Contacts of the helix formed by residues 184 - 199 (chain B) in PDB entry 2BTO
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B GLY* 3.0 18.8 + - - +
183B VAL* 1.3 77.5 - - - +
185B GLU* 1.3 63.2 + - - +
186B PRO* 3.3 4.5 - - - -
187B TYR* 3.1 28.4 + - - +
188B ASN* 3.3 8.8 + - - -
399B PHE* 3.8 36.6 - - + -
402B TRP* 4.5 12.6 - - + +
403B TYR* 2.9 23.9 + - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 3.4 26.6 - - - +
175B PRO* 3.1 32.8 - - + +
176B SER 4.4 8.8 + - - +
183B VAL* 3.4 23.6 - - + +
184B THR* 1.3 77.3 + - - +
186B PRO* 1.4 67.6 - - + +
188B ASN* 3.4 1.7 + - - +
189B THR* 2.9 30.0 + - - -
1433B GTP 3.4 23.5 + - - +
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Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO* 5.4 2.0 - - + -
183B VAL* 3.6 13.0 - - + +
184B THR 3.3 6.1 - - - -
185B GLU* 1.4 94.8 - - + +
187B TYR* 1.3 59.4 + - - +
189B THR* 3.7 5.6 + - - +
190B VAL* 3.3 29.8 + - - +
386B ILE* 4.1 9.7 - - + +
389B ASN* 3.8 19.1 - - + -
390B PHE* 3.5 29.5 - - - +
393B LEU* 3.8 16.8 - - + -
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Residues in contact with TYR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 3.1 18.7 + - - +
186B PRO* 1.3 79.3 - - - +
188B ASN* 1.3 62.3 + - - +
190B VAL* 3.5 1.9 + - - +
191B PHE* 3.0 48.7 + + + -
390B PHE* 3.5 27.8 - + + -
393B LEU* 3.2 51.2 + - + +
394B TRP* 3.3 38.6 + + + -
397B LYS 4.4 0.9 - - - -
398B ALA 3.8 7.6 + - - -
399B PHE* 4.3 19.2 + + + -
400B ALA* 4.8 3.4 + - - -
403B TYR* 3.7 30.7 - + - +
413B ILE* 4.6 1.1 - - + -
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Residues in contact with ASN 188 (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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103B GLY* 3.0 23.1 + - - -
105B PHE* 3.1 29.6 + - + +
143B ILE 3.2 8.0 - - - +
144B GLY 2.8 22.8 + - - +
145B GLY 3.2 24.0 + - - +
149B SER* 3.9 5.5 - - - +
184B THR* 3.3 14.1 + - - -
185B GLU 3.4 1.4 + - - +
187B TYR* 1.3 73.9 - - - +
189B THR* 1.3 66.9 + - - +
191B PHE* 3.4 1.4 + - - +
192B ALA* 3.0 26.3 + - - +
403B TYR* 3.1 18.3 + - - -
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.1 33.2 + - + +
144B GLY* 3.9 0.2 - - - -
174B LEU* 4.4 5.2 - - + -
175B PRO* 3.3 26.6 - - + +
185B GLU 2.9 20.8 + - - -
186B PRO 3.8 4.7 - - - -
188B ASN* 1.3 78.2 - - - +
190B VAL* 1.3 56.7 + - - +
192B ALA* 3.3 2.3 + - - +
193B LEU* 2.9 40.6 + - + +
383B LEU* 6.3 0.2 - - + -
386B ILE* 3.7 28.9 - - + -
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Residues in contact with VAL 190 (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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186B PRO 3.3 18.1 + - - +
187B TYR 3.9 0.4 - - - +
189B THR* 1.3 80.0 - - - +
191B PHE* 1.3 65.8 + - + +
193B LEU* 3.3 24.8 + - + +
194B ASN* 3.5 5.0 + - - +
386B ILE* 4.0 18.2 - - + -
387B CYS* 4.3 15.9 - - - -
390B PHE* 3.6 37.0 - - + -
416B LEU 3.8 26.4 - - - +
417B ARG* 4.2 9.9 - - - -
420B ALA* 4.3 6.5 - - + +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.7 52.0 - + + -
187B TYR* 3.0 39.8 + + + +
188B ASN 3.9 0.2 - - - +
189B THR 3.3 0.2 - - - -
190B VAL* 1.3 80.7 - - + +
192B ALA* 1.3 62.9 + - - +
194B ASN* 3.5 16.1 + - - +
195B THR* 4.2 3.5 + - - -
390B PHE* 3.6 19.3 - + - -
403B TYR* 4.1 20.6 - + + -
408B MET* 4.0 18.4 - - + -
413B ILE* 3.8 36.6 - - + -
416B LEU* 3.8 25.0 - - + +
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Residues in contact with ALA 192 (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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105B PHE* 3.7 7.9 - - - -
141B HIS* 5.9 0.9 - - + -
143B ILE* 3.8 30.1 - - + -
149B SER* 3.9 19.1 - - - +
153B ALA* 4.8 3.5 - - + -
188B ASN 3.0 17.5 + - - +
189B THR 3.7 3.6 - - - +
191B PHE* 1.3 75.0 - - - +
193B LEU* 1.3 64.7 + - - +
