Contacts of the helix formed by residues 208 - 216 (chain B) in PDB entry 5TWV
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 GLU 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B TRP* 4.7 12.1 - - + +
66B LEU* 6.1 1.3 - - - -
205B LYS 5.2 2.5 - - - +
206B PRO 3.4 7.0 + - - +
207B PRO* 1.3 75.2 - - - +
209B ASP* 1.3 65.1 + - - +
210B LEU* 3.3 6.1 - - + +
211B GLN* 3.7 21.8 + - + +
212B ASP* 3.6 17.2 + - - +
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Residues in contact with ASP 209 (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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207B PRO 4.3 0.6 + - - -
208B GLU* 1.3 72.1 - - - +
210B LEU* 1.3 58.8 + - - +
212B ASP* 3.3 9.3 + - - +
213B LEU* 3.0 24.8 + - - +
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Residues in contact with LEU 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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65B TRP* 6.4 2.7 - - + -
208B GLU* 3.3 6.7 - - + +
209B ASP* 1.3 77.6 - - - +
211B GLN* 1.3 58.5 + - - +
213B LEU* 3.1 10.6 + - - +
214B GLY* 2.9 24.8 + - - -
222B VAL* 5.0 15.9 - - + -
224B LEU* 5.6 9.4 - - + -
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Residues in contact with GLN 211 (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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48A ASN* 6.2 4.0 - - - -
63B SER* 5.6 8.1 - - - +
64B THR* 6.2 1.3 - - - -
65B TRP* 5.3 16.7 - - + +
208B GLU* 3.7 21.6 + - + +
209B ASP 3.4 0.2 - - - -
210B LEU* 1.3 78.6 - - - +
212B ASP* 1.3 53.7 + - - +
214B GLY* 2.9 3.8 + - - -
215B VAL* 2.6 38.6 + - - +
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Residues in contact with ASP 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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208B GLU 3.6 10.1 + - - +
209B ASP* 3.3 10.9 + - - +
210B LEU 3.2 0.4 - - - -
211B GLN* 1.3 75.3 - - - +
213B LEU* 1.3 68.2 + - - +
215B VAL* 3.6 11.9 + - - +
216B ARG* 3.9 11.1 + - - +
331C SER* 5.9 8.3 - - - -
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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 ASP 3.0 13.3 + - - +
210B LEU* 3.1 13.2 + - - +
212B ASP* 1.3 80.1 - - - +
214B GLY* 1.3 58.6 + - - +
216B ARG* 3.9 4.2 + - - +
217B PHE* 3.2 20.8 + - - +
220B PRO 6.0 0.4 - - - +
260B LEU* 4.9 22.2 - - + +
263B TYR* 6.0 4.9 - - + -
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Residues in contact with GLY 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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63B SER* 4.9 10.4 - - - -
210B LEU 2.9 13.2 + - - -
211B GLN* 2.9 5.5 + - - -
213B LEU* 1.3 74.0 - - - +
215B VAL* 1.3 58.8 + - - +
216B ARG 3.2 2.0 - - - -
217B PHE* 2.9 34.4 + - - +
220B PRO* 4.5 20.4 + - - +
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Residues in contact with VAL 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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47A LYS* 4.2 15.1 - - + +
48A ASN* 4.4 19.1 - - + +
63B SER* 5.0 8.5 - - - -
211B GLN 2.6 19.0 + - - +
212B ASP* 4.1 9.0 - - - +
213B LEU 3.6 0.4 - - - -
214B GLY* 1.3 73.4 - - - +
216B ARG* 1.3 58.6 + - - +
217B PHE 3.6 1.7 + - - +
329C ASP* 3.3 28.2 - - - +
331C SER* 5.2 2.5 - - - +
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Residues in contact with ARG 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 ASP 3.9 10.0 + - - +
213B LEU 4.1 3.6 - - - +
214B GLY 3.2 0.2 - - - -
215B VAL* 1.3 77.4 - - + +
217B PHE* 1.3 57.9 + - - +
218B LEU 3.9 1.6 + - - -
258B ARG* 5.0 1.7 - - - +
329C ASP* 5.7 3.8 - - - +
332C LYS* 5.8 9.0 - - - +
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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