Contacts of the helix formed by residues 194 - 206 (chain O) in PDB entry 5A0Q
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 194 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42O VAL* 4.0 16.8 - - + +
44O GLY* 3.6 29.6 - - - -
45O LYS 5.2 0.2 - - - +
47O CYS* 3.1 28.2 - - - -
49O VAL* 3.2 16.1 - - - +
193O GLN* 1.3 76.1 - - + +
195O VAL* 1.4 68.9 + - - +
197O THR* 3.1 19.6 + - - -
198O ALA* 3.1 14.6 + - - +
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Residues in contact with VAL 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O CYS* 5.7 2.0 - - - -
49O VAL* 3.6 25.8 - - + -
193O GLN 5.3 3.8 - - - +
194O THR* 1.4 77.1 - - - +
196O GLU* 1.3 57.4 + - - +
198O ALA* 3.4 2.8 + - - +
199O ILE* 2.9 49.9 + - + +
217O VAL* 4.9 3.4 - - + -
219O VAL* 4.3 14.8 - - + -
230O LEU* 3.8 24.5 - - + -
235O ILE* 6.2 1.3 - - - +
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Residues in contact with GLU 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O LYS* 6.0 1.9 - - - +
193O GLN* 3.4 44.2 + - - +
195O VAL* 1.3 77.5 - - - +
197O THR* 1.4 65.8 + - - +
199O ILE* 4.6 3.8 - - - +
200O THR* 2.8 56.3 + - + +
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Residues in contact with THR 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O VAL* 4.1 19.1 - - + +
178O PHE* 4.7 3.5 - - + -
179O LEU* 5.0 10.1 - - + -
182O LYS* 4.1 31.4 - - + -
193O GLN 2.7 22.8 + - - -
194O THR* 3.1 11.6 + - - -
196O GLU* 1.4 82.3 + - - +
198O ALA* 1.4 58.6 + - - +
200O THR* 3.5 3.0 + - - -
201O CYS* 3.0 30.4 + - + +
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Residues in contact with ALA 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O VAL* 4.5 5.8 - - + +
42O VAL* 3.9 17.5 - - + +
49O VAL* 4.1 13.7 - - + -
51O VAL* 3.6 23.6 - - + -
194O THR 3.1 10.2 + - - +
195O VAL 3.4 6.9 + - - +
197O THR* 1.4 79.0 - - - +
199O ILE* 1.4 57.7 + - + +
201O CYS* 3.2 6.2 + - - +
202O LEU* 2.9 35.8 + - - +
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Residues in contact with ILE 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O VAL* 4.8 7.4 - - + -
195O VAL* 2.9 38.5 + - + +
196O GLU* 4.4 2.7 - - - +
198O ALA* 1.4 71.8 - - + +
200O THR* 1.4 61.9 + - + +
202O LEU* 3.3 7.3 + - - +
203O SER* 2.9 28.2 + - - -
210O PHE* 4.2 5.4 - - + -
215O ILE* 4.3 26.7 - - + -
217O VAL* 4.4 24.7 - - + -
230O LEU* 5.2 0.4 - - + -
235O ILE* 4.7 19.3 - - + -
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Residues in contact with THR 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O PHE* 3.9 15.0 - - - -
196O GLU* 2.8 47.8 + - + +
197O THR* 3.5 4.5 + - - -
199O ILE* 1.4 73.5 - - + +
201O CYS* 1.4 60.5 + - - +
203O SER* 4.2 6.7 - - - -
204O THR* 2.9 39.5 + - - -
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Residues in contact with CYS 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O VAL* 4.3 11.7 - - + -
175O SER* 3.4 42.2 - - - -
178O PHE* 3.6 18.4 - - + -
179O LEU* 4.2 15.9 - - + -
197O THR* 3.0 22.3 + - + +
198O ALA* 3.2 8.2 + - - +
200O THR* 1.4 75.4 + - - +
202O LEU* 1.3 62.0 + - - +
205O VAL* 2.9 34.9 + - - +
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Residues in contact with LEU 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR* 3.6 22.0 - - + +
40O VAL* 3.4 28.9 - - + -
51O VAL* 3.4 38.1 - - + -
52O THR 4.3 10.8 - - - +
198O ALA 2.9 29.1 + - - +
199O ILE* 3.3 3.1 + - - +
201O CYS* 1.3 77.0 - - - +
203O SER* 1.4 58.4 + - - +
205O VAL* 4.7 2.5 - - - -
206O LEU* 3.1 42.2 + - + +
210O PHE* 3.4 20.9 - - + -
215O ILE* 4.1 11.9 - - + -
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Residues in contact with SER 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199O ILE* 2.9 19.8 + - - -
200O THR* 3.8 8.3 - - - -
201O CYS 3.2 0.4 - - - -
202O LEU* 1.4 76.6 - - - +
204O THR* 1.3 58.5 + - - +
207O SER* 3.1 6.6 + - - -
208O ILE 3.1 46.2 + - - +
209O ASP* 4.3 12.6 + - - -
210O PHE* 3.5 8.7 - - - -
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Residues in contact with THR 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O PHE* 4.5 24.0 - - + -
200O THR* 2.9 21.8 + - - -
201O CYS 4.2 1.6 - - - -
203O SER* 1.3 76.7 - - - +
205O VAL* 1.3 65.7 + - + +
207O SER* 3.6 13.6 + - - +
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Residues in contact with VAL 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR* 5.4 2.2 - - + -
171O LYS* 3.3 38.8 - - + +
174O GLU* 3.7 15.9 - - + +
175O SER* 3.3 44.2 - - - +
178O PHE* 4.3 10.5 - - + -
201O CYS* 2.9 27.8 + - - +
202O LEU* 4.5 2.0 - - - +
204O THR* 1.3 79.9 - - + +
206O LEU* 1.4 60.5 + - + +
207O SER* 3.1 7.6 + - - -
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Residues in contact with LEU 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O GLY 6.0 0.7 - - - +
38O THR* 3.7 31.4 - - + +
170O VAL* 5.6 1.6 - - + -
171O LYS* 3.5 32.3 - - + +
202O LEU* 3.1 33.5 + - + +
205O VAL* 1.4 74.4 - - + +
207O SER* 1.4 68.1 + - - +
208O ILE* 3.3 17.3 + - + +
210O PHE* 4.0 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