Contacts of the helix formed by residues 221 - 236 (chain B) in PDB entry 1TD2
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 GLY 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ALA* 4.6 0.9 - - - -
21B ALA* 4.4 9.6 - - - -
220B VAL* 1.3 80.1 - - - +
222B VAL* 1.3 67.4 + - - +
224B ASP* 3.0 24.1 + - - +
225B VAL* 3.0 17.7 + - - +
266B LEU* 3.8 7.4 - - - -
288B SO4 3.0 19.2 + - - -
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Residues in contact with VAL 222 (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 PHE* 4.9 10.5 - - + -
209B ARG* 3.9 16.4 - - - +
218B GLN* 5.6 6.1 - - + +
219B PRO* 3.8 14.1 - - + +
220B VAL 3.6 0.6 - - - -
221B GLY* 1.3 75.9 - - - +
223B GLY* 1.3 55.1 + - - +
225B VAL* 3.4 4.3 + - - +
226B THR* 2.7 39.9 + - - +
251B VAL* 3.5 25.6 - - + +
255B MET* 3.7 32.1 - - + -
266B LEU* 3.9 12.5 - - + +
288B SO4 3.1 6.5 + - - +
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Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 3.6 4.5 - - - +
182B LYS* 3.9 26.0 - - - +
222B VAL* 1.3 74.5 - - - +
224B ASP* 1.3 63.9 + - - -
226B THR* 3.7 5.9 - - - -
227B SER* 3.0 29.6 + - - -
288B SO4 2.6 19.6 + - - -
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 3.8 15.1 + - - +
17B ALA 3.8 0.2 - - - -
18B GLY* 2.7 46.3 + - - +
21B ALA* 4.7 1.3 - - + -
22B ALA* 3.6 12.3 - - + +
83B TYR 5.2 0.2 + - - -
112B ASP* 3.9 13.0 - - - +
114B VAL* 4.3 4.7 - - - +
221B GLY* 3.0 15.6 + - - +
223B GLY* 1.3 73.2 - - - +
225B VAL* 1.3 60.9 + - - +
227B SER* 3.5 2.4 + - - -
228B GLY 2.9 23.7 + - - -
288B SO4 3.3 1.6 + - - -
289B PXL 2.8 31.9 + - - -
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Residues in contact with VAL 225 (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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21B ALA* 3.9 22.9 - - + +
22B ALA* 4.6 7.2 - - - +
25B PRO* 4.3 9.6 - - + -
26B MET* 5.6 0.2 - - - +
221B GLY 3.0 14.5 + - - +
222B VAL* 3.6 6.7 - - - +
224B ASP* 1.3 75.9 - - - +
226B THR* 1.3 58.8 + - - +
228B GLY* 3.1 1.4 + - - -
229B LEU* 2.8 54.6 + - + +
251B VAL* 3.9 8.7 - - + -
254B ILE* 3.9 20.2 - - + -
266B LEU* 3.8 20.0 - - + -
268B VAL* 4.4 5.2 - - + -
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Residues in contact with THR 226 (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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180B LEU* 4.2 15.5 - - + -
182B LYS* 4.6 4.5 - - + +
194B PHE* 5.8 1.4 - - - -
196B MET* 3.8 31.6 - - + -
222B VAL* 2.7 28.6 + - - +
223B GLY* 3.7 10.0 - - - -
224B ASP 3.3 0.2 - - - -
225B VAL* 1.3 77.1 - - - +
227B SER* 1.3 56.8 + - - +
230B LEU* 3.0 28.6 + - + +
247B VAL* 3.7 24.2 - - + +
251B VAL* 3.5 15.0 - - - +
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Residues in contact with SER 227 (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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80B LEU* 4.1 8.5 - - - +
110B PHE* 3.7 24.0 - - - -
112B ASP* 2.9 30.0 + - - -
144B ALA* 3.9 13.0 - - - +
180B LEU* 4.9 2.7 - - - +
182B LYS* 4.3 3.8 - - - +
223B GLY 3.0 14.3 + - - -
224B ASP* 3.8 4.3 - - - -
226B THR* 1.3 73.2 - - - +
228B GLY* 1.3 66.3 + - - +
230B LEU* 3.4 3.9 + - - +
231B LEU* 3.1 24.9 + - - +
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Residues in contact with GLY 228 (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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9B GLN* 6.1 0.2 - - - -
22B ALA* 4.8 1.3 - - - -
26B MET* 3.4 34.6 - - - +
80B LEU* 4.4 8.0 - - - +
224B ASP 2.9 16.0 + - - -
225B VAL 3.6 2.2 - - - -
227B SER* 1.3 78.7 - - - +
229B LEU* 1.3 55.9 + - - +
231B LEU* 3.4 1.0 + - - +
232B VAL* 3.1 31.4 + - - +
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Residues in contact with LEU 229 (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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22B ALA 5.3 0.2 - - - +
25B PRO* 3.7 39.5 - - + +
26B MET* 3.8 10.5 - - + +
29B LEU* 4.1 20.6 - - + +
225B VAL* 2.8 37.8 + - + +
226B THR 4.1 0.9 - - - +
