Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 1TUB
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 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 5.1 6.1 - - - +
223A THR* 2.1 32.0 + - - +
224A TYR* 1.3 76.8 - - - +
226A ASN* 1.3 64.6 + - - +
228A ASN* 3.4 14.0 + - - +
229A ARG* 3.9 19.9 + - - +
247B GLN* 2.2 48.0 + - - +
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A CYS* 5.9 0.2 - - - -
219A ILE* 6.4 0.2 - - - +
222A PRO* 4.1 6.8 - - + +
223A THR* 2.6 48.4 + - - +
225A THR* 1.3 85.4 + - - +
227A LEU* 1.3 55.9 + - - +
228A ASN 3.0 4.7 - - - -
229A ARG* 3.0 39.7 + - - +
230A LEU* 3.6 3.6 + - - +
366A GLY* 4.9 11.3 - - - +
326B LYS* 3.8 11.5 + - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASN* 2.0 38.6 - - - +
209A ILE* 1.2 74.5 - - + -
210A TYR* 2.2 43.7 - - + +
223A THR 3.2 1.6 + - - -
224A TYR* 2.7 5.3 + - - +
226A ASN* 1.3 77.2 - - - +
228A ASN* 1.3 66.3 + - - +
229A ARG 3.1 0.4 + - - -
230A LEU* 3.4 2.2 + - - +
231A ILE* 3.4 18.2 + - - +
500A GTP 3.4 3.8 - - - +
326B LYS* 3.2 18.1 - - - +
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 4.0 15.9 + - + +
16A ILE* 4.8 9.9 - - - +
19A ALA* 3.3 18.9 - - + +
171A ILE* 5.3 1.4 - - - +
224A TYR* 2.5 21.9 - - - +
225A THR* 3.4 14.5 - - - +
227A LEU* 1.3 80.7 - - - +
229A ARG* 1.2 53.6 + - + +
231A ILE* 4.0 4.4 - - - +
232A GLY* 2.4 35.1 + - - +
500A GTP 2.2 50.8 + - - +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.7 5.9 - - + +
22A GLU* 4.8 13.3 + - - -
225A THR 3.9 16.3 + - - +
226A ASN* 3.0 25.0 + - - +
228A ASN* 1.2 77.5 - - + +
230A LEU* 1.3 59.3 + - - +
232A GLY* 3.9 2.2 - - - +
233A GLN* 2.5 51.0 + - + +
364A PRO* 4.2 9.1 - - - +
366A GLY* 3.8 23.8 - - - +
367A ASP* 2.6 30.8 + - - -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ILE* 3.1 24.9 - - + -
212A ILE* 2.0 53.4 - - + -
213A CYS* 4.6 3.8 - - - -
226A ASN 3.6 3.3 + - - +
227A LEU* 3.4 11.2 + - - +
228A ASN 3.2 0.2 - - - -
229A ARG* 1.3 83.0 - - - +
231A ILE* 1.3 58.5 + - - +
233A GLN* 4.0 10.0 - - - +
234A ILE* 3.3 20.8 + - - +
272A TYR* 4.8 16.1 - - + +
275A VAL* 5.0 13.2 - - + -
300A ASN 5.7 0.2 - - - +
302A MET* 3.1 22.4 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.4 23.1 - - + -
169A PHE* 5.1 6.9 - - + -
170A SER 5.2 0.9 - - - +
171A ILE* 5.0 7.2 - - + -
204A VAL* 1.4 125.2 - - + -
209A ILE* 2.9 11.7 - - + -
227A LEU* 3.4 8.2 + - + +
228A ASN* 4.0 5.2 - - - +
230A LEU* 1.3 74.3 - - - +
232A GLY* 1.3 67.5 + - - +
233A GLN 3.0 1.8 - - - -
234A ILE* 2.9 20.9 + - + +
235A VAL* 3.6 8.3 + - - +
302A MET* 2.7 21.1 - - + -
500A GTP 5.1 4.3 - - - +
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.9 1.5 - - - +
19A ALA* 3.7 21.8 - - - -
20A CYS* 4.5 11.1 - - - -
23A LEU* 3.4 14.5 - - - +
228A ASN 2.4 28.5 + - - -
229A ARG* 3.8 1.8 - - - -
231A ILE* 1.3 69.0 - - - +
233A GLN* 1.2 63.6 - - - +
