Contacts of the helix formed by residues 227 - 238 (chain f) in PDB entry 5T0J
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 GLY 227 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225f ALA* 3.5 1.5 - - - +
226f PHE* 1.3 96.0 - - - +
228f GLN* 1.3 62.2 + - - -
229f ASP* 3.3 3.9 + - - -
230f LYS* 3.7 17.4 + - - +
231f LEU* 3.5 20.5 - - - +
369f GLY* 4.6 3.4 - - - -
406f ASN* 4.1 15.0 - - - -
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Residues in contact with GLN 228 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226f PHE 3.9 0.2 + - - -
227f GLY* 1.3 69.4 - - - -
229f ASP* 1.3 53.8 + - - +
230f LYS 3.2 2.7 - - - -
231f LEU* 3.1 33.8 + - - +
232f LEU* 2.7 43.3 + - + +
250f SER* 3.2 39.9 + - - +
251f ALA* 4.5 5.6 - - - +
334f ASN* 5.4 0.6 + - - -
335f ARG* 5.1 3.2 - - - +
368f VAL 5.8 0.4 + - - -
369f GLY* 3.2 36.3 + - - +
371f CYS* 4.7 5.6 - - - -
372f ASN* 4.2 18.6 + - - +
406f ASN* 3.7 1.5 + - - +
407f HIS* 5.2 0.2 - - - -
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Residues in contact with ASP 229 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193f HIS* 4.6 6.6 + - - -
195f GLU* 3.1 28.4 - - - +
227f GLY* 3.3 1.7 - - - -
228f GLN* 1.3 78.4 - - - +
230f LYS* 1.3 63.0 + - + +
232f LEU* 4.1 9.1 - - - +
233f THR* 3.1 37.6 + - - +
406f ASN* 4.1 14.4 + - - +
407f HIS* 3.5 36.9 + - + +
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Residues in contact with LYS 230 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190f TYR* 3.2 39.9 - - - -
199f PHE* 6.6 0.4 - - - -
221f PHE* 4.0 28.9 - - + -
222f VAL* 6.3 0.2 - - - -
224f ALA 5.5 0.2 + - - -
225f ALA* 3.6 27.0 - - + +
226f PHE* 4.0 20.4 - - - -
227f GLY* 4.0 15.3 - - - +
228f GLN 3.2 0.6 - - - -
229f ASP* 1.3 81.0 - - + +
231f LEU* 1.3 59.4 + - + +
233f THR* 3.8 2.4 + - - -
234f ASP* 3.0 36.8 + - - +
666f MET* 3.3 18.2 - - - +
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Residues in contact with LEU 231 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222f VAL* 3.8 37.5 - - + +
225f ALA* 3.8 19.1 - - + +
227f GLY 3.5 18.8 - - - +
228f GLN* 3.1 20.7 + - - +
230f LYS* 1.3 78.4 - - + +
232f LEU* 1.3 59.2 + - - +
234f ASP* 4.8 2.0 - - - -
235f ASP* 3.4 21.0 + - - +
248f MET 4.5 1.1 - - - +
249f LEU* 3.7 32.1 - - + +
250f SER 3.4 24.9 - - - +
251f ALA* 3.6 17.3 - - + +
254f SER* 4.5 0.2 - - - +
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Residues in contact with LEU 232 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228f GLN* 2.7 24.7 + - + +
229f ASP* 3.8 15.9 - - - +
230f LYS 3.2 0.4 - - - -
231f LEU* 1.3 75.4 - - - +
233f THR* 1.3 70.4 + - + +
234f ASP 3.2 1.3 - - - -
235f ASP* 3.0 22.4 + - + +
236f GLY 3.7 2.9 + - - -
371f CYS* 6.0 3.6 - - - -
407f HIS* 5.0 9.6 - - + -
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Residues in contact with THR 233 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195f GLU* 4.3 17.7 - - - +
199f PHE* 4.2 20.1 - - + -
200f GLY* 5.9 0.7 - - - -
229f ASP* 3.1 32.2 + - - +
230f LYS* 3.8 4.5 + - - -
232f LEU* 1.3 79.4 - - + +
234f ASP* 1.3 69.1 + - - +
235f ASP 3.4 0.5 + - - -
236f GLY* 3.5 3.5 + - - -
237f ASN* 2.8 28.7 + - - +
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Residues in contact with ASP 234 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199f PHE* 4.9 5.6 - - - -
200f GLY* 3.8 25.0 - - - +
204f SER* 5.8 2.2 - - - -
221f PHE* 3.7 23.4 - - - -
222f VAL* 6.0 4.5 - - + +
230f LYS* 3.0 21.8 + - - +
231f LEU* 4.8 3.1 - - - -
232f LEU 3.2 0.8 - - - -
233f THR* 1.3 84.1 + - - +
235f ASP* 1.3 60.1 + - - +
237f ASN* 3.4 6.3 - - + -
238f LYS* 2.8 40.5 + - - +
249f LEU* 5.5 2.5 - - + -
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Residues in contact with ASP 235 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231f LEU 3.4 15.8 + - - +
232f LEU* 3.0 18.8 + - + +
234f ASP* 1.3 79.5 - - - +
236f GLY* 1.3 61.3 + - - +
238f LYS* 3.4 18.1 + - - +
243f ASN* 5.8 0.3 - - - +
245f ASP* 2.9 29.6 - - - +
246f HIS* 5.3 8.1 + - - +
249f LEU* 3.4 16.4 - - + +
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Residues in contact with GLY 236 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232f LEU 3.7 3.4 + - - -
233f THR 3.5 6.2 + - - -
234f ASP 3.3 0.4 - - - -
235f ASP* 1.3 78.5 - - - +
237f ASN* 1.3 65.0 + - - +
238f LYS 3.4 1.1 + - - +
239f TRP* 4.1 13.3 + - - -
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Residues in contact with ASN 237 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197f ASN* 2.5 40.4 + - - +
200f GLY* 3.3 36.2 - - - +
201f GLY* 3.6 12.4 - - - +
204f SER* 3.1 18.5 + - - -
233f THR* 2.8 21.3 + - - +
234f ASP* 3.2 11.7 + - - +
236f GLY* 1.3 79.2 + - - +
238f LYS* 1.3 58.1 + - - +
239f TRP* 3.1 28.7 - - - -
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Residues in contact with LYS 238 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204f SER* 4.2 8.1 - - - +
218f VAL* 4.3 18.0 - - + +
222f VAL* 4.2 9.1 - - - +
234f ASP* 2.8 21.6 + - - +
235f ASP 3.4 10.9 + - - +
236f GLY 4.7 1.0 - - - +
237f ASN* 1.3 75.5 - - - +
239f TRP* 1.3 61.0 + - - +
240f LEU* 3.6 36.7 + - + +
245f ASP* 3.3 31.8 - - + +
248f MET* 4.2 20.7 - - - +
249f LEU* 3.4 31.6 - - - +
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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