Contacts of the helix formed by residues 213 - 221 (chain B) in PDB entry 4EMS
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO 5.8 0.2 + - - -
180B ALA* 2.9 34.6 + - - +
183B SER* 3.8 17.9 - - - -
184B TRP* 3.9 24.4 - - - +
187B SER* 4.0 3.2 + - - -
188B ARG* 5.3 0.2 + - - -
209B GLY 4.3 1.6 + - - -
211B THR* 3.6 11.9 + - - +
212B GLY* 1.3 77.6 - - - +
214B THR* 1.3 63.0 + - - +
216B LYS* 3.8 2.5 - - - +
217B VAL* 3.5 26.0 + - - +
241B GLN* 2.9 31.3 + - - +
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER* 3.4 25.0 + - - -
186B PHE* 6.0 0.7 - - + -
187B SER* 3.9 18.0 - - - -
190B LEU* 4.8 8.7 - - + -
206B ASP* 3.6 13.4 + - - +
209B GLY* 5.3 1.9 + - - -
212B GLY* 3.3 0.6 - - - -
213B ASN* 1.3 75.5 - - - +
215B SER* 1.3 65.3 + - - +
217B VAL* 3.2 5.4 + - - +
218B ILE* 3.1 42.6 + - + +
265B LEU* 3.9 16.6 - - + -
267B LYS* 4.1 18.2 - - + +
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.4 3.1 - - - +
206B ASP* 2.8 35.7 + - - +
212B GLY 3.5 3.0 + - - -
214B THR* 1.3 76.4 - - - +
216B LYS* 1.3 60.7 + - - +
218B ILE* 3.7 9.6 - - - +
219B ALA* 2.8 33.3 + - - +
227B CYS* 3.9 14.3 - - - +
228B THR 4.8 0.3 + - - -
229B VAL* 3.7 7.9 - - - +
246B LEU* 3.5 27.6 - - - -
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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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188B ARG* 6.4 0.2 - - - +
212B GLY 2.8 19.2 + - - +
213B ASN 3.8 5.4 - - - +
214B THR 3.2 0.2 - - - -
215B SER* 1.3 78.7 - - - +
217B VAL* 1.3 58.6 + - + +
219B ALA* 3.4 3.7 + - - +
220B GLU* 3.0 65.8 + - + +
241B GLN* 3.0 43.2 + - + +
242B THR 3.4 25.8 + - - +
243B HIS* 4.0 13.5 - - + -
246B LEU* 4.1 7.5 - - + +
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Residues in contact with VAL 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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187B SER* 3.3 41.7 - - - +
188B ARG* 3.2 46.2 - - + +
191B VAL* 4.0 12.8 - - + -
213B ASN 3.5 8.2 + - - +
214B THR 3.2 4.8 + - - +
215B SER 3.2 0.6 - - - -
216B LYS* 1.3 75.7 - - + +
218B ILE* 1.3 63.9 + - - +
220B GLU* 3.4 12.2 + - - +
221B THR* 2.7 38.5 + - - +
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Residues in contact with ILE 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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187B SER* 5.7 0.9 - - - -
190B LEU* 4.9 3.4 - - + -
191B VAL* 4.1 21.3 - - + -
198B PHE* 3.9 34.5 - - + -
204B LEU* 4.1 12.6 - - + -
214B THR* 3.1 24.6 + - + +
215B SER* 3.3 7.6 + - - +
217B VAL* 1.3 76.1 - - + +
219B ALA* 1.3 57.1 + - - +
221B THR 3.2 0.3 + - - -
222B PHE* 2.8 32.9 + - + +
225B ILE* 4.2 13.9 - - + -
227B CYS* 3.7 17.0 - - - -
265B LEU* 3.9 28.5 - - + -
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Residues in contact with ALA 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 SER 2.8 20.4 + - - +
216B LYS* 3.8 3.4 - - - +
218B ILE* 1.3 74.5 - - - +
220B GLU* 1.3 61.4 + - - +
222B PHE 3.4 20.6 - - - +
223B PRO* 3.7 8.3 - - - +
225B ILE 4.4 2.2 - - - +
227B CYS* 4.3 13.7 - - + -
243B HIS* 3.7 37.2 + - + +
245B ASN* 4.4 14.3 + - + +
246B LEU* 5.0 1.3 - - + -
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Residues in contact with GLU 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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188B ARG* 4.8 7.3 + - - -
216B LYS* 3.0 54.5 + - - +
217B VAL* 3.8 17.2 - - - +
219B ALA* 1.3 77.7 - - - +
221B THR* 1.3 63.5 + - - +
223B PRO* 4.5 8.1 - - - +
243B HIS* 3.9 21.0 - - + -
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Residues in contact with THR 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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191B VAL* 3.5 25.7 - - + +
195B ARG* 3.7 26.9 + - - +
217B VAL* 2.7 24.3 + - - +
218B ILE 3.8 2.2 - - - -
220B GLU* 1.3 80.2 - - - +
222B PHE* 1.3 86.7 + - + +
223B PRO* 3.4 8.7 - - - +
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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