234A ILE 3.3 0.3 + - - -
235A VAL* 3.4 18.2 + - - +
236A SER 3.6 0.2 + - - -
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.4 23.3 - - + +
229A ARG* 2.5 38.3 + - + +
230A LEU* 4.0 10.7 - - - +
231A ILE 3.0 0.2 - - - -
232A GLY* 1.2 78.2 - - - +
234A ILE* 1.2 70.6 + - - +
235A VAL 2.8 0.4 + - - -
236A SER* 2.6 21.5 + - - +
237A SER* 3.3 4.5 + - - -
272A TYR* 3.9 42.7 - - + -
361A THR 5.5 5.6 + - - -
362A VAL* 5.9 2.4 - - - +
367A ASP* 3.9 25.7 + - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A PHE* 4.5 9.2 - - + -
202A PHE* 5.3 2.7 - - + -
203A MET 6.2 0.2 - - - -
204A VAL* 4.4 9.2 - - + -
230A LEU 3.3 19.7 - - - +
231A ILE* 2.9 16.0 + - - +
233A GLN* 1.2 78.3 - - - +
235A VAL* 1.3 58.8 - - - +
237A SER* 2.1 31.7 + - - +
238A ILE* 3.2 27.5 + - + +
270A ALA* 3.3 41.5 - - + -
271A THR 4.7 2.2 - - - +
272A TYR* 4.4 18.6 - - + -
302A MET* 4.2 12.8 - - + -
376A CYS* 5.8 3.6 - - + -
378A LEU* 4.7 2.0 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 5.8 1.1 - - + -
20A CYS* 3.8 26.0 - - + -
24A TYR* 3.5 25.4 - - + +
138A PHE* 4.7 1.6 - - + -
169A PHE* 2.8 47.8 - - + -
231A ILE 4.0 5.6 - - - +
232A GLY 3.5 9.9 - - - +
233A GLN 2.8 0.4 + - - -
234A ILE* 1.3 73.5 - - - +
236A SER* 1.3 60.7 + - - +
237A SER 2.8 2.0 - - - -
238A ILE* 2.6 25.6 + - + +
239A THR* 2.7 24.1 + - - +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 2.8 35.4 - - - +
24A TYR* 5.5 4.7 - - - -
232A GLY 3.6 1.4 + - - -
233A GLN* 2.6 21.7 + - - +
235A VAL* 1.3 79.7 - - - +
237A SER* 1.3 56.3 + - - +
240A ALA* 2.9 35.6 + - - +
241A SER 3.0 7.3 + - - -
272A TYR* 6.0 0.9 - - - -
320A ARG* 2.9 26.8 + - - -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN 4.1 3.6 - - - -
234A ILE* 2.1 32.3 + - - +
235A VAL 2.8 0.4 - - - -
236A SER* 1.3 79.5 + - - +
238A ILE* 1.3 65.8 + - - +
241A SER* 1.7 34.5 + - - -
272A TYR* 5.8 1.8 - - - -
318A LEU* 3.7 8.2 - - - +
320A ARG* 3.0 18.2 - - - +
376A CYS* 2.9 40.9 - - - +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 5.3 3.6 - - + -
169A PHE* 4.0 17.5 - - + -
202A PHE* 3.9 35.2 - - + -
234A ILE* 3.2 31.9 - - + +
235A VAL* 2.6 12.4 + - - +
237A SER* 1.3 82.4 + - - +
239A THR* 1.3 62.7 + - - +
242A LEU* 3.3 11.4 - - - +
252A LEU* 4.8 2.9 - - + -
255A PHE* 2.7 53.5 - - + -
318A LEU* 4.3 2.2 - - + -
376A CYS* 6.1 0.4 - - + -
378A LEU* 3.8 17.3 - - + -
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A CYS* 4.0 18.3 - - - -
24A TYR* 4.4 16.6 + - - +
28A HIS* 4.4 7.4 - - + -
30A ILE* 4.5 8.2 - - + +
31A GLN* 3.1 27.1 - - - +
167A LEU* 5.8 0.3 - - - +
235A VAL* 2.7 19.6 + - - +
238A ILE* 1.3 76.7 - - - +
240A ALA* 1.3 62.0 + - - +
241A SER 3.0 2.0 - - - -
243A ARG* 2.4 41.3 + - + +
252A LEU* 4.3 6.4 - - - +
255A PHE* 5.0 0.2 - - - -
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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