Contacts of the helix formed by residues 213 - 225 (chain B) in PDB entry 2ORY
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 ASN 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B MET* 3.8 6.3 - - + +
122B ILE* 3.0 22.4 + - - +
124B LYS* 3.0 40.9 + - - +
212B GLY* 1.3 75.9 - - - +
214B ALA* 1.3 58.3 + - - +
215B ASP* 3.3 4.7 + - - +
216B PHE* 2.8 20.8 + - - +
217B ALA* 2.9 25.8 + - - +
281B LYS 3.5 18.0 + - - +
282B LYS* 3.1 21.8 - - + +
283B TYR* 3.9 0.2 - - - +
284B LYS 4.3 2.2 - - - -
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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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213B ASN* 1.3 70.7 - - - +
215B ASP* 1.3 63.3 + - - +
217B ALA* 3.3 1.4 + - - +
218B ASP* 2.9 41.8 + - - +
282B LYS* 2.9 22.6 + - + +
284B LYS* 3.8 29.1 - - + +
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Residues in contact with ASP 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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121B ARG* 3.1 32.1 + - + +
122B ILE* 2.9 47.2 + - - +
123B LEU* 3.8 10.4 - - + +
213B ASN* 3.3 3.1 + - - +
214B ALA* 1.3 80.0 - - - +
216B PHE* 1.3 63.5 + - - +
218B ASP* 3.4 9.0 + - - +
219B TYR* 3.1 24.4 + - - +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 3.9 26.5 - + + -
123B LEU* 3.9 12.2 - - + +
124B LYS 3.5 13.7 - - - +
125B ILE* 3.5 26.9 - - + -
182B THR* 4.3 17.0 - - + -
185B LEU* 3.5 31.9 - - + -
211B ALA* 4.2 15.7 - - + -
212B GLY* 4.2 14.8 - - - -
213B ASN* 2.8 20.9 + - - +
215B ASP* 1.3 78.2 - - - +
217B ALA* 1.3 63.2 + - + +
219B TYR* 3.2 3.3 + - - +
220B PHE* 2.9 30.3 + + + +
284B LYS 5.7 0.2 - - - -
286B ILE* 4.2 19.7 - - + -
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASN 2.9 12.7 + - - +
214B ALA 3.3 4.5 + - - +
216B PHE* 1.3 84.2 - - + +
218B ASP* 1.3 58.4 + - - +
220B PHE* 3.4 1.7 + - - +
221B ASP* 3.0 34.9 + - - +
284B LYS* 3.6 25.1 - - + +
285B GLN 3.5 27.6 - - - +
286B ILE* 4.1 8.7 - - + +
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 5.6 4.6 + - - +
214B ALA* 2.9 25.8 + - - +
215B ASP* 3.9 8.9 + - - +
217B ALA* 1.3 74.0 - - - +
219B TYR* 1.3 67.4 + - - +
221B ASP* 3.3 11.7 + - - +
222B ASP* 3.0 31.5 + - - +
284B LYS* 2.9 30.3 + - - -
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Residues in contact with TYR 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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113B TRP* 4.3 2.0 - - - -
116B ALA* 3.3 25.0 - - + +
117B SER 5.2 1.8 - - - -
118B VAL* 3.7 25.1 - - + -
123B LEU* 3.8 22.0 - - + -
185B LEU* 4.2 14.6 - - + -
189B ASP* 2.5 36.4 + - - -
215B ASP 3.1 17.0 + - - +
216B PHE* 3.6 3.8 - + - +
218B ASP* 1.3 76.1 - - - +
220B PHE* 1.3 65.2 + - - +
222B ASP* 3.1 12.0 + - + +
223B CYS* 2.9 45.0 + - + +
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Residues in contact with PHE 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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181B SER* 3.3 28.7 - - - -
185B LEU* 3.9 34.3 - - + -
203B THR* 4.0 4.9 - - + -
216B PHE* 2.9 20.4 + + + +
217B ALA 3.5 8.3 - - - +
219B TYR* 1.3 78.9 - - - +
221B ASP* 1.3 61.2 + - - +
224B LEU* 2.7 58.5 + - + -
225B GLY* 3.0 5.6 + - - -
228B CYS* 3.8 29.8 - - + -
286B ILE* 3.5 46.7 - - + -
287B LYS* 4.5 0.9 - - + -
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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 ALA* 3.0 24.1 + - - +
218B ASP* 3.6 13.6 - - - +
219B TYR 3.2 0.2 - - - -
220B PHE* 1.3 82.3 - - - +
222B ASP* 1.3 61.1 + - - +
225B GLY* 2.9 28.0 + - - +
226B ASP* 4.2 3.6 + - - +
284B LYS* 5.6 2.6 + - - -
285B GLN 5.0 1.2 - - - +
286B ILE* 3.6 1.6 - - - -
287B LYS* 2.7 48.1 + - - +
288B ALA 4.7 1.2 + - - -
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Residues in contact with ASP 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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218B ASP* 3.0 22.5 + - - +
219B TYR* 3.1 14.1 + - + +
221B ASP* 1.3 81.6 - - - +
223B CYS* 1.3 62.7 + - + +
225B GLY 4.5 0.5 + - - -
226B ASP* 5.6 2.8 + - - +
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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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185B LEU* 4.0 13.2 - - + -
188B LYS* 2.9 54.1 + - - -
189B ASP* 3.9 18.4 - - - -
219B TYR* 2.9 36.6 + - + +
222B ASP* 1.3 81.1 - - - +
224B LEU* 1.3 56.4 + - - +
227B GLN* 3.8 2.1 + - - -
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Residues in contact with LEU 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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184B ALA* 3.8 30.5 - - + +
185B LEU* 3.9 18.2 - - + +
188B LYS* 3.8 19.1 - - + -
201B ILE* 3.5 29.8 - - + +
202B SER* 4.7 0.7 - - - -
203B THR* 3.9 9.6 - - + -
220B PHE* 2.7 44.7 + - + +
223B CYS* 1.3 75.9 - - - +
225B GLY* 1.3 63.9 + - - +
226B ASP 3.3 2.5 - - - -
227B GLN* 2.9 28.2 + - + +
228B CYS* 3.3 7.8 + - - +
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Residues in contact with GLY 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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220B PHE* 3.0 6.9 + - - -
221B ASP* 2.9 31.6 + - - -
222B ASP 4.5 0.2 + - - -
223B CYS 3.8 0.2 - - - -
224B LEU* 1.3 76.3 - - - +
226B ASP* 1.3 63.2 + - - +
227B GLN 3.1 1.4 + - - -
228B CYS 3.2 5.0 + - - -
287B LYS* 3.0 41.6 + - - +
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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