Contacts of the helix formed by residues 224 - 238 (chain U) in PDB entry 1J0B
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 224 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219U PHE* 3.7 24.7 - - - -
220U GLY 4.4 0.2 - - - +
221U GLU* 2.4 56.3 + - - +
223U MET* 1.3 69.5 - - - +
225U SER* 1.3 62.9 + - - +
226U LYS 3.4 0.4 - - - -
227U LEU* 3.7 8.2 - - - +
228U ASP* 3.1 27.0 + - - +
245U ARG* 3.6 22.9 + - - -
248U LEU* 4.6 2.6 - - - +
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Residues in contact with SER 225 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221U GLU* 3.0 29.6 + - - +
222U VAL* 3.9 7.8 - - - +
224U THR* 1.3 79.0 - - - +
226U LYS* 1.3 64.8 + - - +
227U LEU 3.1 2.2 - - - -
228U ASP* 3.1 7.4 + - - +
229U ASN* 2.9 32.3 + - - +
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Residues in contact with LYS 226 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131U PHE* 3.0 42.4 - - + -
156U PRO* 5.6 4.8 - - - +
159U ALA* 6.4 2.9 - - + -
191U SER* 5.0 11.2 - - - +
222U VAL* 2.7 45.9 - - + +
223U MET* 4.6 0.4 - - - -
224U THR 3.4 0.4 - - - -
225U SER* 1.3 82.5 + - - +
227U LEU* 1.3 57.4 + - - +
229U ASN* 3.8 4.9 - - - +
230U LEU* 2.9 34.1 + - + +
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Residues in contact with LEU 227 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192U GLY* 4.4 13.7 - - - +
195U LEU* 3.8 25.6 - - + -
196U ALA* 4.1 19.7 - - + +
223U MET* 3.9 12.5 + - - +
224U THR 3.7 11.4 + - - +
225U SER 3.1 0.2 - - - -
226U LYS* 1.3 78.6 - - - +
228U ASP* 1.3 65.1 + - - +
230U LEU* 3.6 7.0 - - - +
231U ILE* 3.1 40.7 + - + +
245U ARG* 5.3 4.7 - - - +
246U PRO* 3.9 19.1 - - + +
248U LEU* 4.1 21.8 - - + -
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Residues in contact with ASP 228 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224U THR* 3.1 16.7 + - - +
225U SER* 3.1 10.4 + - - +
227U LEU* 1.3 77.2 - - - +
229U ASN* 1.3 62.3 + - - +
230U LEU 2.9 4.5 - - - -
231U ILE* 2.9 17.3 + - - +
232U LYS* 3.0 15.5 + - - +
245U ARG* 2.9 50.2 + - - +
246U PRO* 4.7 4.2 - - - +
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Residues in contact with ASN 229 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225U SER 2.9 16.8 + - - +
226U LYS* 4.2 4.5 - - - +
228U ASP* 1.3 76.8 - - - +
230U LEU* 1.3 57.4 + - - +
231U ILE 3.3 0.2 - - - -
232U LYS* 4.1 21.6 - - - +
233U GLU* 2.8 46.2 + - - +
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Residues in contact with LEU 230 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159U ALA* 4.5 14.1 - - + +
160U SER 4.2 2.5 - - - -
161U PRO* 3.6 38.6 - - + -
164U THR* 4.3 6.7 - - - +
191U SER 4.9 6.1 - - - +
192U GLY 4.3 4.5 - - - +
193U GLY* 4.3 13.0 - - - +
196U ALA* 3.5 27.1 - - + +
226U LYS* 2.9 22.4 + - + +
227U LEU* 3.6 10.8 - - - +
228U ASP 2.9 0.4 - - - -
229U ASN* 1.3 78.9 - - - +
231U ILE* 1.3 58.4 + - + +
233U GLU* 3.3 6.4 - - - +
234U ALA* 3.1 22.3 + - + +
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Residues in contact with ILE 231 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196U ALA* 3.8 33.0 - - + +
199U SER* 4.0 15.9 - - - +
200U LEU* 4.2 22.9 - - + +
227U LEU* 3.1 35.2 - - + +
