Contacts of the helix formed by residues 210 - 221 (chain B) in PDB entry 1EJI
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 ASP 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 2.8 33.2 + - + -
208B ASN 4.1 0.6 + - - -
209B LEU* 1.3 67.3 - - - +
211B TYR* 1.3 66.1 + - - +
212B ALA* 3.5 11.8 - - - +
213B ARG* 3.0 36.7 + - - +
214B LEU* 2.9 24.2 + - - +
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Residues in contact with TYR 211 (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 ALA* 3.9 28.9 + - + -
201B GLY* 5.9 0.2 - - - -
208B ASN* 6.3 0.7 - - + -
209B LEU* 2.9 52.1 + - + +
210B ASP* 1.3 71.2 - - - +
212B ALA* 1.3 58.5 + - - +
214B LEU* 3.6 5.9 - - + +
215B ARG* 2.8 32.9 + - - +
225B LEU* 4.0 1.7 - - + +
227B ALA* 4.3 2.8 - - + +
229B MSE 5.3 2.3 - - - +
232B ILE* 4.0 20.3 - - + +
242B PRO* 4.3 16.8 - - + -
243B SER 4.3 4.5 - - - -
244B PRO* 3.4 41.4 - - + +
247B HIS* 3.7 25.0 - - + +
248B CYS* 3.9 14.8 - - - -
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Residues in contact with ALA 212 (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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210B ASP* 3.0 11.4 + - - +
211B TYR* 1.3 80.6 - - - +
213B ARG* 1.3 62.7 + - - +
215B ARG* 3.3 4.3 - - - +
216B LYS* 3.2 17.0 + - - +
247B HIS* 3.3 30.8 + - + +
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Residues in contact with ARG 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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183B TYR* 3.6 31.5 + - + +
184B ASP* 2.8 34.4 + - - +
187B GLU* 2.7 33.9 + - - -
210B ASP* 3.0 30.6 + - + +
212B ALA* 1.3 76.0 - - - +
214B LEU* 1.3 66.4 + - - +
216B LYS* 3.0 20.6 + - + +
217B ILE* 3.0 36.5 + - + +
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Residues in contact with LEU 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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172B TYR* 4.6 9.0 - - + +
181B ILE* 6.0 1.3 - - + -
183B TYR* 3.8 19.3 - - + +
186B LEU* 3.5 32.1 - - + -
198B ILE* 4.5 15.2 - - + +
200B ALA* 3.4 29.6 - - + -
209B LEU* 4.5 10.1 - - + -
210B ASP 2.9 25.4 + - - +
211B TYR* 3.6 10.1 - - + +
213B ARG* 1.3 76.5 - - - +
215B ARG* 1.3 57.5 + - - +
217B ILE* 3.2 8.2 + - + +
218B ALA* 2.8 29.6 + - - +
225B LEU* 4.0 15.3 - - + +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR 2.8 16.0 + - - +
212B ALA 3.3 6.5 - - - +
214B LEU* 1.3 78.5 - - - +
216B LYS* 1.3 63.2 + - - +
218B ALA* 3.2 4.8 + - - +
219B ASP* 2.5 78.4 + - - +
225B LEU* 3.7 9.4 - - + +
247B HIS* 2.8 47.6 + - + +
248B CYS 5.6 0.6 - - - -
249B HIS* 3.3 34.4 + - - -
270B ARG* 5.4 6.3 - - - +
274B ARG* 5.4 0.4 - - - +
286B TYR* 4.3 7.9 + - - -
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Residues in contact with LYS 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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187B GLU* 3.0 31.2 + - - +
212B ALA 3.2 8.3 + - - +
213B ARG* 3.0 20.5 + - + +
215B ARG* 1.3 80.2 - - - +
217B ILE* 1.3 62.3 + - + +
219B ASP* 3.2 5.4 + - - +
220B ASP* 2.9 57.8 + - - +
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Residues in contact with ILE 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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183B TYR* 3.8 16.2 - - + +
186B LEU* 4.0 17.5 - - + -
187B GLU* 3.6 53.2 - - + +
190B ALA* 4.0 9.6 - - + -
198B ILE* 4.2 10.1 - - + -
213B ARG* 3.0 30.2 + - + +
214B LEU* 3.5 8.5 - - + +
216B LYS* 1.3 76.5 - - + +
218B ALA* 1.3 63.9 + - - +
220B ASP* 3.3 11.5 + - - +
221B ASN* 3.0 36.3 + - - +
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Residues in contact with ALA 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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198B ILE* 4.1 17.7 - - + +
214B LEU 2.8 14.2 + - - +
215B ARG* 3.3 10.8 - - - +
216B LYS 3.2 0.2 - - - -
217B ILE* 1.3 79.5 - - - +
219B ASP* 1.3 56.9 + - - +
221B ASN* 3.2 1.2 + - - -
222B GLY 2.9 7.8 + - - -
223B ALA* 2.7 46.4 + - - +
224B TYR 4.6 0.4 - - - -
225B LEU* 4.1 22.4 - - + +
249B HIS* 5.2 0.9 - - + -
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Residues in contact with ASP 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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215B ARG* 2.5 60.3 + - - +
216B LYS* 3.9 4.5 - - - +
218B ALA* 1.3 75.1 - - - +
220B ASP* 1.3 68.6 + - - +
222B GLY* 2.9 15.4 + - - +
223B ALA 4.5 1.8 - - - +
249B HIS* 4.1 9.7 + - - -
274B ARG* 4.9 4.3 + - - -
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Residues in contact with ASP 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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187B GLU* 3.7 10.2 - - + +
216B LYS* 2.9 56.5 + - - +
217B ILE* 3.4 12.8 - - - +
218B ALA 3.2 0.2 - - - -
219B ASP* 1.3 77.8 - - - +
221B ASN* 1.3 65.7 + - - +
222B GLY 3.6 0.3 + - - -
156D ASP* 5.2 1.9 - - - +
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Residues in contact with ASN 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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187B GLU* 4.9 2.6 + - - +
190B ALA* 3.3 46.0 - - - +
191B SER* 3.4 15.5 - - - +
194B HIS* 5.1 6.7 - - - -
195B PRO* 4.3 21.1 - - + +
198B ILE* 5.4 0.4 - - - +
217B ILE* 3.0 26.4 + - - +
218B ALA* 3.2 3.7 + - - +
219B ASP 3.1 0.2 - - - -
220B ASP* 1.3 84.2 - - - +
222B GLY* 1.3 65.8 + - - +
223B ALA* 3.3 3.4 + - + +
156D ASP* 3.9 26.9 - - + +
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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