Contacts of the helix formed by residues 224 - 238 (chain A) in PDB entry 4IYM
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 SER 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A PHE* 3.9 2.9 - - - -
223A GLY* 1.3 76.1 - - - -
225A THR* 1.3 59.0 + - - +
226A PRO* 3.8 10.9 - - - +
227A ILE* 3.4 27.1 + - - +
228A ALA* 2.9 26.0 + - - +
246A GLY* 4.1 0.2 - - - -
247A GLY* 4.4 5.2 - - - +
381A GLU* 5.2 6.7 - - - -
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Residues in contact with THR 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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224A SER* 1.3 68.7 - - - +
226A PRO* 1.4 75.9 - - + +
228A ALA* 3.2 2.8 + - - +
229A ARG* 2.9 45.2 + - - +
246A GLY* 3.6 5.3 - - - -
247A GLY* 2.9 24.8 + - - +
381A GLU* 5.6 0.2 + - - -
407A TYR* 3.4 19.3 + - + +
453A SER* 2.8 37.6 + - - +
456A PHE* 4.3 3.4 - - + -
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Residues in contact with PRO 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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224A SER* 3.6 14.4 - - - +
225A THR* 1.4 95.0 - - + +
227A ILE* 1.3 67.5 + - + +
229A ARG* 3.5 9.6 + - + +
230A TYR* 3.2 21.3 + - - +
407A TYR* 5.3 4.0 - - - +
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Residues in contact with ILE 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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207A VAL* 6.1 1.6 - - + -
221A PHE* 3.4 30.5 - - + -
224A SER* 3.4 18.6 + - - +
225A THR 3.3 0.4 - - - -
226A PRO* 1.3 79.8 - - + +
228A ALA* 1.3 60.8 + - - +
230A TYR* 3.2 12.9 + - + +
231A VAL* 2.9 36.3 + - + +
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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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221A PHE* 3.5 26.5 - - + -
224A SER 2.9 17.2 + - - +
225A THR* 3.5 7.9 - - - +
227A ILE* 1.3 77.5 - - - +
229A ARG* 1.3 56.7 + - - +
231A VAL 3.5 0.2 + - - -
232A TYR* 3.0 30.7 + - - +
244A CYS* 3.6 13.5 - - + +
245A PHE 4.0 9.6 - - - +
246A GLY* 4.2 2.0 - - - -
456A PHE* 4.0 16.6 - - + -
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Residues in contact with ARG 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 THR* 2.9 27.5 + - - +
226A PRO* 3.6 9.6 - - - +
228A ALA* 1.3 75.4 - - - +
230A TYR* 1.3 59.6 + - - +
232A TYR* 3.4 4.8 + - - +
233A GLY* 3.0 28.1 + - - -
406A GLU* 5.4 2.8 + - - -
453A SER* 3.4 29.9 - - - +
456A PHE* 3.3 38.1 - - + -
236B ALA 5.1 1.4 - - - +
237B MSE 5.3 5.6 - - + +
238B ASN 5.0 4.6 + - - -
239B GLY* 4.8 8.3 - - - +
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Residues in contact with TYR 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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204A LYS* 3.1 26.8 + - + -
207A VAL* 5.2 4.0 - - + -
208A ASP* 2.7 29.9 + - - -
211A LEU* 4.3 9.2 - - + -
226A PRO 3.2 10.4 + - - +
227A ILE* 3.2 18.2 + - + +
229A ARG* 1.3 79.5 - - - +
231A VAL* 1.3 66.6 + - + +
233A GLY* 5.4 0.2 - - - -
234A THR* 2.6 60.6 + - - +
237B MSE 5.4 8.0 - - + +
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Residues in contact with VAL 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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144A ILE* 4.1 8.7 - - + -
207A VAL* 4.2 22.4 - - + -
211A LEU* 3.8 20.6 - - + +
219A VAL* 4.1 7.6 - - + -
