Contacts of the helix formed by residues 287 - 298 (chain A) in PDB entry 3Q29
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 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LYS* 6.2 2.7 - - - +
282A GLU 4.3 4.7 - - - +
283A ASN* 3.6 24.0 + - - +
284A TYR* 2.7 23.7 + - - -
285A LEU 2.7 5.7 + - - -
286A LEU* 1.3 77.4 - - - +
288A ASP* 1.3 68.4 + - - +
289A GLU* 4.0 6.4 + - - +
290A GLY 3.4 7.6 + - - -
291A LEU* 2.9 24.8 + - - +
305A LEU* 3.3 11.2 - - - -
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Residues in contact with ASP 288 (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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287A THR* 1.3 74.4 - - - +
289A GLU* 1.3 59.0 + - - +
292A GLU* 3.0 32.4 + - - +
305A LEU* 3.6 2.2 - - - +
307A SER* 2.7 39.2 + - - +
308A TYR* 3.5 29.6 + - + -
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Residues in contact with GLU 289 (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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287A THR* 3.3 6.3 + - - +
288A ASP* 1.3 78.8 - - - +
290A GLY* 1.3 58.8 + - - +
292A GLU* 4.0 11.0 - - - +
293A ALA* 3.5 18.7 + - - +
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Residues in contact with GLY 290 (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 VAL* 3.8 15.6 - - - +
284A TYR 3.5 21.3 - - - -
285A LEU* 3.5 6.7 - - - -
287A THR* 3.4 7.1 + - - -
288A ASP 3.2 0.4 - - - -
289A GLU* 1.3 77.2 - - - +
291A LEU* 1.3 63.9 + - - +
292A GLU 3.1 1.3 - - - -
293A ALA* 3.2 13.3 + - - +
294A VAL* 3.3 17.0 + - - +
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Residues in contact with LEU 291 (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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109A ILE* 4.1 15.9 - - + +
285A LEU* 3.3 26.9 + - + +
286A LEU* 4.3 12.3 - - + -
287A THR 2.9 16.8 + - - +
290A GLY* 1.3 75.9 - - - +
292A GLU* 1.3 57.6 + - - +
294A VAL* 3.6 2.8 + - - +
295A ASN* 2.9 30.3 + - - +
300A LEU* 4.0 22.5 - - + +
303A VAL* 4.0 22.2 - - + -
305A LEU* 3.5 39.3 - - + +
308A TYR* 3.9 15.4 - - + -
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Residues in contact with GLU 292 (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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288A ASP 3.0 19.6 + - - +
289A GLU* 4.1 9.8 - - - +
291A LEU* 1.3 75.2 - - - +
293A ALA* 1.3 57.9 + - - +
296A LYS* 2.7 62.3 + - + +
308A TYR* 3.3 21.9 - - + +
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Residues in contact with ALA 293 (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 GLY* 3.3 29.6 - - - +
23A GLU* 4.1 18.4 - - + +
24A VAL* 4.0 9.0 - - + +
289A GLU 3.5 12.6 + - - +
290A GLY 3.2 10.0 + - - +
292A GLU* 1.3 80.5 - - - +
294A VAL* 1.3 62.0 + - - +
296A LYS* 3.7 6.7 + - - +
297A ASP* 3.5 9.9 + - - +
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Residues in contact with VAL 294 (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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12A ILE* 5.7 5.2 - - + -
16A LYS* 6.0 0.2 - - + -
17A GLY* 3.8 21.7 - - - +
20A GLY* 4.0 6.7 - - - -
21A LEU* 3.8 26.5 - - + +
24A VAL* 4.4 1.8 - - + -
285A LEU* 3.9 22.4 - - + -
290A GLY 3.3 12.9 + - - +
291A LEU* 4.0 4.9 - - - +
292A GLU 3.2 0.2 - - - -
293A ALA* 1.3 73.2 - - - +
295A ASN* 1.3 67.2 + - - +
297A ASP* 3.0 5.4 + - - +
298A LYS 3.0 24.3 + - - +
300A LEU* 3.9 29.6 - - + -
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Residues in contact with ASN 295 (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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291A LEU 2.9 21.1 + - - +
292A GLU 3.6 3.4 - - - +
294A VAL* 1.3 78.7 - - - +
296A LYS* 1.3 64.2 + - + +
298A LYS 3.2 6.0 - - - -
299A PRO* 3.2 34.0 - - - +
300A LEU* 3.0 32.8 + - + +
301A GLY 4.5 5.2 + - - +
303A VAL* 4.8 4.0 - - + +
308A TYR* 3.9 23.6 + - + +
312A LEU* 5.2 6.2 - - - +
317A ARG* 6.2 0.2 - - - +
318A ILE* 5.9 1.0 - - - +
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Residues in contact with LYS 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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234A SER* 5.1 1.4 + - - -
292A GLU* 2.7 48.0 + - + +
293A ALA* 4.1 6.3 - - - +
295A ASN* 1.3 75.5 - - + +
297A ASP* 1.3 60.9 + - - +
299A PRO* 5.7 0.3 - - - +
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Residues in contact with ASP 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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16A LYS 4.6 0.2 - - - +
17A GLY* 3.1 18.0 - - - -
18A TYR 3.5 0.3 + - - -
19A ASN* 3.1 21.3 + - - +
20A GLY* 2.9 32.5 + - - +
234A SER* 3.0 22.9 + - - -
293A ALA 3.5 6.1 + - - +
294A VAL 3.0 9.3 + - - +
296A LYS* 1.3 82.1 - - - +
298A LYS* 1.3 71.9 + - - +
299A PRO* 4.6 0.2 - - - -
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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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14A GLY 5.4 4.0 + - - -
15A ASP* 3.9 14.9 + - - +
16A LYS* 3.7 9.4 - - - -
17A GLY* 3.6 29.1 + - - +
18A TYR* 6.2 2.2 - - - -
231A TRP* 3.5 27.1 + - + +
234A SER* 4.0 6.5 - - - -
235A ASN* 3.5 33.4 + - - +
294A VAL* 3.0 18.4 + - - +
295A ASN* 3.2 4.6 - - - +
297A ASP* 1.3 91.4 - - - +
299A PRO* 1.3 73.3 - - - +
300A LEU* 3.4 5.4 + - - +
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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