228B GLY* 1.3 72.3 - - - +
230B LEU* 1.3 61.8 + - - +
232B VAL* 3.3 4.4 + - - +
233B LYS* 2.9 34.0 + - - +
246B HIS* 6.2 0.7 - - + -
247B VAL* 3.6 18.6 - - + +
250B ALA* 4.2 24.0 - - + -
251B VAL* 4.6 6.5 - - + +
254B ILE* 5.4 1.1 - - + -
275B ILE* 4.5 5.2 - - + -
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Residues in contact with LEU 230 (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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110B PHE* 4.4 14.4 - - + -
142B ILE* 5.2 3.4 - - + -
180B LEU* 3.5 39.0 - - + -
196B MET* 6.6 0.2 - - + -
198B LEU* 4.1 21.5 - - + -
226B THR* 3.0 20.2 + - + +
227B SER 3.7 3.8 - - - +
228B GLY 3.3 0.2 - - - -
229B LEU* 1.3 73.2 - - - +
231B LEU* 1.3 67.1 + - - +
233B LYS* 3.1 3.1 + - - +
234B LEU* 3.0 41.2 + - + +
243B ALA* 3.8 34.8 - - + +
244B LEU* 4.5 5.8 - - + +
247B VAL* 3.5 11.2 - - + +
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Residues in contact with LEU 231 (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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5B ILE* 3.8 30.1 - - + -
26B MET* 5.2 0.4 - - + -
78B ALA* 3.8 15.3 - - + -
80B LEU* 3.8 11.7 - - + -
108B LYS* 5.4 2.5 - - + -
110B PHE* 3.7 44.1 - - + -
142B ILE* 4.4 14.4 - - + -
227B SER 3.1 14.2 + - - +
228B GLY 3.7 4.7 - - - +
230B LEU* 1.3 76.3 - - - +
232B VAL* 1.3 63.5 + - - +
234B LEU* 3.9 5.3 - - + +
235B LEU* 3.0 55.0 + - + +
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Residues in contact with VAL 232 (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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3B LYS* 6.2 0.7 - - + -
5B ILE* 3.6 25.4 - - + -
26B MET* 3.7 20.4 - - + -
29B LEU* 4.1 20.2 - - + -
31B ALA* 3.8 25.8 - - + -
228B GLY 3.1 16.4 + - - +
229B LEU* 3.5 9.9 - - - +
230B LEU 3.1 0.2 - - - -
231B LEU* 1.3 78.1 - - - +
233B LYS* 1.3 63.8 + - - +
235B LEU* 3.3 2.5 + - - +
236B GLN* 3.0 45.5 + - + +
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Residues in contact with LYS 233 (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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29B LEU* 4.5 11.6 - - + +
229B LEU 2.9 22.6 + - - +
230B LEU* 3.7 4.3 - - - +
232B VAL* 1.3 75.6 - - - +
234B LEU* 1.3 62.6 + - - +
236B GLN* 3.1 22.9 + - - +
237B GLY 3.3 0.2 + - - -
238B ALA* 3.0 38.1 + - + +
242B GLU* 4.9 3.2 + - - +
243B ALA* 3.8 21.3 - - + +
246B HIS* 2.8 53.4 + - + +
247B VAL* 4.1 10.1 - - + -
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Residues in contact with LEU 234 (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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110B PHE* 5.7 0.2 - - + -
142B ILE* 4.5 16.2 - - + -
178B ILE* 4.4 23.8 - - + -
198B LEU* 5.4 1.1 - - + -
230B LEU* 3.0 41.2 + - + +
231B LEU* 3.9 7.0 - - + +
233B LYS* 1.3 76.5 - - - +
235B LEU* 1.3 60.6 + - + +
237B GLY* 2.9 20.1 + - - -
238B ALA 3.8 18.0 + - - +
239B THR 4.7 1.3 - - - +
240B LEU* 4.4 20.9 - - + +
243B ALA* 4.1 16.6 - - + -
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Residues in contact with LEU 235 (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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3B LYS* 3.0 40.4 + - + +
5B ILE* 3.8 19.1 - - + -
77B ASP* 4.3 27.4 - - + +
78B ALA* 3.8 15.7 - - + -
108B LYS* 5.0 11.7 - - + -
231B LEU* 3.0 46.7 + - + +
232B VAL* 3.7 3.8 - - - +
234B LEU* 1.3 76.3 - - + +
236B GLN* 1.3 59.1 + - - +
237B GLY 3.2 1.3 + - - -
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Residues in contact with GLN 236 (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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3B LYS* 4.6 19.8 - - + +
29B LEU* 3.2 27.3 + - - +
30B GLY* 4.0 15.0 + - - -
31B ALA* 4.3 3.0 - - - +
232B VAL* 3.0 37.6 + - + +
233B LYS* 3.5 19.3 - - - +
234B LEU 3.1 0.8 - - - -
235B LEU* 1.3 79.7 - - - +
237B GLY* 1.3 58.5 + - - +
238B ALA* 3.5 0.9 - - + +
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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