Contacts of the helix formed by residues 183 - 197 (chain J) in PDB entry 5T0G
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 THR 183 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG* 4.1 4.7 - - - +
181J ILE* 3.1 4.6 - - - +
182J GLU* 1.3 81.4 - - - +
184J ASP* 1.3 55.8 + - - +
185J ASP* 3.3 6.5 - - - -
186J LEU* 3.0 21.0 + - - +
187J THR* 2.7 33.4 + - - -
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Residues in contact with ASP 184 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J GLY* 6.1 0.2 - - - -
38J ARG* 5.3 4.6 - - - +
39J ASP* 3.5 25.6 + - - +
40J ILE* 3.3 42.1 + - + +
183J THR* 1.3 70.7 - - - +
185J ASP* 1.3 67.2 + - - +
187J THR* 2.9 19.0 + - - -
188J ILE* 3.1 23.3 + - + +
212J ARG* 5.6 1.9 - - - +
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Residues in contact with ASP 185 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J THR* 3.3 5.8 - - - -
184J ASP* 1.3 77.7 - - - +
186J LEU* 1.3 60.4 + - - +
188J ILE* 3.9 10.6 + - - +
189J LYS* 3.7 17.2 + - - +
228J TYR* 5.6 5.0 - - - -
231J GLU* 5.3 1.2 - - - +
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Residues in contact with LEU 186 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J GLU* 3.9 37.0 - - + +
180J ALA* 4.8 7.4 - - + -
181J ILE* 4.7 3.4 - - + -
182J GLU* 4.8 2.9 - - + +
183J THR* 3.0 22.2 + - - +
185J ASP* 1.3 77.0 - - - +
187J THR* 1.3 61.6 + - - +
189J LYS* 3.5 12.0 + - + -
190J LEU* 2.8 30.5 + - + +
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Residues in contact with THR 187 (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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35J VAL* 5.2 10.1 - - - -
40J ILE* 4.9 10.3 - - - -
42J VAL* 5.5 4.5 - - - -
181J ILE* 3.6 19.9 - - - +
183J THR 2.7 17.3 + - - -
184J ASP* 2.9 16.8 + - - -
186J LEU* 1.3 73.1 - - - +
188J ILE* 1.3 63.2 + - - +
190J LEU* 3.0 8.7 + - - +
191J VAL* 2.9 27.4 + - - +
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Residues in contact with ILE 188 (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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184J ASP* 3.1 18.3 + - + +
185J ASP* 4.1 9.0 - - - +
187J THR* 1.3 75.7 - - - +
189J LYS* 1.3 59.1 + - - +
191J VAL* 2.9 26.4 + - + +
192J ILE* 3.0 10.4 + - - +
210J VAL* 4.2 32.5 - - + -
220J LEU* 4.9 14.6 - - + -
228J TYR* 3.5 44.9 - - + +
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Residues in contact with LYS 189 (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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185J ASP 3.7 10.3 + - - +
186J LEU* 3.5 17.4 + - + +
188J ILE* 1.3 78.7 - - - +
190J LEU* 1.3 56.8 + - - +
192J ILE* 3.5 11.3 + - + +
193J LYS* 2.9 27.5 + - - +
228J TYR* 5.1 6.6 - - + +
231J GLU* 3.5 27.8 - - + +
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Residues in contact with LEU 190 (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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35J VAL* 4.6 17.0 - - + -
171J PHE* 5.5 4.7 - - + -
175J ASN* 3.1 45.8 - - + +
180J ALA* 4.2 15.3 - - + -
181J ILE* 3.9 25.4 - - + +
186J LEU* 2.8 19.8 + - + +
187J THR* 3.0 13.6 + - - +
189J LYS* 1.3 76.9 - - - +
191J VAL* 1.3 58.0 + - - +
193J LYS* 3.3 8.5 + - + -
194J ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 191 (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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33J VAL* 4.4 18.4 - - + -
34J GLY* 5.7 1.3 - - - +
35J VAL* 4.2 16.6 - - + +
42J VAL* 3.7 27.1 - - + +
43J LEU 3.6 20.6 - - - +
44J GLY* 4.6 2.2 - - - -
187J THR 2.9 13.9 + - - +
188J ILE* 2.9 8.9 + - + +
190J LEU* 1.3 75.4 - - - +
192J ILE* 1.3 59.9 + - - +
194J ALA* 3.1 6.0 + - + +
195J LEU* 2.9 31.2 + - + +
206J ILE* 6.0 4.0 - - + -
208J LEU* 4.8 8.1 - - + -
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Residues in contact with ILE 192 (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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188J ILE 3.0 11.3 + - - +
189J LYS* 3.8 12.3 - - - +
191J VAL* 1.3 76.9 - - - +
193J LYS* 1.3 58.1 + - - +
195J LEU* 3.7 6.1 - - - +
196J LEU* 2.9 29.0 + - - +
206J ILE* 5.9 4.9 - - + -
225J ILE 5.8 0.9 - - - +
228J TYR* 4.7 23.3 - - + +
229J VAL* 5.3 3.1 - - + +
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Residues in contact with LYS 193 (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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171J PHE* 3.3 26.5 - - + -
189J LYS 2.9 19.1 + - - +
190J LEU* 3.7 11.7 - - + +
191J VAL 3.2 0.4 - - - -
192J ILE* 1.3 75.7 - - - +
194J ALA* 1.3 61.4 + - - +
196J LEU* 3.6 16.7 + - - +
197J GLU* 3.9 4.2 + - - +
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Residues in contact with ALA 194 (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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33J VAL* 5.3 11.7 - - + -
35J VAL* 6.2 3.1 - - + -
168J VAL* 4.5 13.0 - - + +
171J PHE* 3.7 19.4 - - + +
172J LEU* 4.8 8.7 - - + -
175J ASN* 4.7 10.5 - - - +
190J LEU 2.9 16.3 + - - +
191J VAL* 3.1 8.0 + - + +
193J LYS* 1.3 77.9 - - - +
195J LEU* 1.3 59.9 + - - +
196J LEU 3.5 0.5 + - - -
197J GLU* 3.6 7.1 + - - +
198J VAL* 3.5 17.1 + - - +
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Residues in contact with LEU 195 (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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33J VAL* 5.2 11.1 - - + +
191J VAL* 2.9 17.1 + - + +
192J ILE* 4.0 4.5 - - - +
194J ALA* 1.3 75.5 - - - +
196J LEU* 1.3 53.2 + - - +
197J GLU 3.3 0.2 - - - -
198J VAL* 2.8 20.6 - - + +
201J SER* 2.3 31.7 + - - -
206J ILE* 3.5 36.4 - - + +
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Residues in contact with LEU 196 (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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192J ILE 2.9 16.6 + - - +
193J LYS* 3.7 12.3 - - - +
194J ALA 3.2 0.6 - - - -
195J LEU* 1.3 73.3 - - - +
197J GLU* 1.3 55.3 + - - +
199J VAL 5.2 0.3 - - - +
201J SER* 2.7 29.6 + - - -
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Residues in contact with GLU 197 (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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167J SER* 5.0 9.7 + - - +
168J VAL* 4.7 9.7 - - - +
171J PHE* 4.5 27.4 - - + -
193J LYS 3.9 4.5 + - - +
194J ALA 3.6 9.3 + - - +
195J LEU 3.3 0.2 - - - -
196J LEU* 1.3 76.8 - - - +
198J VAL* 1.3 58.0 + - - +
199J VAL 4.2 2.4 + - - +
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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