Contacts of the helix formed by residues 230 - 242 (chain A) in PDB entry 5ID6
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 THR 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASN* 3.4 16.6 - - - +
66A LEU* 3.6 37.5 - - + +
67A HIS* 3.2 27.3 + - + +
226A ASN 5.2 1.3 - - - +
227A PHE 3.8 9.9 + - - +
228A VAL 4.0 0.2 - - - +
229A LEU* 1.3 78.1 - - + +
231A GLN* 1.3 65.5 + - - +
232A GLU* 3.3 13.8 + - - +
233A GLY* 3.4 10.0 + - - -
234A ILE* 3.0 23.0 + - - +
279A GLN* 6.0 0.2 - - - +
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Residues in contact with GLN 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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59A LEU* 4.3 15.6 - - + +
63A ASN* 2.3 50.2 + - - +
229A LEU 4.2 0.2 + - - -
230A THR* 1.3 69.4 - - - +
232A GLU* 1.3 90.9 + - + +
234A ILE* 3.2 10.3 + - + +
235A ASP* 2.8 26.8 + - - +
278A LYS* 3.0 42.6 + - + +
279A GLN* 5.4 10.6 + - - +
280A VAL* 5.7 0.9 - - - +
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Residues in contact with GLU 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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67A HIS* 3.0 33.5 + - - -
230A THR* 3.3 3.3 + - - +
231A GLN* 1.3 107.4 + - + +
233A GLY* 1.3 52.0 + - - +
235A ASP* 2.8 11.6 + - - +
236A VAL* 2.7 43.9 + - + +
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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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219A PHE* 4.8 0.7 - - - -
227A PHE* 3.6 38.7 - - - -
228A VAL* 3.2 11.1 - - - +
230A THR* 3.4 10.5 + - - -
232A GLU* 1.3 77.8 - - - +
234A ILE* 1.3 55.7 + - - +
236A VAL* 3.7 4.2 - - - +
237A TYR* 2.9 29.6 + - - +
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Residues in contact with ILE 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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179A ASN* 3.8 10.8 - - - +
228A VAL* 3.3 21.8 - - + +
229A LEU 4.0 10.1 - - - +
230A THR 3.0 21.3 + - - +
231A GLN* 3.3 14.6 - - + +
233A GLY* 1.3 75.1 - - - +
235A ASP* 1.3 59.7 + - - +
237A TYR* 3.3 1.5 + - - +
238A ASN* 2.8 42.6 + - - +
276A LEU* 3.8 25.1 - - + +
277A TYR 3.5 20.2 - - - +
278A LYS* 3.9 25.4 - - + -
279A GLN* 4.5 9.4 - - - +
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Residues in contact with ASP 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 GLN* 2.8 14.4 + - - +
232A GLU* 2.8 10.4 + - - +
234A ILE* 1.3 70.5 - - - +
236A VAL* 1.3 57.4 + - + +
238A ASN* 3.4 5.4 + - - +
239A ALA* 2.8 37.2 + - - +
244A PHE* 6.5 0.9 - - + -
278A LYS* 2.5 40.8 + - - +
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Residues in contact with VAL 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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210A LEU* 4.4 14.8 - - + +
211A ASN* 4.5 13.9 - - + +
214A TYR* 6.5 0.2 - - + -
219A PHE* 4.0 24.5 - - + -
227A PHE* 4.8 7.2 - - + -
232A GLU* 2.7 30.2 + - + +
233A GLY* 3.7 9.2 - - - +
235A ASP* 1.3 73.4 - - + +
237A TYR* 1.3 62.2 + - - +
239A ALA* 3.3 7.2 + - - +
240A ILE* 3.0 33.4 + - + +
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Residues in contact with TYR 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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183A TYR* 3.7 30.0 + + - -
186A ASN* 2.6 37.2 + - - +
219A PHE* 3.8 31.2 - + + -
220A PHE* 4.1 13.7 - + - -
228A VAL* 3.7 13.7 - - + -
233A GLY 2.9 20.3 + - - +
234A ILE 3.5 3.8 - - - +
236A VAL* 1.3 77.4 - - - +
238A ASN* 1.3 76.0 + - - +
240A ILE* 3.0 28.3 + - + +
241A ILE* 3.2 33.0 + - + +
276A LEU* 3.5 27.6 - - + -
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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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234A ILE* 2.8 25.3 + - - +
235A ASP* 4.1 5.6 + - - +
237A TYR* 1.3 80.9 - - - +
239A ALA* 1.3 56.6 + - - +
241A ILE* 3.6 7.9 - - - +
242A GLY* 2.7 29.1 + - - -
275A PRO* 3.4 16.1 - - + +
276A LEU* 2.9 48.9 + - - +
278A LYS* 6.1 0.6 - - - +
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Residues in contact with ALA 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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206A LYS* 5.4 0.3 - - - +
210A LEU* 3.4 32.0 - - + +
235A ASP 2.8 19.1 + - - +
236A VAL* 3.6 1.3 - - - +
238A ASN* 1.3 74.7 - - - +
240A ILE* 1.3 63.1 + - - +
243A GLY* 2.8 44.7 + - - +
244A PHE* 3.8 13.7 - - + -
254A GLY* 4.3 0.9 - - - -
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Residues in contact with ILE 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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206A LYS* 3.8 20.7 - - + +
210A LEU* 4.5 12.5 - - + +
211A ASN* 5.3 3.1 - - - +
216A VAL* 4.3 19.3 - - + -
219A PHE* 3.9 36.8 - - + -
220A PHE* 4.6 7.4 - - + -
236A VAL* 3.0 23.2 + - + +
237A TYR* 3.0 19.8 + - + +
239A ALA* 1.3 77.4 - - - +
241A ILE* 1.3 51.0 + - + +
254A GLY* 3.2 6.2 - - - -
255A LEU* 2.8 52.1 + - + +
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Residues in contact with ILE 241 (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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220A PHE* 5.8 2.7 - - + -
237A TYR* 3.2 42.6 + - + +
238A ASN* 3.6 5.8 - - - +
240A ILE* 1.3 78.7 - - + +
242A GLY* 1.3 64.2 + - - +
254A GLY* 3.3 1.0 - - - -
255A LEU* 3.1 13.7 + - + +
256A ASN* 3.1 60.1 + - - +
257A GLU* 4.2 0.2 - - - +
273A PHE* 3.8 21.5 - - + +
274A LYS 3.6 17.7 - - - +
275A PRO* 3.7 18.4 - - + -
492A LEU* 5.9 1.6 - - + -
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Residues in contact with GLY 242 (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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238A ASN 2.7 19.5 + - - -
241A ILE* 1.3 78.4 - - - +
243A GLY* 1.3 55.7 + - - +
256A ASN* 5.4 2.2 - - - +
257A GLU* 2.8 23.5 - - - +
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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