Contacts of the helix formed by residues 212 - 223 (chain B) in PDB entry 2E52
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 MET 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A TYR* 3.8 19.3 - - + -
145B PHE* 3.7 29.4 - - + -
148B TYR* 3.8 32.3 - - + -
156B PHE* 4.5 4.5 - - + -
166B LEU* 3.7 25.8 - - + +
171B HIS* 6.1 0.2 - - + -
210B ASN* 2.9 27.3 + - - +
211B PHE* 1.3 94.5 - - + +
213B ARG* 1.3 60.1 + - - +
215B PHE* 3.7 22.8 - - + +
216B ASN* 2.9 32.9 + - - +
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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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298A TYR* 3.6 36.5 - - + +
299A LEU* 6.1 0.2 - - - -
210B ASN* 4.4 1.2 + - - +
211B PHE 3.3 0.4 - - - -
212B MET* 1.3 77.4 - - - +
214B ASP* 1.3 90.4 + - - +
216B ASN* 3.5 2.8 + - - +
217B LYS* 3.2 22.3 + - - +
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Residues in contact with ASP 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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194B PHE* 4.2 2.1 - - - -
198B GLN* 2.8 40.3 + - - +
201B LYS* 5.6 3.6 - - - +
211B PHE* 3.3 8.9 + - - +
213B ARG* 1.3 104.5 + - - +
215B PHE* 1.3 65.4 + - - +
217B LYS* 3.5 12.5 + - + +
218B TYR* 3.0 24.8 + - - +
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Residues in contact with PHE 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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165B LEU* 3.8 20.9 - - + -
166B LEU 4.7 7.2 - - - -
167B PHE* 4.2 14.8 - + - -
171B HIS* 3.8 44.0 - + - -
191B LEU* 3.7 27.4 - - + -
194B PHE* 3.7 39.4 - + + -
211B PHE* 2.7 21.4 + + - +
212B MET* 3.3 24.9 + - - +
214B ASP* 1.3 72.1 - - - +
216B ASN* 1.3 58.2 + - - +
218B TYR* 3.2 5.5 + + - +
219B PHE* 2.8 40.6 + + + +
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Residues in contact with ASN 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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297A LEU 2.8 28.5 + - - -
298A TYR* 3.2 20.5 + - - +
299A LEU* 4.2 12.8 - - + +
145B PHE* 4.4 7.8 - - - -
171B HIS* 2.8 31.9 + - - -
212B MET 2.9 19.5 + - - +
213B ARG 3.8 1.1 - - - +
214B ASP 3.4 0.2 - - - -
215B PHE* 1.3 72.4 - - - +
217B LYS* 1.3 56.9 + - - +
219B PHE* 3.4 4.6 + - - +
220B MET* 2.9 35.9 + - - +
230B LEU* 4.2 12.2 - - + +
234B LEU* 4.5 6.1 - - - +
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Residues in contact with LYS 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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299A LEU* 5.5 1.9 - - - +
201B LYS* 5.1 9.4 - - - +
213B ARG 3.2 13.9 + - - +
214B ASP* 3.6 16.6 - - + +
215B PHE 3.3 0.2 - - - -
216B ASN* 1.3 75.5 - - - +
218B TYR* 1.3 79.2 + - - +
220B MET* 3.3 10.7 + - + +
221B ASP* 2.8 45.0 + - + +
102C ASN* 3.5 25.3 + - - +
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Residues in contact with TYR 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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190B GLN* 2.6 45.0 + - + +
191B LEU* 4.4 5.8 - - + -
194B PHE* 3.4 41.8 - + + -
197B LYS* 3.5 34.4 + - + +
201B LYS* 4.2 11.4 - - - -
214B ASP 3.0 18.9 + - - +
215B PHE* 3.4 8.5 - + - +
217B LYS* 1.3 89.8 - - - +
219B PHE* 1.3 60.4 + - - +
221B ASP* 3.4 1.7 + - - +
222B LEU* 2.9 41.9 + - + +
102C ASN* 3.6 27.1 - - + +
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Residues in contact with PHE 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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167B PHE* 4.5 1.1 - + - -
171B HIS* 3.7 45.3 - + + -
174B ILE* 4.1 11.7 - - + -
175B LEU* 3.6 28.7 - - + -
191B LEU* 4.1 8.7 - - + -
215B PHE* 2.8 38.5 + + + +
216B ASN* 3.4 8.1 - - - +
218B TYR* 1.3 80.9 - - - +
220B MET* 1.3 62.5 + - - +
222B LEU* 3.4 1.2 + - - -
223B PHE* 3.0 55.0 + + - +
225B ILE* 3.7 22.7 - - + -
230B LEU* 4.2 15.9 - - + -
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Residues in contact with MET 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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299A LEU* 3.8 24.0 - - - -
216B ASN 2.9 20.1 + - - +
217B LYS* 3.5 8.3 - - + +
219B PHE* 1.3 76.6 - - - +
221B ASP* 1.3 56.1 + - - +
224B LYS* 2.9 27.9 + - - -
225B ILE* 3.1 36.0 + - + +
226B ASP* 4.0 1.6 - - - -
227B LYS* 3.5 41.1 - - + +
230B LEU* 3.5 19.1 - - + -
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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 LYS* 2.8 41.1 + - + +
218B TYR 3.8 3.3 - - - +
220B MET* 1.3 72.8 - - - +
222B LEU* 1.3 62.5 + - - +
224B LYS* 2.8 47.4 + - - +
101C PHE* 5.6 2.8 - - - -
102C ASN* 4.4 17.2 - - - +
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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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186B PHE* 3.1 33.3 - - + -
187B SER 4.0 19.3 - - - +
188B PHE 4.6 2.2 - - - +
190B GLN* 4.0 16.6 - - + -
191B LEU* 3.4 34.8 - - + +
218B TYR* 2.9 26.8 + - + +
219B PHE* 4.0 2.7 - - - +
221B ASP* 1.3 84.5 + - - +
223B PHE* 1.3 85.7 + - + +
224B LYS* 3.6 7.7 + - - +
101C PHE* 5.9 7.6 - - + -
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Residues in contact with PHE 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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175B LEU* 3.9 18.2 - - + -
180B LEU* 4.0 23.3 - - + +
186B PHE* 3.6 26.8 - + - -
188B PHE* 3.5 36.8 - + - -
191B LEU* 3.7 26.0 - - + -
219B PHE* 3.0 53.3 + + - +
222B LEU* 1.3 98.4 - - + +
224B LYS* 1.3 70.4 + - - +
225B ILE* 3.3 20.5 + - + +
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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