Contacts of the helix formed by residues 209 - 219 (chain J) in PDB entry 5TJ4
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 209 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150J ASN* 3.6 15.0 - - - +
152J GLN* 3.7 18.2 - - + -
207J ASP 3.6 3.7 + - - +
208J THR* 1.3 75.1 - - - +
210J TYR* 1.3 65.3 + - - +
211J SER* 2.9 23.7 + - - -
212J ILE* 3.1 24.5 + - - +
213J ALA* 3.1 22.7 + - - +
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Residues in contact with TYR 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASP* 4.5 14.4 - - + +
150J ASN* 3.4 23.6 - - + +
156J PHE* 4.1 21.1 - + - -
209J ASP* 1.3 75.4 + - - +
211J SER* 1.3 62.4 + - - +
213J ALA* 4.2 2.8 - - - +
214J GLU* 3.1 56.6 + - + +
227J ASN* 3.3 35.0 + - - -
230J TRP* 3.2 31.6 + + - -
231J ALA* 4.0 5.4 - - - +
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Residues in contact with SER 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209J ASP* 2.9 15.5 + - - -
210J TYR* 1.3 77.8 - - - +
212J ILE* 1.3 62.2 + - - +
214J GLU* 4.0 4.9 - - - +
215J ALA* 2.9 31.7 + - - +
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Residues in contact with ILE 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J MET* 3.6 24.5 - - + -
207J ASP* 3.7 16.4 - - + +
208J THR* 3.8 6.1 - - + -
209J ASP* 3.1 36.0 + - - +
211J SER* 1.3 77.7 - - - +
213J ALA* 1.3 57.7 + - - +
215J ALA* 3.4 5.4 + - - +
216J ALA* 2.8 29.7 + - + +
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Residues in contact with ALA 213 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J MET* 3.6 33.5 - - - +
149J PHE* 3.6 20.0 - - - +
150J ASN 4.1 1.3 - - - +
208J THR* 4.1 5.1 - - + +
209J ASP 3.1 14.7 + - - +
210J TYR* 4.2 2.7 - - + +
212J ILE* 1.3 77.0 - - - +
214J GLU* 1.3 65.7 + - - +
216J ALA* 3.4 2.5 + - - +
217J PHE* 3.1 24.6 + - - +
222J THR* 4.8 1.0 - - - +
225J THR* 4.2 7.0 + - - +
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Residues in contact with GLU 214 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J TYR* 3.1 51.0 + - + +
211J SER* 4.0 4.8 - - - +
213J ALA* 1.3 76.5 - - - +
215J ALA* 1.3 63.3 + - - +
217J PHE* 3.4 2.2 + - - -
218J ASN* 3.0 43.9 + - - +
225J THR* 5.5 3.1 - - - -
227J ASN* 5.2 9.6 - - - +
231J ALA* 4.2 12.5 - - + +
234J ASN* 3.6 32.1 - - - +
235J ILE* 5.8 1.6 - - + -
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Residues in contact with ALA 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211J SER 2.9 19.7 + - - +
212J ILE* 3.5 7.0 - - - +
214J GLU* 1.3 76.9 - - - +
216J ALA* 1.3 57.3 + - - +
218J ASN* 3.3 4.0 + - - +
219J LYS* 2.9 33.2 + - - +
221J GLU* 5.5 0.2 - - - -
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Residues in contact with ALA 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J MET* 3.6 31.9 - - + -
212J ILE* 2.8 21.5 + - + +
213J ALA 3.9 2.9 - - - +
214J GLU 3.4 0.2 - - - -
215J ALA* 1.3 73.3 - - - +
217J PHE* 1.3 58.8 + - - +
219J LYS 3.7 0.2 + - - -
220J GLY 3.3 2.6 + - - -
221J GLU* 2.8 50.9 + - + +
222J THR* 3.4 6.4 + - + -
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Residues in contact with PHE 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J ILE* 3.7 32.3 - - + -
117J TYR 3.7 2.7 - - - -
118J ASN* 3.7 22.7 + - + -
213J ALA 3.1 17.2 + - - +
214J GLU* 3.9 3.4 - - - +
216J ALA* 1.3 75.8 - - - +
218J ASN* 1.3 70.4 + - - +
220J GLY* 3.1 15.6 + - - -
222J THR* 3.6 23.6 - - + +
223J ALA 3.6 21.3 - - - -
224J MET* 3.7 23.3 - - - -
225J THR* 3.9 16.6 - - + -
235J ILE* 4.3 21.5 - - + -
240J VAL* 3.6 15.5 - - + +
242J TYR* 4.3 4.9 - - + -
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Residues in contact with ASN 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J GLU* 3.0 30.3 + - - +
215J ALA* 4.0 4.0 - - - +
217J PHE* 1.3 80.2 - - - +
219J LYS* 1.3 58.1 + - - +
220J GLY 3.2 3.2 + - - -
234J ASN* 3.2 40.6 + - - +
235J ILE* 3.3 23.3 - - - +
238J SER* 3.9 21.4 - - - +
239J ALA* 4.9 2.8 + - - +
240J VAL* 3.6 17.5 - - - +
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Residues in contact with LYS 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J LYS* 5.7 0.5 + - - -
215J ALA 2.9 17.3 + - - +
216J ALA 4.1 0.7 - - - +
217J PHE 3.3 0.2 - - - -
218J ASN* 1.3 75.6 - - - +
220J GLY* 1.3 61.1 + - - +
221J GLU* 3.3 30.9 + - - +
240J VAL* 5.2 0.2 - - - -
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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