Contacts of the helix formed by residues 190 - 206 (chain G) in PDB entry 5T0J
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 190 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G CYS* 5.0 0.4 - - - -
188G ASP 4.0 4.4 + - - +
189G TRP* 1.3 75.0 - - - +
191G PHE* 1.3 66.4 + - - +
192G GLU* 3.8 13.6 + - - +
193G GLN* 2.9 33.6 + - - +
194G THR* 3.0 13.4 + - - +
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Residues in contact with PHE 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G CYS* 5.0 7.5 - - + -
49G VAL* 5.1 1.1 - - + -
190G THR* 1.3 73.4 - - - +
192G GLU* 1.3 67.5 + - - +
194G THR* 2.8 25.0 + - - -
195G VAL* 3.2 26.9 - - + +
219G VAL* 3.6 36.1 - - + -
221G THR* 4.8 5.8 - - + -
228G ARG* 6.3 0.2 - - - -
230G LEU* 3.9 25.4 - - + -
234G GLU* 4.8 7.9 - - - -
238G HIS* 3.3 41.1 - + - -
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Residues in contact with GLU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR* 3.2 11.5 - - - +
191G PHE* 1.3 86.9 + - - +
193G GLN* 1.3 58.4 + - - +
195G VAL* 4.0 2.9 - - - +
196G GLU* 3.0 27.9 + - - +
238G HIS* 3.6 35.9 - - + +
241G ALA* 5.7 7.2 - - + -
242G LEU* 5.6 0.9 - - - +
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Residues in contact with GLN 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G LYS* 3.6 11.7 + - - +
185G LYS* 4.1 17.2 - - + +
188G ASP 5.8 0.2 - - - +
189G TRP* 4.1 28.9 - - + +
190G THR* 2.9 28.9 + - - +
192G GLU* 1.3 77.8 - - - +
194G THR* 1.3 58.7 + - - +
196G GLU* 3.3 10.0 + - - +
197G THR* 3.0 35.3 + - - +
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Residues in contact with THR 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLY* 4.7 2.9 - - - +
47G CYS* 3.6 24.4 - - - -
49G VAL* 3.3 32.0 - - + +
189G TRP* 3.6 30.3 - - + -
190G THR 3.0 12.3 + - - +
191G PHE* 2.8 26.7 + - - -
193G GLN* 1.3 76.9 - - - +
195G VAL* 1.3 60.6 + - - +
197G THR* 2.5 23.5 + - - -
198G ALA* 3.3 9.5 + - - +
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Residues in contact with VAL 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G VAL* 4.9 9.6 - - + -
191G PHE* 3.2 44.0 + - + +
192G GLU* 4.1 3.8 - - - +
194G THR* 1.3 76.2 + - - +
196G GLU* 1.3 66.6 + - - +
198G ALA* 3.0 16.6 + - + +
199G ILE* 3.2 30.0 - - + +
217G VAL* 5.5 6.1 - - + -
230G LEU* 4.6 13.0 - - + -
235G ILE* 5.7 4.5 - - + +
238G HIS* 3.9 28.3 - - + -
242G LEU* 4.6 3.8 - - + -
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Residues in contact with GLU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G LYS* 5.2 2.2 - - - +
192G GLU 3.0 19.6 + - - +
193G GLN* 3.5 15.9 - - - +
194G THR 3.3 0.2 - - - -
195G VAL* 1.3 77.1 - - - +
197G THR* 1.3 49.8 + - - +
199G ILE* 3.6 1.2 + - - +
200G THR* 2.7 44.4 + - + +
242G LEU* 3.8 28.4 - - + +
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Residues in contact with THR 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G VAL* 4.9 8.8 - - - +
179G LEU* 4.1 12.3 - - + +
182G LYS* 3.4 22.0 - - + +
185G LYS* 4.5 0.2 - - - +
189G TRP* 3.9 30.4 - - + -
193G GLN* 3.0 25.9 + - - +
194G THR* 2.5 28.6 + - - -
196G GLU* 1.3 75.2 - - - +
198G ALA* 1.3 60.1 + - - +
200G THR* 3.3 7.4 + - - -
201G CYS* 3.2 28.4 + - - +
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Residues in contact with ALA 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G VAL* 4.6 11.2 - - + -
51G VAL* 3.9 31.9 - - + +
194G THR 3.3 11.0 + - - +
195G VAL* 3.0 15.7 + - + +
