Contacts of the helix formed by residues 220 - 232 (chain B) in PDB entry 3E0D
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ALA* 6.2 0.7 - - + -
215B TYR* 3.6 17.3 - - + -
216B VAL* 3.3 15.6 + - - +
217B ARG* 2.9 37.3 + - - +
219B GLU* 1.3 84.3 - - - +
221B ALA* 1.3 57.2 + - - +
222B ARG 3.4 0.7 - - - -
223B ALA* 3.2 13.8 + - + +
224B HIS* 2.9 30.5 + - - +
564B ARG* 4.9 11.3 + - - -
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Residues in contact with ALA 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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215B TYR* 3.8 24.2 - - + +
218B LYS 3.4 15.3 + - - +
219B GLU 3.2 1.6 - - - -
220B ASP* 1.3 76.9 - - - +
222B ARG* 1.3 57.8 + - + +
224B HIS* 3.3 5.5 + - - +
225B GLU* 2.8 27.5 + - - +
247B ASP* 3.8 34.8 - - + +
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Residues in contact with ARG 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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219B GLU 4.2 5.7 + - - +
220B ASP 3.4 0.4 - - - -
221B ALA* 1.3 76.4 - - - +
223B ALA* 1.3 60.0 + - - +
225B GLU* 3.0 23.5 + - - +
226B VAL* 2.9 39.0 + - + +
236B LEU* 3.5 41.6 - - - +
241B ARG* 5.4 3.0 - - - +
511B TYR* 5.4 2.1 + - - -
557B GLN* 4.4 17.0 + - - +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 5.6 1.3 - - + -
219B GLU 4.8 2.3 + - - +
220B ASP* 3.2 18.9 + - + +
222B ARG* 1.3 75.4 - - - +
224B HIS* 1.3 57.8 + - - +
226B VAL* 3.3 14.5 - - - +
227B LEU* 3.1 24.3 + - - +
561B VAL* 5.8 3.1 - - + -
564B ARG* 4.9 15.9 - - + +
565B LEU* 3.9 21.4 - - + +
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Residues in contact with HIS 224 (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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20B ASN 3.0 28.4 + - - -
22B ALA* 3.8 23.7 - - + +
214B HIS* 3.9 8.2 - - - +
215B TYR* 3.5 29.9 - + + -
220B ASP 2.9 13.2 + - - +
221B ALA 3.4 8.5 + - - +
223B ALA* 1.3 75.8 - - - +
225B GLU* 1.3 66.3 + - - +
227B LEU* 3.0 20.4 + - + +
228B LEU* 3.1 34.2 + - + +
244B PHE* 3.8 39.7 - + - +
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Residues in contact with GLU 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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221B ALA 2.8 14.7 + - - +
222B ARG* 3.0 33.3 + - + +
224B HIS* 1.3 81.0 + - - +
226B VAL* 1.3 60.8 + - + +
228B LEU* 3.7 8.4 + - - +
229B ALA* 3.4 16.6 + - - +
236B LEU* 4.8 3.2 - - - +
241B ARG* 3.4 33.2 + - - +
242B TRP 4.5 2.8 - - - +
243B ARG* 3.5 35.0 + - + +
244B PHE 5.3 4.5 + - - +
247B ASP* 5.4 4.4 - - - +
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Residues in contact with VAL 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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222B ARG* 2.9 23.6 + - + +
223B ALA* 3.3 16.8 - - - +
225B GLU* 1.3 75.5 - - + +
227B LEU* 1.3 66.3 + - - +
228B LEU 3.2 0.4 - - - -
229B ALA* 3.0 19.6 + - + +
230B ILE* 3.0 19.7 + - + +
236B LEU* 4.4 21.5 - - + -
507B VAL* 5.5 1.6 - - + -
510B VAL* 4.5 10.0 - - + +
511B TYR* 4.5 18.2 - - + +
561B VAL* 4.1 15.0 - - + -
565B LEU* 3.9 22.9 - - + -
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Residues in contact with LEU 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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18B LEU 5.6 3.1 - - - +
19B LEU 4.6 2.9 - - - +
20B ASN* 4.3 12.6 - - - +
21B GLY 3.3 28.3 - - - +
22B ALA* 3.9 17.5 - - + -
223B ALA 3.1 14.0 + - - +
224B HIS* 3.0 14.0 + - + +
226B VAL* 1.3 77.3 - - - +
228B LEU* 1.3 57.4 + - + +
230B ILE* 2.9 32.0 + - + +
231B GLN* 3.1 40.9 + - - +
565B LEU* 5.5 5.4 - - + -
568B LEU* 4.0 25.4 - - + -
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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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19B LEU 4.0 1.6 - - - +
20B ASN* 3.7 29.4 - - + +
224B HIS* 3.1 25.5 + - + +
225B GLU* 3.7 8.7 - - - +
227B LEU* 1.3 80.6 - - + +
229B ALA* 1.3 50.5 + - - +
231B GLN* 3.4 2.5 + - - +
232B SER* 2.7 38.2 + - - -
242B TRP* 3.6 59.2 - - + +
243B ARG* 4.2 2.0 - - - -
244B PHE* 3.6 37.0 - - + +
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Residues in contact with ALA 229 (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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225B GLU 3.4 11.4 + - - +
226B VAL* 3.0 12.9 + - + +
228B LEU* 1.3 77.7 - - - +
230B ILE* 1.3 57.1 + - - +
232B SER* 4.2 7.0 - - - -
233B LYS* 3.0 18.8 + - - -
234B THR* 3.1 24.0 + - - +
235B THR 4.7 5.4 - - - +
236B LEU* 5.5 1.3 - - - -
241B ARG* 5.3 9.4 - - - +
242B TRP 4.8 2.2 + - - +
510B VAL* 3.6 27.3 - - + +
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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
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226B VAL* 3.0 17.4 + - + +
227B LEU* 2.9 18.2 + - + +
229B ALA* 1.3 78.0 - - - +
231B GLN* 1.3 74.4 + - - +
233B LYS* 3.3 23.0 - - - +
506B ASP* 3.7 45.5 - - + +
507B VAL* 4.5 4.9 - - + +
510B VAL* 3.5 19.1 - - + -
565B LEU* 4.2 24.9 - - + -
570B ARG* 4.9 4.7 - - - +
14E T 4.5 5.7 + - - +
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Residues in contact with GLN 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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18B LEU 4.2 9.3 + - - +
19B LEU* 3.0 47.3 - - + +
227B LEU* 3.1 34.1 + - - +
228B LEU 3.9 4.9 - - - +
230B ILE* 1.3 90.0 + - - +
232B SER* 1.3 60.3 + - - +
233B LYS* 3.1 15.9 + - - +
242B TRP* 4.2 15.9 - - + -
570B ARG* 5.3 6.3 - - - +
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Residues in contact with SER 232 (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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228B LEU 2.7 22.9 + - - -
229B ALA* 4.2 0.7 - - - -
231B GLN* 1.3 71.0 - - - +
233B LYS* 1.3 68.9 + - - +
234B THR* 3.4 25.0 + - - +
240B GLU 5.1 0.9 + - - -
241B ARG* 4.2 2.4 - - - -
242B TRP* 3.5 33.7 + - - +
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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