Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 5TSQ
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A THR 4.4 4.8 - - - +
253A VAL* 2.8 26.7 + - - +
254A MET* 4.6 0.2 - - - +
293A LYS 4.1 0.6 + - - -
294A LEU* 1.3 68.1 - - - +
296A PHE* 1.3 59.4 + - - +
297A SER* 3.5 6.6 + - - -
298A LYS* 3.1 42.6 + - + +
299A TYR* 2.9 29.3 + - - +
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Residues in contact with PHE 296 (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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196A GLN* 3.3 26.9 - - + +
198A LEU* 3.4 22.0 - - + -
200A THR* 4.0 16.4 - - + -
203A VAL* 4.0 11.0 - - + -
293A LYS* 6.0 0.7 - - - +
294A LEU* 3.2 18.7 + - + +
295A ASP* 1.3 73.8 + - - +
297A SER* 1.3 71.5 + - - +
299A TYR* 3.4 0.9 + - - +
300A TRP* 3.1 59.6 + + + -
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Residues in contact with SER 297 (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 ARG* 4.8 1.3 + - - +
295A ASP* 3.3 5.7 + - - -
296A PHE* 1.3 87.7 - - - +
298A LYS* 1.3 57.4 + - - +
300A TRP* 3.5 2.9 + - - +
301A ASP* 2.9 42.7 + - - +
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Residues in contact with LYS 298 (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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250A ASP* 2.7 30.0 + - + +
252A THR* 2.8 19.0 + - - -
253A VAL* 3.9 26.9 - - + -
295A ASP* 3.1 32.4 + - + +
297A SER* 1.3 76.4 - - - +
299A TYR* 1.3 63.6 + - - +
301A ASP* 3.3 8.6 + - + +
302A LEU* 2.9 32.5 + - + +
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Residues in contact with TYR 299 (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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21A LEU* 5.1 0.2 - - + -
197A ALA* 3.7 14.6 - - + -
239A VAL* 2.8 23.4 + - - +
242A PRO* 3.2 29.9 - - + +
243A CYS* 3.6 33.5 + - - -
246A ALA* 3.9 17.3 - - + -
253A VAL* 3.8 7.7 - - + +
294A LEU* 4.0 26.2 - - + -
295A ASP 2.9 17.6 + - - +
296A PHE 3.6 3.4 - - - +
298A LYS* 1.3 75.2 - - - +
300A TRP* 1.3 101.9 + + - +
302A LEU* 3.1 16.2 + - - +
303A VAL* 3.2 22.5 + - + +
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Residues in contact with TRP 300 (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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17A VAL* 5.3 1.1 - - + -
197A ALA 3.8 11.4 - - - -
198A LEU 3.1 32.4 + - - +
199A ALA* 4.1 3.1 - - + -
203A VAL* 3.6 35.2 - - + -
206A ARG* 4.1 13.7 - - - +
207A VAL* 5.4 2.2 - - + -
222A LEU* 5.1 9.6 - - + -
239A VAL* 3.7 30.1 - - + -
296A PHE* 3.1 51.3 + + + +
297A SER* 4.3 2.0 - - - +
299A TYR* 1.3 99.6 - + - +
301A ASP* 1.3 60.2 + - - +
303A VAL* 3.2 34.5 + - + +
304A ILE* 2.9 38.8 + - + +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 2.8 43.1 + - - +
297A SER* 2.9 31.0 + - - +
298A LYS* 3.6 8.5 - - + +
299A TYR 3.2 0.2 - - - -
300A TRP* 1.3 76.4 - - - +
302A LEU* 1.3 58.0 + - + +
304A ILE* 4.0 0.7 - - - +
305A ASP* 2.9 32.2 + - - +
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Residues in contact with LEU 302 (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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21A LEU* 3.4 21.8 - - + +
25A ASN* 3.8 24.5 + - - +
246A ALA* 4.2 27.6 - - + +
249A ILE* 4.0 20.4 - - + -
250A ASP* 4.9 6.3 - - + -
253A VAL* 4.5 6.1 - - + -
298A LYS* 2.9 33.1 + - + +
299A TYR* 3.1 7.8 + - - +
301A ASP* 1.3 78.3 - - + +
303A VAL* 1.3 62.2 + - - +
305A ASP* 3.8 7.0 - - + +
306A ALA* 3.0 19.1 + - - +
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Residues in contact with VAL 303 (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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17A VAL* 4.0 22.7 - - + +
21A LEU* 4.1 20.9 - - + -
207A VAL* 5.6 2.0 - - + -
218A ILE* 6.0 1.1 - - + -
242A PRO* 4.5 6.7 - - + -
299A TYR* 3.2 32.4 + - + +
