Contacts of the helix formed by residues 213 - 227 (chain B) in PDB entry 3EIJ
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 ALA 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A HIS* 4.1 20.6 - - + +
211B GLY 3.7 1.2 + - - -
212B LYS* 1.3 73.0 - - - +
214B SER* 1.3 60.5 + - - +
215B HIS 3.3 0.5 + - - -
216B ARG* 3.4 56.2 + - - +
217B GLU* 4.3 1.7 + - - +
353B GLU* 4.3 10.5 - - - +
355B GLU* 4.5 7.4 - - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A HIS* 4.2 20.1 - - - -
397A THR* 5.0 11.0 - - - +
399A ASP* 3.9 17.8 - - - +
400A GLN* 6.1 1.3 - - - -
212B LYS* 4.0 21.2 + - - +
213B ALA* 1.3 78.4 - - - +
215B HIS* 1.3 73.6 + - - +
216B ARG 3.2 0.9 + - - -
217B GLU* 3.6 8.6 + - - +
218B MET* 3.4 27.4 + - - +
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Residues in contact with HIS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 3.3 58.5 - + + +
177B GLU* 5.1 6.7 - - - -
207B LEU 5.4 0.7 - - - -
208B ALA* 4.0 11.7 - - - -
211B GLY* 4.0 7.4 - - - -
212B LYS* 3.0 55.3 + - + +
214B SER* 1.3 85.1 + - - +
216B ARG* 1.3 57.4 + - - +
218B MET* 3.8 5.0 - - - -
219B THR* 2.8 33.9 + - - -
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA* 4.2 19.7 + - + +
209B LEU* 5.3 2.7 + - - +
213B ALA* 3.5 44.9 + - - +
214B SER 3.2 0.8 - - - -
215B HIS* 1.3 73.9 - - - +
217B GLU* 1.3 65.9 + - - +
219B THR 3.1 2.1 + - - -
220B SER* 3.0 20.4 + - - -
260B LEU* 3.4 48.0 - - - +
263B GLN* 4.7 8.4 + - - +
264B PHE* 3.4 36.0 - - + -
353B GLU* 3.3 33.5 + - - +
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Residues in contact with GLU 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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399A ASP* 3.3 30.3 - - - +
213B ALA 4.3 0.8 + - - -
214B SER* 3.6 7.0 + - - +
215B HIS 3.5 0.4 - - - -
216B ARG* 1.3 77.9 - - - +
218B MET* 1.3 61.2 + - - +
220B SER* 3.1 7.6 + - - -
221B LYS* 3.0 42.8 + - + +
267B ARG* 2.8 43.1 + - - +
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Residues in contact with MET 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 4.5 10.1 - - + -
399A ASP* 4.3 27.6 - - + +
402A LYS* 5.9 5.2 - - - +
175B TYR* 2.4 40.3 + - + +
176B PHE* 2.8 58.6 - - + +
179B GLY* 3.7 19.3 - - - +
214B SER* 3.4 18.3 + - - +
215B HIS* 3.7 12.1 - - - +
216B ARG 3.2 0.6 - - - -
217B GLU* 1.3 76.0 - - - +
219B THR* 1.3 58.2 + - - +
221B LYS* 3.5 7.1 + - + -
222B LEU 3.0 15.1 + - - -
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Residues in contact with THR 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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176B PHE* 3.0 23.1 - - - -
204B ALA* 3.4 32.5 + - + +
205B VAL* 3.8 10.5 - - + -
208B ALA* 3.2 8.4 - - - +
215B HIS 2.8 24.4 + - - -
216B ARG 3.1 5.6 + - - -
218B MET* 1.3 76.2 - - - +
220B SER* 1.3 58.5 + - - +
222B LEU* 3.2 8.0 + - - +
223B LEU* 2.9 32.3 + - + +
264B PHE* 3.8 17.5 - - + -
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ARG 3.0 9.2 + - - -
217B GLU* 3.1 9.3 + - - -
219B THR* 1.3 76.5 - - - +
221B LYS* 1.3 63.4 + - - +
223B LEU* 3.2 9.8 + - - +
224B SER* 3.0 23.9 + - - -
264B PHE* 3.5 24.2 + - - -
267B ARG* 3.3 44.6 + - - +
271B ASP* 4.3 2.4 - - - +
273B ILE* 5.3 0.7 - - - +
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP* 3.4 23.8 + - - +
