Contacts of the helix formed by residues 220 - 235 (chain I) 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 GLY 220 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G GLU 2.4 19.2 - - - +
149G ARG* 3.8 10.1 - - - -
218I ARG 2.5 12.9 + - - -
219I PHE* 1.3 71.0 - - - +
221I GLU* 1.3 66.2 + - - +
222I VAL* 3.5 2.5 - - - -
223I MET* 3.2 24.9 + - - +
224I THR 3.6 3.8 + - - -
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Residues in contact with GLU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G GLU* 2.3 30.4 - - - +
144G LEU* 2.9 28.4 - - + +
147G GLU* 2.6 71.5 + - + +
149G ARG* 2.9 37.6 - - + +
220I GLY* 1.3 69.4 - - - +
222I VAL* 1.3 61.9 + - + +
223I MET 2.7 12.8 + - - -
225I SER* 2.7 15.2 + - - -
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Residues in contact with VAL 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G ARG* 5.9 4.9 - - - +
131I PHE* 4.8 15.2 - - + -
220I GLY* 4.4 1.1 - - - -
221I GLU* 1.3 83.7 - - + +
223I MET* 1.3 58.1 + - - +
225I SER* 3.7 8.3 - - - -
226I LYS* 2.9 50.6 - - + +
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Residues in contact with MET 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I PHE* 6.2 3.6 - - + -
189I ALA* 4.0 19.3 - - + +
190I GLY* 3.8 26.5 - - - +
191I SER 5.3 4.3 - - - +
192I GLY* 5.3 9.9 - - - -
215I ALA* 4.0 22.0 - - + -
217I GLY* 4.6 9.6 - - - +
218I ARG 5.4 1.1 - - - +
219I PHE* 4.7 8.7 - - + -
220I GLY* 3.2 25.8 - - - +
221I GLU 2.7 9.3 + - - -
222I VAL* 1.3 75.4 - - - +
224I THR* 1.3 59.1 + - - +
226I LYS* 3.5 4.7 - - - +
227I LEU* 2.9 27.8 + - - +
248I LEU* 3.9 20.2 - - + -
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Residues in contact with THR 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G ARG 3.6 13.9 - - - +
147G GLU* 2.7 22.4 - - - +
219I PHE* 2.8 37.9 - - + -
220I GLY 3.6 1.2 + - - -
221I GLU 3.5 2.4 + - - -
223I MET* 1.3 79.6 - - - +
225I SER* 1.3 59.1 + - - +
227I LEU* 3.1 11.1 - - - +
228I ASP* 3.0 30.4 + - - +
245I ARG* 3.7 28.7 + - - +
248I LEU* 3.9 4.9 - - - +
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Residues in contact with SER 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G GLU* 2.6 34.0 + - - -
221I GLU* 2.7 28.1 + - - -
222I VAL* 3.7 2.8 - - - -
224I THR* 1.3 77.2 - - - +
226I LYS* 1.3 67.5 + - - +
227I LEU 3.1 1.1 - - - -
228I ASP* 3.4 10.3 + - - +
229I ASN* 3.2 19.4 + - - +
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Residues in contact with LYS 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I PHE* 2.9 39.0 - - + -
134I MET* 5.3 8.8 - - - +
156I PRO* 5.9 1.0 - - - +
159I ALA* 5.8 7.6 - - - -
191I SER 5.4 7.4 - - - +
222I VAL* 2.9 51.4 - - + +
223I MET* 3.5 6.0 - - - +
224I THR 3.4 0.4 - - - -
225I SER* 1.3 79.6 + - - +
227I LEU* 1.3 53.4 + - - +
229I ASN* 3.2 4.4 + - - +
230I LEU* 2.7 45.2 + - + +
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Residues in contact with LEU 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I GLY* 3.9 17.0 - - - +
195I LEU* 4.5 12.1 - - + -
196I ALA* 3.6 37.5 - - + +
223I MET* 2.9 21.3 + - - +
224I THR* 3.1 9.4 - - - +
226I LYS* 1.3 79.0 - - - +
228I ASP* 1.3 56.1 + - - +
230I LEU* 2.7 28.8 + - + +
231I ILE* 2.7 26.2 + - + +
245I ARG* 4.8 7.4 - - - +
246I PRO* 4.3 18.8 - - + -
