Contacts of the helix formed by residues 196 - 210 (chain B) in PDB entry 1T0R
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 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 2.6 47.6 + - - +
191B ASP 3.8 1.2 + - - -
192B VAL* 2.8 41.2 + - + +
195B ASN* 1.3 70.7 - - - +
197B PRO* 1.3 59.1 - - - +
198B ALA* 2.6 32.9 + - - +
199B TRP* 2.7 30.0 + - + -
200B GLN* 3.1 11.8 + - - -
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Residues in contact with PRO 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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123B ARG* 4.4 8.7 - - - +
195B ASN 3.4 8.9 - - - +
196B ASP* 1.3 88.0 - - - +
198B ALA* 1.3 60.1 + - - +
199B TRP 3.1 1.4 + - - -
200B GLN* 3.6 19.5 + - + +
302B ALA* 3.4 18.2 - - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.8 13.5 - - - +
124B PHE* 4.1 15.3 - - + -
196B ASP* 2.6 24.5 + - - +
197B PRO* 1.3 73.4 - - - +
199B TRP* 1.3 60.1 + - + +
202B PHE* 5.1 1.2 + - - -
299B ALA 4.9 0.5 - - - +
302B ALA* 3.3 21.7 - - - +
303B TYR* 3.2 30.9 + - - +
306B ALA* 4.0 12.6 - - + -
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Residues in contact with TRP 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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123B ARG* 2.8 23.4 + - - +
124B PHE* 3.7 9.1 - - - +
127B PRO* 3.6 21.7 - - + +
128B ALA* 4.0 11.9 - - - -
131B LEU* 3.9 27.8 - - + -
192B VAL* 3.5 30.9 - - + +
193B TRP* 3.6 44.4 - + + +
196B ASP* 2.7 16.8 + - + +
198B ALA* 1.3 83.8 - - + +
200B GLN* 1.3 58.8 + - - +
201B GLY 3.2 2.9 - - - -
202B PHE* 3.3 10.9 + + + +
203B ARG* 2.8 27.5 + - - +
234B LEU* 3.6 25.1 - - + -
303B TYR* 3.7 28.9 - + - -
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Residues in contact with GLN 200 (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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21A LYS* 5.7 0.9 - - - -
22A TYR* 2.6 31.3 + - + +
193B TRP 3.0 25.6 + - - -
194B GLU 3.0 19.5 + - - -
195B ASN* 4.7 2.9 - - - +
196B ASP 3.1 25.4 + - - +
197B PRO* 3.6 15.1 + - + +
199B TRP* 1.3 76.2 - - - +
201B GLY* 1.3 66.4 + - - +
203B ARG* 3.1 21.6 + - - -
204B GLU* 3.0 28.8 + - - +
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Residues in contact with GLY 201 (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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199B TRP 3.2 1.0 - - - -
200B GLN* 1.3 80.7 - - - +
202B PHE* 1.3 59.4 + - - +
204B GLU* 3.9 2.4 - - - +
205B LEU* 3.3 15.9 + - - +
295B LEU 4.2 3.1 - - - +
298B LYS* 3.5 35.9 + - - -
299B ALA* 3.4 16.0 - - - +
302B ALA* 4.0 13.0 - - - +
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Residues in contact with PHE 202 (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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131B LEU* 3.9 20.6 - - + -
193B TRP* 4.4 5.4 - - + -
198B ALA 5.1 1.3 - - - -
199B TRP* 3.3 10.6 + + + +
201B GLY* 1.3 75.0 - - - +
203B ARG* 1.3 64.9 + - - +
205B LEU* 3.4 9.7 + - + +
206B ILE* 3.1 28.5 + - - +
226B THR* 5.5 0.4 - - + -
229B ALA* 3.5 16.4 - - + -
230B VAL* 3.5 39.9 - - + -
233B ALA* 3.4 34.5 - - + -
234B LEU* 3.9 9.9 - - + -
299B ALA* 3.5 38.8 + - + +
300B ILE* 4.6 1.3 - - + -
303B TYR* 3.9 18.2 - + + -
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Residues in contact with ARG 203 (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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18A TRP* 3.9 6.3 - - - -
19A THR 2.4 30.7 + - - -
21A LYS* 3.2 36.2 - - - +
22A TYR* 4.0 4.3 - - + -
193B TRP* 3.4 48.6 - - + -
194B GLU* 2.6 44.8 + - - +
199B TRP 2.8 21.5 + - - +
200B GLN* 3.1 16.7 + - - +
202B PHE* 1.3 71.6 - - - +
204B GLU* 1.3 65.7 + - - +
206B ILE* 3.6 1.0 - - - +