300A TRP* 3.2 34.3 + - + +
302A LEU* 1.3 77.2 - - - +
304A ILE* 1.3 66.0 + - + +
306A ALA* 3.3 4.2 + - - +
307A LEU* 3.1 35.9 + - + +
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Residues in contact with ILE 304 (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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203A VAL* 4.7 1.3 - - + +
206A ARG* 3.8 45.8 - - + +
207A VAL* 3.7 43.5 - - + +
210A VAL* 4.0 13.7 - - + -
300A TRP* 2.9 26.4 + - + +
301A ASP 4.0 0.4 - - - +
303A VAL* 1.3 78.8 - - + +
305A ASP* 1.3 59.4 + - - +
307A LEU* 3.1 9.0 + - + +
308A GLN* 2.9 47.9 + - - +
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Residues in contact with ASP 305 (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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25A ASN* 4.4 14.0 + - - -
26A PRO* 4.5 0.3 - - - +
301A ASP 2.9 19.5 + - - +
302A LEU* 3.8 7.0 - - + +
304A ILE* 1.3 77.1 - - - +
306A ALA* 1.3 58.8 + - - +
308A GLN* 3.2 18.3 + - - +
309A ARG* 2.8 69.8 + - - +
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Residues in contact with ALA 306 (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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20A LEU 3.7 21.8 - - - +
21A LEU* 3.8 19.5 - - + -
24A GLY* 3.9 20.0 - - - -
25A ASN* 4.1 1.8 - - + +
302A LEU 3.0 16.9 + - - +
303A VAL 3.6 4.7 - - - +
304A ILE 3.3 0.2 - - - -
305A ASP* 1.3 79.8 + - - +
307A LEU* 1.3 57.5 + - + +
309A ARG* 3.3 2.1 + - - +
310A ILE* 3.0 35.4 + - - +
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Residues in contact with LEU 307 (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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17A VAL* 6.4 1.3 - - + -
20A LEU* 3.9 36.6 - - + -
207A VAL* 4.2 33.0 - - + -
210A VAL* 4.0 23.4 - - + +
212A THR* 4.6 2.5 + - - +
214A PRO* 5.0 2.9 - - + +
215A ALA* 4.3 16.8 - - + +
218A ILE* 4.2 15.5 - - + -
303A VAL* 3.1 26.3 + - + +
304A ILE* 3.5 9.2 - - + +
306A ALA* 1.3 75.7 - - + +
308A GLN* 1.3 63.1 + - - +
310A ILE* 3.4 8.6 + - + +
311A GLY* 3.1 20.3 + - - +
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Residues in contact with GLN 308 (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 ARG* 6.0 0.2 - - - +
210A VAL* 4.3 20.7 - - + +
212A THR* 5.7 0.7 - - - -
304A ILE* 2.9 35.3 + - + +
305A ASP* 3.5 22.4 - - - +
307A LEU* 1.3 77.4 - - - +
309A ARG* 1.3 63.1 + - + +
311A GLY* 3.2 14.4 + - - -
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Residues in contact with ARG 309 (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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24A GLY* 3.3 28.5 - - - +
26A PRO* 3.7 28.6 - - - +
305A ASP* 2.8 51.4 + - - +
306A ALA 3.8 0.9 - - - +
308A GLN* 1.3 74.7 - - + +
310A ILE* 1.3 67.8 + - - +
311A GLY* 3.4 0.5 + - - -
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Residues in contact with ILE 310 (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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20A LEU* 3.6 47.8 - - + +
23A TYR* 3.8 28.0 - - + -
24A GLY* 3.9 8.1 - - - -
56A ALA* 4.0 21.8 - - + +
214A PRO* 4.2 15.7 - - + -
306A ALA 3.0 20.7 + - - +
307A LEU* 3.8 7.9 - - + +
308A GLN 3.3 0.2 - - - -
309A ARG* 1.3 76.1 - - - +
311A GLY* 1.3 72.8 + - - +
312A ASP 3.5 1.6 + - - -
313A PRO* 4.0 11.0 - - + +
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Residues in contact with GLY 311 (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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212A THR* 3.5 21.3 + - - -
214A PRO* 3.5 17.5 - - - +
307A LEU 3.1 10.5 + - - +
308A GLN 3.2 14.0 + - - -
309A ARG 4.3 0.9 - - - -
310A ILE* 1.3 79.6 - - - +
312A ASP* 1.3 58.0 + - - -
313A PRO* 3.3 7.8 - - - +
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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