Contacts of the helix formed by residues 227 - 238 (chain K) 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 LEU 227 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191K SER 5.4 1.8 - - - -
192K GLY* 3.7 28.7 - - - +
195K LEU* 4.2 9.2 - - + -
196K ALA* 3.8 20.2 - - + +
223K MET* 2.9 15.6 + - - +
224K THR* 5.2 1.1 - - - +
226K LYS* 1.3 80.3 - - - +
228K ASP* 1.3 71.3 + - - +
229K ASN 3.3 0.2 - - - -
230K LEU* 3.1 24.1 + - - +
231K ILE* 3.2 12.4 + - + +
245K ARG* 4.6 7.9 - - - +
246K PRO* 3.4 38.6 - - + -
248K LEU* 4.5 19.7 - - + -
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Residues in contact with ASP 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K THR 2.5 30.4 - - - +
225K SER* 4.0 7.1 - - - +
227K LEU* 1.3 86.0 - - - +
229K ASN* 1.3 60.7 + - - +
230K LEU 3.1 1.7 + - - -
231K ILE* 4.1 4.9 + - - +
232K LYS* 2.9 27.6 + - - +
245K ARG* 3.1 41.7 + - - +
246K PRO* 4.9 1.2 - - - +
108V LEU* 6.1 1.3 - - + -
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Residues in contact with ASN 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K SER 3.5 16.0 + - - +
226K LYS* 4.1 5.1 - - - +
227K LEU 3.3 0.4 - - - -
228K ASP* 1.3 78.9 - - - +
230K LEU* 1.3 60.0 + - - +
232K LYS* 3.1 16.1 - - - +
233K GLU* 3.0 44.0 + - - +
319U ASP* 2.6 56.4 + - - +
322U LEU* 3.3 16.8 - - + +
323U SER* 3.5 6.0 + - - -
108V LEU* 4.4 9.4 - - + +
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Residues in contact with LEU 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K ALA* 3.2 32.3 - - + +
161K PRO* 4.0 16.2 - - + -
164K THR* 3.5 26.0 - - - +
191K SER 5.3 0.9 - - - +
192K GLY 3.8 11.7 - - - +
193K GLY* 3.9 11.2 - - - -
196K ALA* 3.6 20.0 - - + -
226K LYS 3.4 16.2 + - - +
227K LEU* 3.1 15.1 + - - +
229K ASN* 1.3 78.2 - - - +
231K ILE* 1.3 65.3 + - - +
233K GLU* 3.4 6.3 + - - +
234K ALA* 3.3 14.6 + - - +
323U SER* 6.1 1.3 - - - -
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Residues in contact with ILE 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K THR* 5.9 0.7 - - - -
196K ALA* 3.7 28.5 - - + +
199K SER* 3.6 29.4 - - - +
200K LEU* 4.5 20.9 - - + -
203K SER* 6.5 0.4 - - - -
227K LEU* 3.2 15.4 + - + +
228K ASP* 4.1 5.6 + - - +
230K LEU* 1.3 72.0 - - - +
232K LYS* 1.3 52.6 + - - +
233K GLU 2.7 7.6 + - - -
234K ALA* 2.9 6.3 + - - +
235K ALA* 2.6 34.9 + - + +
242K VAL* 3.9 30.7 - - + -
244K VAL 5.9 0.9 - - - +
245K ARG* 5.6 2.2 - - - -
246K PRO* 4.3 17.7 - - + -
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Residues in contact with LYS 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K ASP 2.9 27.6 + - - +
229K ASN* 3.1 21.3 - - - +
231K ILE* 1.3 73.9 - - - +
233K GLU* 1.3 62.2 + - - +
235K ALA* 3.7 12.9 - - - +
236K GLU* 3.3 36.0 + - - +
242K VAL* 4.4 16.8 - - + +
109U LYS* 5.7 4.9 - - - +
319U ASP* 2.4 49.0 + - - +
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Residues in contact with GLU 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PRO* 3.9 19.7 - - + +
229K ASN* 3.0 38.8 + - - +
230K LEU* 3.4 5.5 + - - +
231K ILE 2.7 6.7 + - - -
232K LYS* 1.3 81.4 - - - +
234K ALA* 1.3 59.1 + - - +
235K ALA 3.0 1.1 - - - -
236K GLU* 3.1 10.3 + - - +
237K LEU* 3.0 25.5 + - - +
319U ASP 4.5 2.9 - - - -
320U LYS* 3.7 27.9 + - + +
323U SER* 2.6 42.9 + - - -
324U LEU* 4.8 0.2 - - - +
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Residues in contact with ALA 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PRO* 3.8 12.9 - - + +
164K THR* 3.3 24.2 - - + -
165K LEU* 5.6 2.0 - - + -
200K LEU* 3.2 24.9 - - + -
230K LEU 3.3 7.8 + - - +
231K ILE* 2.9 5.0 + - - +
233K GLU* 1.3 78.2 - - - +
235K ALA* 1.3 56.5 + - - +
236K GLU 3.0 1.6 - - - -
237K LEU* 3.3 10.5 - - + +
238K LEU* 2.9 35.8 + - + +
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Residues in contact with ALA 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K LEU* 4.1 2.6 - - + +
231K ILE* 2.6 19.7 + - + +
232K LYS* 3.7 15.5 - - - +
234K ALA* 1.3 78.0 - - - +
236K GLU* 1.3 58.0 + - + +
239K GLY 3.0 1.7 - - - -
240K VAL* 2.4 62.7 + - + +
242K VAL* 4.0 20.4 - - + +
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Residues in contact with GLU 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ARG* 4.6 9.2 + - - +
232K LYS* 3.3 28.3 + - - +
233K GLU* 3.1 11.6 + - - +
234K ALA 3.0 0.4 - - - -
235K ALA* 1.3 79.1 - - + +
237K LEU* 1.3 65.4 - - - +
238K LEU 3.2 1.6 - - - -
239K GLY* 2.9 15.9 + - - +
105U LYS* 3.2 27.3 + - - +
107U GLU* 5.2 3.9 - - - +
109U LYS* 5.8 1.0 + - - -
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Residues in contact with LEU 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LYS* 4.1 10.4 + - - -
12K PHE* 3.3 54.1 - - + -
161K PRO* 4.3 14.4 - - + +
162K ILE* 3.4 32.8 - - + +
165K LEU* 5.0 2.7 - - + -
233K GLU 3.0 14.0 + - - +
234K ALA* 3.3 11.0 - - - +
236K GLU* 1.3 78.0 - - - +
238K LEU* 1.3 61.1 + - + +
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Residues in contact with LEU 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ARG* 4.7 3.3 + - - -
8K LEU* 2.8 66.5 - - + +
9K LEU* 3.4 21.1 - - + -
11K LYS* 5.5 5.4 + - - +
12K PHE* 4.6 7.2 - - + -
165K LEU* 3.9 16.2 - - + -
168K VAL* 3.8 21.3 - - + -
200K LEU* 3.7 28.5 - - + -
204K ILE* 4.0 10.8 - - + -
234K ALA 2.9 10.6 + - - +
237K LEU* 1.3 79.0 - - + +
239K GLY* 1.3 59.8 + - - +
240K VAL* 3.3 8.5 - - + -
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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