402A LYS* 3.8 33.7 - - - +
403A ARG* 5.0 10.3 - - - +
406A GLU* 4.0 16.7 + - - -
175B TYR* 4.0 4.3 - - - +
181B THR* 4.5 2.2 - - - +
217B GLU* 3.0 36.4 + - + +
218B MET* 3.7 12.8 - - + +
220B SER* 1.3 75.3 - - - +
222B LEU* 1.3 57.0 + - - +
224B SER* 3.3 7.1 + - - -
225B ASP* 2.9 42.1 + - - +
267B ARG* 3.9 9.6 - - - +
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Residues in contact with LEU 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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172B ILE* 4.8 11.2 - - + -
175B TYR* 3.8 27.7 + - + +
176B PHE* 5.6 0.4 - - + -
181B THR* 3.9 19.5 - - - +
184B VAL* 3.8 33.9 - - + -
200B VAL* 5.5 2.5 - - + -
204B ALA* 4.3 24.2 - - + -
218B MET 3.0 14.3 + - - +
219B THR* 3.2 9.6 - - - +
221B LYS* 1.3 77.3 - - - +
223B LEU* 1.3 58.0 + - + +
225B ASP* 4.0 0.2 - - - +
226B LEU* 2.8 60.4 + - + +
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Residues in contact with LEU 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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200B VAL* 5.3 0.9 - - + -
201B PRO* 3.5 44.4 - - + -
204B ALA* 4.6 5.2 - - + -
205B VAL* 4.3 17.9 - - + -
219B THR* 2.9 29.2 + - + +
220B SER* 3.2 8.5 + - - +
222B LEU* 1.3 80.3 - - + +
224B SER* 1.3 61.7 + - - +
226B LEU* 5.4 3.1 - - + -
227B CYS* 3.1 27.4 + - - +
231B MET* 3.8 11.3 - - + +
236B VAL* 5.4 2.2 - - + -
240B PHE* 4.3 22.2 - - + -
264B PHE* 5.0 5.8 - - + -
268B ALA* 5.7 1.1 - - + -
273B ILE* 3.8 18.5 - - + +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER 3.0 11.7 + - - -
221B LYS* 3.6 7.0 - - - -
223B LEU* 1.3 78.3 - - - +
225B ASP* 1.3 66.6 + - - +
227B CYS* 3.4 17.3 - - - +
267B ARG* 5.9 0.2 - - - -
271B ASP* 3.4 39.8 + - - +
273B ILE* 4.0 14.7 - - - +
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Residues in contact with ASP 225 (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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402A LYS* 5.7 1.7 + - - -
442A GLN* 4.3 4.9 + - - -
181B THR* 3.1 43.4 + - + +
221B LYS* 2.9 22.3 + - - +
222B LEU 4.0 1.6 - - - +
224B SER* 1.3 80.5 + - - +
226B LEU* 1.3 65.7 + - - +
227B CYS 3.5 3.3 + - - +
229B THR* 3.6 15.1 + - - -
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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
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181B THR* 4.6 3.4 - - + +
184B VAL* 4.7 1.1 - - + -
185B ALA* 3.9 31.2 - - + +
188B LEU* 4.2 20.9 - - + -
200B VAL* 4.3 12.3 - - + -
222B LEU* 2.8 58.1 + - + +
223B LEU* 5.0 2.7 - - + +
225B ASP* 1.3 70.9 - - + +
227B CYS* 1.3 67.0 + - - +
228B GLY 3.3 0.3 + - - -
229B THR* 3.1 3.4 + - - -
230B VAL* 3.1 47.5 + - + +
231B MET* 3.3 22.1 + - + -
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Residues in contact with CYS 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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223B LEU 3.1 19.1 + - - +
224B SER 3.4 11.0 - - - +
225B ASP 3.3 4.2 - - - +
226B LEU* 1.3 76.1 - - - +
228B GLY* 1.3 61.4 + - - +
229B THR* 4.4 0.7 + - - -
231B MET* 3.4 13.4 - - + +
232B SER* 4.0 2.2 - - - -
233B THR* 3.8 34.1 - - - -
236B VAL* 3.9 11.4 - - + -
273B ILE* 3.7 33.8 - - + +
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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