Contacts of the helix formed by residues 209 - 216 (chain B) in PDB entry 5E0T
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 LEU 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B CYS* 3.8 31.2 - - + +
151B LEU* 3.6 26.2 - - + +
152B SER* 3.9 12.1 - - - +
155B GLY 3.5 23.6 - - - +
156B ASP* 3.0 14.8 + - - +
157B ALA 3.7 20.9 - - - +
158B VAL* 3.6 30.7 - - + +
171B ALA* 4.7 0.2 - - + -
208B ALA* 1.3 69.2 - - - +
210B ARG* 1.3 58.0 + - - +
212B LEU* 3.2 10.5 + - + +
213B ASN* 2.8 39.8 + - - -
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Residues in contact with ARG 210 (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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156B ASP* 4.4 2.9 + - - +
208B ALA* 4.8 4.3 - - + -
209B LEU* 1.3 80.4 - - - +
211B TYR* 1.3 99.2 + - + +
213B ASN* 3.4 8.9 + - - +
214B PHE* 3.3 52.3 + - + -
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Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.2 7.0 - - + -
41B ASP* 3.3 27.5 + - + -
42B SER* 5.5 0.7 + - - -
43B SER* 3.3 20.0 + - - -
45B VAL* 3.8 18.4 - - + -
46B SER* 4.0 14.4 - - - -
208B ALA* 3.2 25.7 + - + +
210B ARG* 1.3 110.1 + - + +
212B LEU* 1.3 66.4 + - - +
214B PHE* 3.1 20.8 + + - +
215B PHE* 3.1 32.3 + - + -
251B LEU* 4.0 20.9 - - + -
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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
----------------------------------------------------------
144B PHE* 4.4 10.5 - - + -
148B CYS* 3.9 25.8 - - - -
158B VAL* 3.5 31.9 - - + -
160B ILE* 4.8 8.5 - - + -
169B PHE* 6.4 0.7 - - + -
207B PHE* 4.2 8.3 - - + -
208B ALA 3.3 9.3 + - - +
209B LEU* 3.2 10.6 + - + +
211B TYR* 1.3 76.2 - - - +
213B ASN* 1.3 58.6 + - - +
215B PHE* 2.9 38.5 + - + +
216B THR* 3.1 17.5 + - - +
235B LEU* 3.9 24.7 - - + -
237B VAL* 4.3 6.5 - - + -
251B LEU* 4.1 8.7 - - + -
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Residues in contact with ASN 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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145B ALA 4.8 1.0 - - - +
148B CYS* 3.3 29.6 + - - +
149B ARG* 3.8 7.1 + - - +
152B SER* 2.8 29.9 + - - -
209B LEU 2.8 26.0 + - - +
210B ARG* 3.7 7.9 - - - +
211B TYR 3.2 0.2 - - - -
212B LEU* 1.3 73.7 - - - +
214B PHE* 1.3 63.3 + - + +
216B THR* 3.1 18.4 + - - -
217B LYS* 3.6 19.5 - - - +
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Residues in contact with PHE 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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18B ALA 4.6 6.8 - - - +
21B ASP* 3.6 36.1 - - + +
22B LEU* 3.8 34.4 - - + +
210B ARG* 3.3 63.1 + - + -
211B TYR* 3.1 20.9 + + - +
213B ASN* 1.3 77.1 - - + +
215B PHE* 1.3 64.0 + - + +
217B LYS* 3.1 31.1 + - - +
249B TYR* 5.0 1.3 - - - -
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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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22B LEU* 4.0 10.5 - - + -
46B SER* 3.7 24.2 - - - -
47B LEU 5.5 0.2 - - - -
144B PHE* 5.6 0.7 - - + -
211B TYR* 3.1 24.2 - - + -
212B LEU* 2.9 29.3 + - + +
214B PHE* 1.3 78.1 - - + +
216B THR* 1.3 60.5 + - + +
218B ALA* 3.0 28.1 + - - +
237B VAL* 4.0 20.0 - - + -
239B TYR* 3.5 6.9 + - - +
249B TYR* 3.2 59.6 - + + -
250B TYR 4.2 3.4 - - - -
251B LEU* 3.8 31.6 - - + -
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Residues in contact with THR 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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144B PHE* 3.6 26.9 - - + -
145B ALA* 3.9 25.1 + - + +
148B CYS* 4.8 4.7 - - + -
212B LEU 3.1 13.2 + - - +
213B ASN* 3.1 20.3 + - - -
214B PHE 3.1 0.2 - - - -
215B PHE* 1.3 73.4 - - - +
217B LYS* 1.3 60.0 + - - +
218B ALA 2.9 5.4 - - - -
219B THR* 2.6 35.1 + - - +
220B PRO* 4.5 0.3 - - - +
239B TYR* 3.4 18.2 - - - +
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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