197G THR* 1.3 77.2 - - - +
199G ILE* 1.3 66.7 + - + +
201G CYS* 3.2 22.2 - - - -
202G LEU* 3.3 11.3 + - - +
217G VAL* 5.3 4.9 - - + -
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Residues in contact with ILE 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G VAL* 3.2 35.1 + - + +
196G GLU 3.6 1.1 + - - +
198G ALA* 1.3 82.4 - - + +
200G THR* 1.3 54.0 - - + +
202G LEU* 3.1 8.8 + - + +
203G SER* 2.5 51.6 + - - +
209G ASP* 4.3 15.4 - - + +
215G ILE* 6.3 4.5 - - + -
217G VAL* 6.1 4.3 - - + -
235G ILE* 6.4 2.7 - - + -
239G LEU* 4.1 23.6 - - + -
242G LEU* 3.7 36.8 - - + -
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Residues in contact with THR 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G PHE* 3.6 16.5 - - - -
182G LYS* 3.8 18.2 - - - +
196G GLU* 2.7 26.6 + - + +
197G THR* 3.3 11.8 + - - -
199G ILE* 1.3 79.2 - - + +
201G CYS* 1.3 61.3 + - - +
203G SER* 3.3 10.0 + - - +
204G THR* 3.2 27.4 + - - +
242G LEU* 6.0 4.5 - - + -
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Residues in contact with CYS 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G VAL* 4.4 20.9 - - - -
42G VAL* 5.9 0.7 - - - -
51G VAL* 4.5 3.8 - - - -
175G SER* 3.6 22.6 + - - +
178G PHE* 3.7 6.5 - - + -
179G LEU* 3.7 20.2 - - + -
197G THR 3.2 15.4 + - - +
198G ALA* 3.2 19.7 - - - -
199G ILE 3.3 0.2 - - - -
200G THR* 1.3 82.1 + - - +
202G LEU* 1.3 65.7 + - - +
204G THR* 2.6 23.1 + - - +
205G VAL* 3.2 14.6 + - - +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G VAL* 4.2 21.8 - - + -
53G GLN* 4.8 10.3 - - + +
198G ALA 3.3 13.2 + - - +
199G ILE* 3.1 9.7 + - + +
201G CYS* 1.3 83.5 - - - +
203G SER* 1.3 53.1 + - - +
205G VAL* 4.4 4.9 - - - +
206G LEU* 2.6 62.8 + - + -
207G SER 3.3 3.5 + - - -
209G ASP* 3.3 33.2 - - - +
210G PHE* 5.4 3.8 - - + -
215G ILE* 4.4 19.5 - - + -
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Residues in contact with SER 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G ILE* 2.5 33.5 + - - +
200G THR* 3.3 11.2 + - - +
202G LEU* 1.3 72.7 - - - +
204G THR* 1.3 60.5 + - - +
207G SER* 3.1 35.9 + - - +
209G ASP* 3.1 25.3 + - - -
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Residues in contact with THR 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G GLU* 4.3 7.5 + - - +
175G SER* 4.8 0.2 - - - -
178G PHE* 3.5 43.9 - - + +
200G THR 3.2 12.9 + - - +
201G CYS* 2.6 25.1 + - - +
203G SER* 1.3 77.6 - - - +
205G VAL* 1.3 68.7 + - - +
206G LEU 5.1 0.3 - - - -
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Residues in contact with VAL 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G THR* 4.7 9.9 - - + +
171G LYS* 3.5 46.5 - - + +
174G GLU* 4.0 12.1 - - + -
175G SER* 3.6 33.9 - - - +
201G CYS 3.2 16.4 + - - +
202G LEU* 3.9 5.2 - - - +
204G THR* 1.3 84.7 + - - +
206G LEU* 1.3 78.3 + - + +
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Residues in contact with LEU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G THR* 5.6 4.3 - - - +
53G GLN* 5.0 15.5 - - + +
171G LYS* 5.4 7.2 - - + -
202G LEU* 2.6 44.6 + - + +
203G SER 4.0 0.2 - - - -
204G THR 5.1 0.2 - - - -
205G VAL* 1.3 93.1 - - + +
207G SER* 1.3 74.6 + - - +
208G ILE* 3.1 23.9 + - + +
210G PHE* 4.4 18.6 - - + -
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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
------------------------------------------------------------
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