GLU* 3.5 32.5 - - + +
259A LEU* 3.5 29.6 - - + +
262A ALA* 3.6 20.6 - - + -
265A ARG* 5.1 0.9 - - - +
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Residues in contact with ASP 232 (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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228A ARG 3.1 19.6 - - - +
229A LYS* 3.0 11.9 + - - +
231A TYR* 1.4 74.1 - - - +
233A SER* 1.4 54.1 + - - +
235A ILE* 3.7 4.6 - - - +
236A ARG* 2.8 35.6 + - - +
262A ALA* 3.5 22.0 - - - +
265A ARG* 3.3 27.2 + - - +
266A ALA* 5.3 3.8 - - - +
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Residues in contact with SER 233 (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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229A LYS* 3.1 14.6 + - - +
230A SER* 3.5 12.0 - - - -
231A TYR 3.3 0.2 - - - -
232A ASP* 1.4 74.6 - - - +
234A VAL* 1.4 59.0 + - - +
236A ARG* 3.6 6.3 + - - +
237A GLU* 3.0 28.4 + - - +
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Residues in contact with VAL 234 (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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191A VAL* 3.8 33.0 - - + -
220A GLU* 3.8 21.3 - - + +
221A LYS 3.7 23.1 - - - +
222A VAL* 4.0 11.2 - - + -
230A SER 3.3 14.1 + - - +
231A TYR 3.2 8.4 + - - +
233A SER* 1.4 75.6 - - - +
235A ILE* 1.4 52.1 - - - +
237A GLU* 3.2 8.2 + - - +
238A LEU* 2.8 36.5 + - + +
259A LEU* 3.8 13.2 - - + -
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Residues in contact with ILE 235 (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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231A TYR 2.8 20.9 + - - +
232A ASP* 3.8 7.2 - - - +
234A VAL* 1.4 74.1 - - - +
236A ARG* 1.4 55.8 + - - +
238A LEU* 3.2 13.9 + - + +
239A LEU* 3.0 30.7 + - + +
259A LEU* 3.6 35.2 - - + +
262A ALA* 3.8 19.1 - - + +
263A ALA* 3.8 15.5 - - + +
266A ALA* 3.8 29.4 - - + -
268A ALA* 4.0 16.8 - - + -
270A PHE* 5.0 2.9 - - + -
272A TRP* 4.1 12.1 - - + -
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Residues in contact with ARG 236 (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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232A ASP 2.8 21.9 + - - +
233A SER* 3.8 6.7 - - - +
235A ILE* 1.4 70.9 - - - +
237A GLU* 1.4 59.0 + - - +
239A LEU* 3.1 29.2 + - + +
240A GLN* 3.2 12.0 + - - +
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Residues in contact with GLU 237 (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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218A THR* 4.0 14.9 + - - +
220A GLU* 3.9 27.8 - - - +
233A SER 3.0 19.4 + - - +
234A VAL 3.5 5.2 - - - +
236A ARG* 1.4 75.5 - - - +
238A LEU* 1.4 61.4 + - - +
240A GLN* 3.4 21.0 + - - +
241A LYS* 4.2 1.4 + - - +
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Residues in contact with LEU 238 (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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189A SER* 3.7 29.8 - - - -
190A THR 5.0 0.9 - - - +
191A VAL* 3.9 31.2 - - + -
218A THR* 4.3 9.6 - - + -
220A GLU* 4.9 5.2 - - + -
234A VAL* 2.8 19.9 + - + +
235A ILE* 3.4 29.2 - - + +
237A GLU* 1.4 74.3 - - - +
239A LEU* 1.4 63.0 + - - +
241A LYS* 3.5 21.3 + - - +
242A PRO* 5.1 0.2 - - - +
244A ALA 5.0 0.9 - - - +
247A VAL* 4.1 20.6 - - + -
259A LEU* 5.1 0.7 - - + -
270A PHE* 3.8 21.5 - - + -
272A TRP* 4.4 7.0 - - + -
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Residues in contact with LEU 239 (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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235A ILE* 3.0 31.0 + - + +
236A ARG* 3.1 15.7 + - + +
238A LEU* 1.4 72.9 - - - +
240A GLN* 1.4 62.3 + - - +
241A LYS 3.1 3.7 + - - -
242A PRO* 3.3 23.2 - - - +
266A ALA* 4.7 10.3 - - + +
268A ALA* 3.9 25.6 - - + -
270A PHE* 4.3 10.8 - - + -
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Residues in contact with GLN 240 (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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236A ARG 3.2 10.4 + - - +
237A GLU* 3.4 18.4 - - - +
238A LEU 3.3 0.2 - - - -
239A LEU* 1.4 75.9 - - - +
241A LYS* 1.3 61.4 + - + +
242A PRO* 3.3 8.7 - - - +
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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