207B GLU* 2.9 42.0 + - + +
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Residues in contact with GLU 204 (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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22A TYR* 3.3 45.8 - - + -
200B GLN* 3.0 18.0 + - - +
201B GLY 3.9 3.8 - - - +
203B ARG* 1.3 75.5 - - - +
205B LEU* 1.3 66.5 + - - +
207B GLU* 4.0 0.7 - - - +
208B LYS* 3.1 55.1 + - + +
295B LEU* 3.7 10.7 - - + +
298B LYS* 3.0 31.3 + - - +
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Residues in contact with LEU 205 (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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201B GLY 3.3 12.7 + - - +
202B PHE* 3.5 16.8 - - + +
204B GLU* 1.3 80.3 - - - +
206B ILE* 1.3 60.2 + - - +
208B LYS* 3.4 2.1 + - - +
209B ALA* 2.8 28.9 + - - +
225B VAL* 4.9 4.3 - - + -
226B THR* 3.3 45.5 - - + +
229B ALA* 4.7 0.9 - - + -
292B TRP* 3.9 25.2 - - + +
295B LEU* 3.9 28.2 - - + +
296B ALA* 4.1 22.0 - - + +
299B ALA* 4.2 10.3 - - + -
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Residues in contact with ILE 206 (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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18A TRP* 4.6 8.7 - - + -
131B LEU* 3.5 20.6 - - + -
134B ALA* 3.2 34.5 - - + -
135B LEU* 5.0 6.1 - - + +
193B TRP* 3.3 31.0 - - + -
202B PHE* 3.1 14.1 + - + +
203B ARG* 3.6 6.3 - - - +
205B LEU* 1.3 77.1 - - + +
207B GLU* 1.3 65.5 + - - +
209B ALA* 4.2 5.6 - - + -
210B LEU* 2.7 39.4 + - + +
222B ILE* 6.4 1.3 - - + -
226B THR* 3.7 25.6 - - + -
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Residues in contact with GLU 207 (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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18A TRP* 2.7 43.5 + - + +
20A PRO* 3.3 14.3 - - + +
21A LYS 2.8 21.8 + - - -
22A TYR* 2.9 20.8 + - + -
23A VAL* 3.7 26.2 + - + +
28A LEU* 4.3 2.4 - - + +
203B ARG* 2.9 38.1 + - + +
204B GLU 4.0 2.0 - - - +
206B ILE* 1.3 84.0 - - + +
208B LYS* 1.3 63.1 + - - +
210B LEU* 3.3 16.7 + - - +
211B ILE* 3.8 4.9 + - - +
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Residues in contact with LYS 208 (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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22A TYR* 3.9 18.6 - - + +
23A VAL* 3.9 17.9 - - + -
204B GLU* 3.1 45.9 + - + +
207B GLU* 1.3 76.9 - - - +
209B ALA* 1.3 62.6 + - - +
211B ILE* 3.1 22.1 + - + +
212B ALA* 3.8 2.9 + - - +
292B TRP* 3.5 22.1 - - + -
295B LEU* 4.0 21.3 - - + +
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Residues in contact with ALA 209 (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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205B LEU 2.8 18.7 + - - +
206B ILE* 3.9 7.9 - - + +
208B LYS* 1.3 76.5 - - - +
210B LEU* 1.3 61.4 + - - +
211B ILE 3.1 1.8 + - - -
212B ALA* 3.3 17.3 + - - +
218B ALA* 5.8 0.2 - - - +
221B ALA* 4.0 10.5 - - + -
222B ILE* 3.7 29.8 - - + +
226B THR* 4.2 11.9 - - - +
292B TRP* 3.4 20.8 - - + -
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Residues in contact with LEU 210 (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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18A TRP* 4.1 25.4 - - + -
28A LEU* 3.7 22.9 - - + -
116A ARG* 2.9 31.5 + - - +
134B ALA* 3.8 16.4 - - + +
137B MET* 4.3 11.4 - - + -
138B GLY* 3.6 37.0 - - - +
141B TYR* 5.6 2.5 - - + +
206B ILE* 2.7 28.8 + - + +
207B GLU* 3.5 7.4 - - - +
208B LYS 3.1 0.8 - - - -
209B ALA* 1.3 77.6 - - + +
211B ILE* 1.3 57.4 + - - +
212B ALA 3.5 0.7 - - - -
213B TRP* 3.5 9.4 - - - -
222B ILE* 5.0 4.7 - - + -
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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