228U ASP* 2.9 7.8 + - - +
230U LEU* 1.3 76.4 - - - +
232U LYS* 1.3 63.5 + - - +
233U GLU 2.8 6.2 + - - -
234U ALA* 4.4 3.5 - - - +
235U ALA* 2.9 29.4 + - + +
242U VAL* 4.3 20.6 - - + -
245U ARG* 6.0 0.4 - - - -
246U PRO* 4.7 9.4 - - + -
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Residues in contact with LYS 232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228U ASP 3.0 12.8 + - - +
229U ASN* 4.1 25.1 - - - +
231U ILE* 1.3 76.2 - - - +
233U GLU* 1.3 63.7 + - - +
235U ALA* 4.1 5.7 - - - +
236U GLU* 3.4 45.5 + - - +
242U VAL* 4.5 23.5 - - + +
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Residues in contact with GLU 233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161U PRO* 3.4 25.5 - - + +
229U ASN* 2.8 47.4 + - - +
230U LEU* 3.3 8.7 - - - +
231U ILE 2.8 1.6 - - - -
232U LYS* 1.3 83.3 - - + +
234U ALA* 1.3 59.5 + - - +
235U ALA 3.1 1.3 - - - -
236U GLU* 3.0 27.4 + - - +
237U LEU* 3.2 9.0 + - - +
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Residues in contact with ALA 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161U PRO* 3.3 40.4 - - + +
164U THR* 4.0 9.0 - - + -
165U LEU* 4.8 1.2 - - + +
196U ALA* 6.4 0.2 - - + -
200U LEU* 3.4 23.3 - - + +
230U LEU* 3.1 9.6 + - + +
231U ILE* 3.4 2.0 + - - +
233U GLU* 1.3 75.1 - - - +
235U ALA* 1.3 59.2 + - - +
236U GLU 3.1 5.4 - - - -
237U LEU* 3.3 20.6 + - - +
238U LEU* 3.5 9.4 + - - +
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Residues in contact with ALA 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200U LEU* 3.4 30.0 - - + +
231U ILE* 2.9 20.2 + - + +
232U LYS* 4.3 4.7 - - - -
234U ALA* 1.3 76.4 - - - +
236U GLU* 1.3 59.7 + - - +
237U LEU 3.3 0.7 - - - -
238U LEU 4.0 1.8 - - - -
239U GLY 3.9 0.2 - - - -
240U VAL* 2.5 48.2 + - + +
242U VAL* 4.5 15.9 - - + +
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Residues in contact with GLU 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ARG* 5.1 3.0 + - - +
232U LYS* 3.4 38.3 + - - +
233U GLU* 3.0 17.3 + - - +
235U ALA* 1.3 78.9 - - - +
237U LEU* 1.3 64.2 + - - +
238U LEU 3.3 0.4 - - - -
239U GLY* 3.4 10.7 + - - -
240U VAL 4.8 0.2 - - - -
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Residues in contact with LEU 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LYS* 4.3 11.4 + - - -
12U PHE* 3.8 33.4 - - + -
161U PRO* 4.3 8.5 - - + +
162U ILE* 3.2 48.2 - - + +
165U LEU* 4.8 2.7 - - + -
233U GLU 3.2 10.3 + - - +
234U ALA* 3.3 11.9 - - - +
235U ALA 3.3 0.2 - - - -
236U GLU* 1.3 82.0 - - - +
238U LEU* 1.3 62.5 + - + +
239U GLY 3.3 1.1 + - - -
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Residues in contact with LEU 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U LEU* 3.5 41.3 - - + +
9U LEU* 3.6 13.9 - - + -
11U LYS* 6.0 2.5 - - - +
12U PHE* 3.4 30.7 - - + -
165U LEU* 3.7 21.8 - - + -
168U VAL* 4.0 12.8 - - + -
200U LEU* 3.9 16.8 - - + -
204U ILE* 3.9 24.9 - - + -
234U ALA 3.5 8.8 + - - +
235U ALA 4.0 0.4 - - - -
236U GLU 3.3 0.2 - - - -
237U LEU* 1.3 75.9 - - - +
239U GLY* 1.3 57.1 + - - +
240U VAL* 3.0 20.6 + - + -
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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