Contacts of the helix formed by residues 211 - 218 (chain B) in PDB entry 5E9W
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 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LYS* 3.1 21.8 + - - +
184B ILE* 4.1 7.0 - - + +
203B ASP* 3.9 22.5 - - - +
206B CYS 5.4 1.0 + - - +
209B GLY* 3.1 1.0 - - - -
210B GLY* 1.3 74.5 - - - +
212B LEU* 1.3 65.2 + - - +
213B LEU 3.2 2.2 - - - -
214B LYS* 2.9 47.3 + - + +
215B TRP* 3.1 24.5 + - - +
282B SER* 4.8 0.5 + - - -
284B GLN* 3.6 26.5 - - - +
501B SAH 4.1 9.1 + - - +
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Residues in contact with LEU 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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203B ASP* 5.4 1.0 + - - +
209B GLY* 3.1 24.1 + - - +
210B GLY 3.5 0.2 - - - -
211B ASP* 1.3 76.5 - - - +
213B LEU* 1.3 63.3 + - - +
215B TRP* 3.2 8.7 + - - +
216B LYS* 3.0 21.0 + - - +
223B LEU* 3.7 26.7 - - + -
225B CYS* 4.0 14.4 - - - -
236B CYS* 3.5 30.5 - - - +
239B ARG* 3.7 22.0 - - + -
240B TYR* 3.7 18.6 - - + +
243B MET* 3.8 15.3 - - + -
253B PHE* 3.8 14.9 - - + -
257B PHE* 5.2 0.4 - - + -
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Residues in contact with LEU 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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209B GLY 4.8 0.4 + - - -
210B GLY 4.8 4.4 + - - +
211B ASP 3.2 0.8 - - - -
212B LEU* 1.3 78.8 - - - +
214B LYS* 1.3 59.0 + - + +
216B LYS* 3.3 23.6 + - + +
217B LYS* 2.9 59.6 + - + +
243B MET* 4.3 11.6 - - + -
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Residues in contact with LYS 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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177B ASN* 2.6 44.4 + - - +
180B LYS* 4.1 3.1 - - - -
181B SER* 3.3 37.5 - - - +
184B ILE* 4.0 26.7 - - + +
188B LEU* 4.6 4.9 - - - +
210B GLY 2.9 17.0 + - - -
211B ASP* 2.9 36.7 + - - +
213B LEU* 1.3 76.7 - - + +
215B TRP* 1.3 65.2 + - - +
217B LYS* 3.3 8.8 + - - +
218B GLY* 3.1 18.5 + - - -
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Residues in contact with TRP 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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184B ILE* 3.5 40.2 - - + -
188B LEU* 3.9 18.2 - - + -
201B VAL* 3.6 33.7 - - + -
203B ASP* 3.5 20.4 + - - -
211B ASP* 3.1 30.5 + - - +
212B LEU* 3.2 5.1 + - - +
214B LYS* 1.3 75.9 - - - +
216B LYS* 1.3 61.5 + - - +
218B GLY* 3.2 2.8 + - - +
219B ARG 3.2 15.4 + - - -
220B ILE* 3.5 44.3 + - + +
223B LEU* 3.8 20.1 - - + +
253B PHE* 3.8 10.5 - - + -
280B ILE* 4.3 11.7 - - + -
282B SER* 3.5 28.9 - - - -
315B ILE* 5.0 0.7 - - + -
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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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212B LEU 3.0 13.4 + - - +
213B LEU* 3.6 21.2 - - + +
215B TRP* 1.3 77.0 - - - +
217B LYS* 1.3 60.4 + - + +
219B ARG* 3.0 23.9 + - - +
243B MET* 3.7 31.9 + - + +
246B ARG* 6.1 3.2 - - - +
249B SER* 4.0 20.4 + - - +
250B GLU* 4.1 29.7 - - - +
251B TYR 5.0 10.7 - - - +
252B ILE* 4.5 8.5 - - + +
253B PHE* 3.5 14.5 - - + -
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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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213B LEU* 2.9 52.3 + - + +
214B LYS* 3.3 7.3 + - - +
216B LYS* 1.3 79.2 - - + +
218B GLY* 1.3 59.2 + - - +
219B ARG* 3.2 8.8 + - - +
411B LEU* 5.5 9.1 - - - +
414B ARG* 5.6 4.9 - - - +
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Residues in contact with GLY 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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188B LEU* 3.7 24.0 - - - -
192B ARG* 2.3 44.0 + - - -
214B LYS 3.1 9.7 + - - -
215B TRP 3.2 4.0 + - - -
216B LYS 3.2 0.4 - - - -
217B LYS* 1.3 76.9 - - - +
219B ARG* 1.3 55.0 + - - +
220B ILE* 3.2 6.0 + - - +
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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