248I LEU* 4.3 22.4 - - + -
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Residues in contact with ASP 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I THR* 3.0 21.4 + - - +
225I SER* 3.4 10.0 + - - +
227I LEU* 1.3 78.3 - - - +
229I ASN* 1.3 57.3 + - - +
231I ILE* 3.8 7.7 + - - +
232I LYS* 3.3 24.0 + - - +
245I ARG* 2.5 53.7 + - - +
246I PRO* 4.9 4.7 - - - +
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Residues in contact with ASN 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I SER 3.2 7.6 + - - +
226I LYS* 3.2 8.3 + - - +
227I LEU 3.1 0.6 - - - -
228I ASP* 1.3 75.8 - - - +
230I LEU* 1.3 58.9 + - - +
231I ILE 3.1 2.0 - - - -
232I LYS* 3.0 40.0 + - + +
233I GLU* 2.6 56.8 + - - +
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Residues in contact with LEU 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I ALA* 3.4 31.0 - - + +
160I SER 5.1 0.4 - - - -
161I PRO* 4.9 1.9 - - + +
164I THR* 3.1 26.5 - - - +
191I SER 3.9 21.3 - - - +
192I GLY* 4.2 13.5 - - - +
193I GLY* 4.3 3.4 - - - +
196I ALA* 3.4 14.6 - - + -
226I LYS* 2.7 23.8 + - + +
227I LEU* 2.7 16.0 + - - +
229I ASN* 1.3 77.3 - - - +
231I ILE* 1.3 56.2 + - - +
233I GLU* 4.3 5.1 - - - +
234I ALA* 3.0 23.4 + - + +
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Residues in contact with ILE 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I ALA* 3.5 45.1 - - + +
199I SER* 4.0 16.4 - - - -
200I LEU* 4.0 13.8 - - + +
227I LEU* 2.7 26.1 + - + +
228I ASP* 4.0 9.0 - - - +
230I LEU* 1.3 74.5 - - - +
232I LYS* 1.3 56.1 + - - +
234I ALA* 3.1 5.2 + - - +
235I ALA* 2.6 39.2 + - + +
242I VAL* 3.8 26.9 - - + -
246I PRO* 4.2 19.5 - - + -
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Residues in contact with LYS 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228I ASP 3.3 14.8 + - - +
229I ASN* 3.0 30.4 + - - +
231I ILE* 1.3 79.4 - - - +
233I GLU* 1.3 60.2 + - - +
235I ALA* 2.5 36.1 + - - +
236I GLU* 3.1 24.3 + - + +
242I VAL* 4.6 15.7 - - + -
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Residues in contact with GLU 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO* 3.9 27.1 - - + +
229I ASN* 2.6 54.5 + - - +
230I LEU* 4.3 3.5 - - - +
232I LYS* 1.3 77.2 - - + +
234I ALA* 1.3 58.7 + - - +
235I ALA 3.0 4.2 + - - -
236I GLU* 3.0 29.4 + - - +
237I LEU* 3.7 4.9 + - - +
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Residues in contact with ALA 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO* 3.1 40.9 - - + +
164I THR* 3.4 19.5 - - + -
165I LEU* 3.8 14.4 - - - +
200I LEU* 3.2 12.2 - - + +
230I LEU 3.0 20.2 + - - +
231I ILE 3.1 4.1 + - - +
233I GLU* 1.3 77.4 - - - +
235I ALA* 1.3 56.2 + - - +
236I GLU 3.4 0.7 - - - -
237I LEU* 4.3 4.9 + - - +
238I LEU* 3.9 5.4 - - - +
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Residues in contact with ALA 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I LEU* 3.4 23.1 - - + -
231I ILE* 2.6 13.1 + - + +
232I LYS* 2.5 25.3 + - - +
234I ALA* 1.3 72.7 - - - +
236I GLU* 1.3 59.7 + - - +
237I LEU 3.5 0.7 - - - -
238I LEU* 3.9 4.8 + - - -
239I GLY 3.7 8.8 + - - -
240I VAL* 3.3 25.7 + - - +
242I VAL* 4.3 17.9 - - + +
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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