194B ASN 3.1 0.9 + - - -
195B THR* 3.2 7.4 + - - -
196B LEU* 3.1 25.2 + - + +
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Residues in contact with LEU 193 (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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143B ILE* 4.5 12.1 - - + -
174B LEU* 5.4 3.4 - - + -
189B THR* 2.9 31.0 + - + +
190B VAL* 3.3 23.0 + - + +
192B ALA* 1.3 76.0 - - - +
194B ASN* 1.3 51.8 + - - +
196B LEU* 3.1 7.2 + - + +
197B ARG* 2.7 37.2 + - - +
205B ILE* 6.0 0.2 - - + -
271B PHE* 3.7 32.0 - - + -
383B LEU* 3.9 29.8 - - + -
386B ILE* 5.1 4.0 - - + -
387B CYS* 5.6 3.1 - - - -
420B ALA* 4.5 19.1 - - + -
423B LEU* 5.2 6.3 - - + -
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Residues in contact with ASN 194 (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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157B GLU* 5.2 3.2 + - - -
190B VAL 3.5 5.5 + - - +
191B PHE 3.5 8.1 + - - +
192B ALA 3.1 0.6 + - - -
193B LEU* 1.3 76.5 - - - +
195B THR* 1.3 64.9 + - - +
197B ARG* 3.1 5.4 + - - +
198B ARG* 2.8 54.8 + - - +
416B LEU* 3.5 36.3 - - + +
419B SER* 2.5 35.2 + - - +
420B ALA* 5.8 3.1 - - - +
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Residues in contact with THR 195 (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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105B PHE* 5.6 0.9 - - - -
109B TYR* 4.7 1.4 - - - -
153B ALA* 3.4 44.1 - - - +
156B ILE* 4.3 12.3 - - + -
157B GLU* 2.7 33.8 + - + -
191B PHE 4.7 2.4 + - - -
192B ALA 3.2 9.2 + - - -
194B ASN* 1.3 82.2 + - - +
196B LEU* 1.3 58.0 + - + +
198B ARG* 4.4 2.2 - - - +
199B SER* 2.8 36.5 + - - +
200B ALA 3.4 4.0 + - - -
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Residues in contact with LEU 196 (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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141B HIS* 4.1 5.4 - - + -
143B ILE* 4.1 38.4 - - + -
153B ALA* 6.5 0.7 - - - -
156B ILE* 3.8 20.2 - - + -
170B SER* 3.2 34.8 - - - +
172B ALA* 4.3 1.6 - - + -
192B ALA* 3.1 20.0 + - + +
193B LEU* 3.1 13.0 + - + +
195B THR* 1.3 78.3 - - + +
197B ARG* 1.3 51.0 + - - +
200B ALA* 3.4 16.5 - - + +
203B CYS* 4.1 15.5 - - - +
270B HIS* 2.7 28.5 + - - -
271B PHE* 3.9 15.4 - - + -
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Residues in contact with ARG 197 (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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193B LEU 2.7 13.3 + - - +
194B ASN* 3.3 9.6 - - - +
196B LEU* 1.3 77.6 - - - +
198B ARG* 1.3 85.5 + - - +
267B PRO 4.7 2.6 - - - +
268B SER* 5.6 13.7 + - - +
270B HIS* 2.9 26.2 - - + +
271B PHE* 4.0 8.2 - - + -
419B SER* 3.4 28.7 + - - -
420B ALA* 5.5 0.4 - - - +
422B GLU* 3.3 45.4 + - - +
423B LEU* 3.7 42.3 - - + +
426B SER* 5.3 3.0 + - - -
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Residues in contact with ARG 198 (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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194B ASN* 2.8 46.8 + - - +
195B THR* 4.5 1.6 - - - +
197B ARG* 1.3 107.9 - - + +
199B SER* 1.3 67.0 + - - +
200B ALA 4.8 1.1 - - - -
270B HIS* 5.1 0.2 - - - -
419B SER* 5.3 1.8 + - - -
422B GLU* 5.0 3.4 + - - -
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Residues in contact with SER 199 (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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156B ILE* 4.0 15.2 - - - +
157B GLU* 4.0 22.5 + - - +
160B LYS* 3.4 32.1 - - - +
195B THR* 2.8 23.5 + - - +
198B ARG* 1.3 81.9 + - - +
200B ALA* 1.3 65.8 + - - +
201B ASP* 3.5 2.6 + - - +
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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
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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