Contacts of the helix formed by residues 212 - 223 (chain B) in PDB entry 4I6J
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 SER 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B ASP* 2.8 26.8 + - - -
210B HIS 4.1 0.8 - - - -
211B VAL* 1.3 74.8 - - - +
213B PRO* 1.3 68.7 - - - +
214B ALA* 4.0 8.9 + - - +
215B GLY* 2.3 32.9 + - - -
216B ILE* 3.2 4.7 + - - -
234B HIS* 5.2 2.5 - - - -
235B LEU* 4.0 2.0 - - - -
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Residues in contact with PRO 213 (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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212B SER* 1.3 87.4 - - - +
214B ALA* 1.3 63.4 + - - +
215B GLY 3.1 0.3 + - - -
216B ILE* 3.4 17.2 + - + +
217B LEU* 3.4 19.8 + - + +
234B HIS* 3.9 33.7 - - + +
235B LEU* 3.7 21.9 - - + +
237B SER* 5.2 13.2 + - - +
240B LEU* 6.0 0.9 - - - +
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Residues in contact with ALA 214 (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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186B ASP* 4.2 2.0 - - - +
212B SER* 3.0 9.6 - - - +
213B PRO* 1.3 81.0 - - - +
215B GLY* 1.3 63.1 + - - +
217B LEU* 3.6 21.4 - - - +
218B CYS* 4.1 4.0 + - - +
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Residues in contact with GLY 215 (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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186B ASP* 3.0 34.2 + - - +
189B LEU* 4.9 6.7 - - - +
211B VAL* 4.3 3.4 - - - -
212B SER 2.3 23.3 + - - -
214B ALA* 1.3 70.3 - - - +
216B ILE* 1.3 65.8 + - - +
217B LEU 3.2 0.7 + - - -
218B CYS* 3.4 15.4 + - - +
219B VAL* 4.3 4.0 + - - +
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Residues in contact with ILE 216 (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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189B LEU* 5.0 0.9 - - + -
203B LEU* 5.1 0.9 - - + -
205B MET* 4.4 18.4 - - + -
211B VAL* 4.0 5.9 - - + +
212B SER 3.2 3.1 + - - +
213B PRO* 3.4 9.8 + - + +
215B GLY* 1.3 73.2 - - - +
217B LEU* 1.3 52.6 + - - +
219B VAL* 2.5 51.6 + - + +
220B ALA* 3.2 5.6 + - + +
229B LEU* 4.8 7.2 - - + -
231B LEU* 3.9 26.9 - - + -
235B LEU* 2.9 63.5 - - + +
240B LEU* 4.4 11.9 - - + -
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Residues in contact with LEU 217 (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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213B PRO* 3.4 15.1 + - + +
214B ALA* 3.6 18.4 - - - +
215B GLY 3.2 0.2 - - - -
216B ILE* 1.3 77.5 - - - +
218B CYS* 1.3 55.8 + - - +
220B ALA* 3.3 6.2 + - - +
221B ASP* 2.9 37.5 + - + +
237B SER* 4.8 4.7 - - - +
239B GLU* 3.8 46.2 - - + +
240B LEU* 4.4 10.2 - - + +
243B ALA* 4.0 12.8 - - + -
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Residues in contact with CYS 218 (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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189B LEU* 6.3 1.3 - - + -
190B LYS* 3.7 36.8 - - + +
193B VAL* 4.0 10.8 - - + +
214B ALA 4.1 3.6 + - - +
215B GLY 3.4 12.4 + - - +
216B ILE 2.9 1.0 + - - -
217B LEU* 1.3 77.5 - - - +
219B VAL* 1.3 58.0 + - + +
221B ASP* 4.2 4.5 - - - -
222B GLN* 3.0 55.6 + - - +
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Residues in contact with VAL 219 (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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189B LEU* 4.1 36.3 - - + -
192B LEU* 5.0 1.8 - - + -
193B VAL* 3.9 18.6 - - + -
200B LEU* 4.4 7.9 - - + -
203B LEU* 4.1 23.6 - - + -
215B GLY 4.6 1.8 - - - +
216B ILE* 2.5 27.1 + - + +
218B CYS* 1.3 71.4 - - + +
220B ALA* 1.3 64.1 + - - +
223B CYS* 3.0 39.5 + - - +
226B LEU* 4.2 13.6 - - + +
229B LEU* 5.9 0.2 - - + -
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Residues in contact with ALA 220 (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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216B ILE* 3.2 6.1 + - + +
217B LEU 3.7 6.7 - - - +
219B VAL* 1.3 81.1 - - - +
221B ASP* 1.3 64.2 + - - +
223B CYS 3.9 3.6 - - - +
226B LEU* 4.7 11.9 - - + +
229B LEU* 6.1 0.7 - - + -
240B LEU* 3.5 32.5 - - + -
243B ALA* 4.0 15.1 - - + +
244B LEU* 4.3 11.4 - - + -
249B HIS* 3.4 26.3 + - - -
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Residues in contact with ASP 221 (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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217B LEU* 2.9 22.6 + - + +
218B CYS* 3.7 7.1 - - - +
220B ALA* 1.3 81.3 - - - +
222B GLN* 1.3 69.1 + - - +
224B HIS* 3.4 19.2 + - - -
243B ALA* 4.6 11.0 - - + +
248B LYS* 5.6 1.9 - - - +
249B HIS* 5.4 0.3 - - - -
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Residues in contact with GLN 222 (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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193B VAL* 3.3 33.1 - - + +
194B ALA* 5.5 2.1 - - - +
197B SER* 3.9 15.4 + - - +
218B CYS* 3.0 36.2 + - - +
219B VAL 4.6 0.2 - - - +
221B ASP* 1.3 86.6 - - - +
223B CYS* 1.3 60.5 + - - +
224B HIS* 3.3 21.0 + - - -
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Residues in contact with CYS 223 (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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193B VAL* 4.0 22.7 - - - -
197B SER* 3.8 28.3 - - - +
200B LEU* 4.0 35.9 - - + +
219B VAL* 3.0 24.4 + - + +
220B ALA 3.9 2.9 - - - +
221B ASP 3.5 0.4 - - - -
222B GLN* 1.3 75.8 - - - +
224B HIS* 1.3 63.5 + - - +
225B GLY 3.1 6.8 + - - +
226B LEU* 3.5 14.3 + - + +
249B HIS* 3.6 12.5 + - - -
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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