Contacts of the helix formed by residues 225 - 239 (chain B) in PDB entry 1JSC
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 GLU 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B VAL* 4.6 1.7 - - - +
219B MET 3.9 5.0 - - - +
220B VAL* 3.8 4.7 - - + -
221B LYS* 3.3 40.7 + - - +
222B SER* 3.0 19.1 + - - +
224B GLU* 1.3 80.4 - - - +
226B LEU* 1.3 62.5 + - - +
227B PRO* 3.5 0.7 - - - -
228B LEU* 3.3 15.1 + - + +
229B ARG* 2.6 67.9 + - + +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 3.4 39.5 - - - +
97B ILE* 4.3 9.4 - - + -
98B PHE* 4.4 9.0 - - + +
220B VAL* 3.8 16.1 - - + +
222B SER 3.4 3.0 + - - -
223B VAL* 3.3 17.2 + - + +
225B GLU* 1.3 78.1 - - - +
227B PRO* 1.3 72.1 - - + +
229B ARG* 3.4 0.9 + - - -
230B ILE* 3.1 46.8 + - + +
247B VAL* 5.5 0.2 - - + -
249B LEU* 3.7 29.6 - - + -
253B VAL* 5.4 2.0 - - + -
254B THR* 4.9 9.4 - - + -
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Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.8 15.0 - - + -
97B ILE* 3.7 22.7 - - + -
101B MET* 4.0 22.4 - - + +
223B VAL 3.6 9.4 - - - +
224B GLU 3.6 11.0 - - - +
226B LEU* 1.3 94.8 - - + +
228B LEU* 1.3 61.4 + - - +
230B ILE* 3.3 2.3 + - - +
231B ASN* 3.0 27.4 + - - -
262B ILE* 3.9 10.1 - - + -
266B THR 3.3 13.7 - - - +
267B THR* 4.0 13.0 - - + -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLU 5.3 0.4 - - - +
225B GLU* 3.3 17.0 + - + +
226B LEU 3.2 0.2 - - - -
227B PRO* 1.3 78.8 - - - +
229B ARG* 1.3 90.6 + - - +
231B ASN* 3.2 5.2 + - + +
232B GLU* 3.0 50.3 + - + +
265B LYS 5.5 0.4 - - - +
266B THR* 3.1 45.5 + - + -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 4.2 7.5 - - - -
218B VAL* 4.2 29.3 - - + +
220B VAL* 3.9 23.3 - - + -
225B GLU* 2.6 53.9 + - + +
226B LEU 4.0 2.9 - - - +
228B LEU* 1.3 90.7 - - - +
230B ILE* 1.3 57.4 + - - +
232B GLU* 2.8 39.6 + - - +
233B ALA* 2.8 31.4 + - - +
247B VAL* 4.5 5.5 - - + +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.9 28.3 - - + +
101B MET* 3.7 42.2 - - + -
102B MET* 5.3 1.8 - - - -
105B GLN* 4.6 4.9 - - + -
187B PHE* 4.0 19.1 - - + -
226B LEU* 3.1 33.7 + - + +
227B PRO 3.6 6.7 - - - +
228B LEU 3.2 0.2 - - - -
229B ARG* 1.3 76.4 - - + +
231B ASN* 1.3 63.8 + - - +
233B ALA* 3.2 6.6 + - - +
234B PHE* 3.1 51.0 + - + -
247B VAL* 5.5 0.7 - - + -
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 3.3 27.3 - - - +
105B GLN* 2.7 32.8 + - - +
227B PRO 3.0 9.9 + - - +
228B LEU* 3.7 4.9 - - + +
230B ILE* 1.3 76.9 - - - +
232B GLU* 1.3 63.2 + - + +
234B PHE* 3.4 2.3 + - - +
235B GLU* 3.0 23.8 + - - +
266B THR 3.2 24.0 + - - +
267B THR 3.3 14.3 - - - -
268B LEU 3.6 3.9 + - - +
269B PRO* 3.3 17.1 - - + +
270B SER* 4.3 17.1 + - - +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.7 20.2 - - + -
228B LEU* 3.0 36.5 + - + +
229B ARG* 2.8 41.8 + - - +
231B ASN* 1.3 78.0 - - + +
233B ALA* 1.3 64.0 + - - +
235B GLU* 3.1 11.7 + - - +
236B ILE* 2.9 34.8 + - + +
270B SER* 5.3 3.1 - - - +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B VAL* 4.1 10.5 - - + -
216B TRP* 3.7 12.0 - - + -
229B ARG 2.8 16.9 + - - +
230B ILE* 3.2 7.2 + - - +
232B GLU* 1.3 77.2 - - - +
234B PHE* 1.3 56.8 + - - +
237B ALA* 3.0 31.4 + - - +
245B VAL* 3.4 18.6 - - + +
247B VAL* 3.6 26.0 - - + -
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Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B MET* 3.9 13.9 - - + -
105B GLN* 3.5 41.7 - - + +
107B VAL* 3.7 31.2 - - + -
156B PRO* 3.8 28.7 - - + -
158B VAL* 3.9 8.5 - - + -
185B VAL* 4.0 31.2 - - + -
187B PHE* 4.1 6.7 - + - -
230B ILE* 3.1 41.6 + - + +
231B ASN 4.0 2.5 - - - +
233B ALA* 1.3 74.4 - - - +
235B GLU* 1.3 58.9 + - - +
237B ALA* 4.5 0.4 - - - -
238B THR* 2.7 38.5 + - + +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ASN 3.0 17.7 + - - +
232B GLU* 3.1 9.6 + - - +
234B PHE* 1.3 78.9 - - - +
236B ILE* 1.3 66.8 + - + +
238B THR* 3.6 4.2 + - - -
239B SER* 2.9 35.8 + - - +
270B SER* 3.0 46.3 + - - +
271B ASN 4.6 2.4 - - - +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 2.9 54.3 + - + +
216B TRP* 3.5 46.0 - - + -
232B GLU* 2.9 22.4 + - + +
233B ALA 4.1 1.6 - - - +
235B GLU* 1.3 83.8 - - + +
237B ALA* 1.3 59.4 + - - +
238B THR 3.2 0.9 + - - -
239B SER* 3.5 9.3 + - - -
245B VAL* 3.9 15.5 - - + -
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B PRO* 5.3 0.2 - - + -
183B PRO* 3.5 6.7 - - + +
184B MET 4.0 15.3 - - - +
185B VAL* 4.1 10.3 - - + -
215B LYS* 4.7 0.2 - - - -
233B ALA 3.0 19.3 + - - +
234B PHE* 4.1 3.1 - - - +
236B ILE* 1.3 77.9 - - - +
238B THR* 1.3 62.6 + - + +
242B PRO* 3.3 6.1 - - - +
243B GLY 3.1 43.1 + - - +
245B VAL* 3.8 12.1 - - + +
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY 6.1 0.7 - - - +
156B PRO* 4.0 35.9 - - + -
183B PRO* 4.1 8.5 - - + -
234B PHE* 2.7 23.3 + - + +
235B GLU* 3.6 5.4 + - - -
236B ILE 3.2 0.6 - - - -
237B ALA* 1.3 82.4 - - + +
239B SER* 1.3 58.5 + - - +
240B GLY 5.1 0.2 - - - +
242B PRO* 4.7 11.2 - - - +
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 2.7 27.5 + - - -
235B GLU* 2.9 24.4 + - - +
236B ILE* 3.5 9.6 + - - -
238B THR* 1.3 76.5 - - - +
240B GLY* 1.3 64.7 + - - +
241B ARG 3.2 4.5 + - - +
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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