221A PHE* 3.7 44.4 - - + -
227A ILE* 2.9 28.7 + - + +
228A ALA 4.0 2.9 - - - +
230A TYR* 1.3 78.6 - - + +
232A TYR* 1.3 59.0 + - - +
235A ALA* 2.8 34.8 + - + +
244A CYS* 3.9 5.4 - - - -
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Residues in contact with TYR 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 ALA 3.0 20.4 + - - +
229A ARG* 3.6 4.5 - - - +
231A VAL* 1.3 78.0 - - - +
233A GLY* 1.3 61.9 + - - +
235A ALA* 3.7 1.6 - - - +
236A ALA* 3.1 25.6 + - + +
242A ALA* 3.7 30.1 - - + +
244A CYS* 3.7 12.8 - - - -
456A PHE* 3.5 31.2 - + + -
457A GLY* 3.5 34.7 + - - -
236B ALA* 3.3 37.0 - - + +
239B GLY 4.2 5.2 - - - -
240B LYS 2.8 29.0 + - - -
241B ARG* 3.7 5.4 - - - -
242B ALA* 4.4 3.1 + - - +
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Residues in contact with GLY 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 ARG 3.0 14.7 + - - -
232A TYR* 1.3 76.1 - - - +
234A THR* 1.3 57.2 + - - +
236A ALA* 3.4 3.1 + - - +
237A MSE 2.9 32.4 + - - +
233B GLY 4.5 0.5 - - - +
236B ALA* 4.0 2.9 - - - -
237B MSE 3.6 41.8 - - - +
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Residues in contact with THR 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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208A ASP* 5.3 0.9 - - - +
211A LEU* 3.9 27.8 - - + -
212A THR* 5.5 4.3 - - + -
230A TYR* 2.6 49.4 + - + +
233A GLY* 1.3 71.5 - - - +
235A ALA* 1.3 67.0 + - - +
237A MSE 3.1 8.2 + - + +
238A ASN* 2.9 42.4 + - - +
237B MSE 4.2 4.7 - - - -
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Residues in contact with ALA 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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211A LEU* 3.9 18.3 - - + +
219A VAL* 4.6 7.6 - - + -
231A VAL 2.8 24.1 + - - +
232A TYR 3.7 3.6 - - - +
234A THR* 1.3 71.9 - - - +
236A ALA* 1.3 62.8 + - - +
238A ASN* 3.0 14.0 + - - +
239A GLY 3.2 0.2 + - - -
240A LYS* 3.1 36.0 + - + +
242A ALA* 3.8 21.3 - - + -
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Residues in contact with ALA 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 TYR* 3.1 11.9 + - + +
233A GLY 3.7 1.8 - - - +
235A ALA* 1.3 76.6 - - - +
237A MSE 1.3 58.1 + - - +
239A GLY* 2.8 16.8 + - - -
240A LYS 3.9 2.7 + - - -
242A ALA* 5.1 2.4 - - + +
229B ARG 5.0 1.7 - - - +
232B TYR* 3.4 44.2 - - + +
233B GLY* 4.2 5.6 + - - -
236B ALA* 3.2 35.0 - - + -
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Residues in contact with MSE 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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233A GLY 2.9 23.8 + - - +
234A THR* 3.1 11.4 + - + +
236A ALA* 1.3 76.8 - - - +
238A ASN* 1.3 63.5 + - - +
239A GLY 3.3 0.8 + - - -
229B ARG* 5.3 4.8 + - - +
230B TYR* 5.4 2.5 - - + +
233B GLY* 3.4 26.5 - - - +
234B THR* 3.8 13.2 - - + +
237B MSE 3.3 32.1 - - + -
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Residues in contact with ASN 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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211A LEU 3.2 26.4 + - - +
212A THR* 3.6 25.7 - - - +
234A THR* 2.9 35.3 + - - +
235A ALA 3.0 9.1 + - - +
237A MSE 1.3 83.7 - - - +
239A GLY* 1.3 58.2 + - - +
240A LYS* 3.3 14.7 + - - +
229B ARG* 5.2 5.2 + - - -
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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