Contacts of the helix formed by residues 294 - 308 (chain A) in PDB entry 2OG9
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 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY* 3.8 16.6 - - - -
123A ASP* 3.7 4.5 - - - -
124A VAL* 4.3 5.4 - - - -
289A ALA* 2.8 23.3 + - - +
290A PRO* 4.3 2.3 + - - -
292A VAL* 4.0 0.3 - - - +
293A GLY* 1.3 78.8 - - - +
295A ILE* 1.3 67.0 + - - -
296A THR 3.4 2.0 - - - -
297A PRO* 3.4 2.3 - - - +
298A PHE* 3.2 22.8 + - - +
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Residues in contact with ILE 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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123A ASP* 2.9 4.0 + - - -
124A VAL* 4.2 19.4 - - + +
127A TRP* 3.5 54.3 - - + +
138A LEU* 3.6 24.7 - - + -
142A LEU* 5.2 2.9 - - + -
289A ALA* 4.9 0.4 - - - -
294A GLY* 1.3 69.9 - - - -
296A THR* 1.3 61.1 + - - +
298A PHE* 3.2 6.9 + - - +
299A LEU* 2.8 43.2 + - + +
320A LEU* 3.8 22.4 - - + -
324A LEU* 4.0 19.3 - - + -
363A LEU* 5.6 0.2 - - + -
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Residues in contact with THR 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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95A ILE* 3.5 8.1 - - - +
96A ALA* 4.3 22.9 + - + +
99A TRP* 4.3 10.8 - - + -
123A ASP* 2.7 29.3 + - - -
127A TRP* 3.2 16.7 + - - +
295A ILE* 1.3 78.8 - - - +
297A PRO* 1.3 71.6 - - + +
299A LEU* 3.3 13.7 + - - +
300A LYS* 3.4 35.8 + - - +
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 3.7 18.6 - - + +
270A ALA* 4.4 12.7 - - + +
292A VAL* 3.4 20.6 - - + +
293A GLY* 3.3 36.8 - - - +
294A GLY 3.4 5.2 - - - +
296A THR* 1.3 98.3 - - + +
298A PHE* 1.3 59.0 + - - -
300A LYS* 3.1 17.1 + - + +
301A ILE* 3.0 28.8 + - - +
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Residues in contact with PHE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 3.4 45.7 - - + +
288A ASP 4.5 0.2 - - - -
289A ALA* 3.7 24.0 - - + -
292A VAL* 4.2 1.9 - - + +
294A GLY 3.2 19.6 + - - +
295A ILE* 3.2 8.7 + - - +
297A PRO* 1.3 77.7 - - - +
299A LEU* 1.3 62.4 + - + +
301A ILE* 3.2 12.0 + - - +
302A ALA* 2.8 38.2 + - + -
312A LEU* 4.2 7.9 - - + -
314A PRO* 4.0 18.2 - - + -
321A HIS* 3.8 11.9 - + - -
324A LEU* 3.7 39.0 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 3.8 33.9 - - + -
142A LEU* 4.1 17.9 - - + -
295A ILE* 2.8 27.2 + - + +
296A THR* 3.7 6.7 - - - +
297A PRO 3.2 0.2 - - - -
298A PHE* 1.3 80.2 - - + +
300A LYS* 1.3 61.5 + - + +
302A ALA* 3.3 8.8 + - + +
303A SER* 2.8 29.7 + - - +
324A LEU* 4.4 20.4 - - + -
327A ALA* 6.0 2.7 - - + -
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Residues in contact with LYS 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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96A ALA* 5.6 5.9 - - - +
99A TRP* 5.4 7.1 - - - -
100A ASP* 5.0 9.7 + - - -
270A ALA* 4.7 12.8 - - + -
296A THR* 3.4 32.8 + - - +
297A PRO* 3.1 15.0 + - + +
299A LEU* 1.3 77.3 - - + +
301A ILE* 1.3 62.6 + - - +
303A SER* 3.3 7.6 + - - -
304A LEU* 3.1 30.0 + - + +
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Residues in contact with ILE 301 (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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270A ALA* 3.6 28.3 - - + +
273A HIS* 3.5 37.7 - - + +
277A ILE* 4.4 1.2 - - + +
285A LEU* 3.6 25.8 - - + -
287A PRO* 4.1 14.6 - - + -
292A VAL* 4.0 25.1 - - + -
297A PRO 3.0 15.6 + - - +
298A PHE* 3.4 8.1 - - - +
300A LYS* 1.3 77.9 - - - +
302A ALA* 1.3 58.0 + - - +
304A LEU* 3.1 10.9 + - + +
305A ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 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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287A PRO* 6.0 0.4 - - - +
298A PHE* 2.8 31.1 + - + +
299A LEU* 3.7 12.8 - - + +
300A LYS 3.3 0.2 - - - -
301A ILE* 1.3 77.9 - - - +
303A SER* 1.3 57.1 + - - +
305A ALA* 4.4 5.4 - - - -
306A GLU* 2.8 30.8 + - - +
312A LEU* 5.1 6.1 - - + -
328A TYR* 3.5 21.8 - - + -
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Residues in contact with SER 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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299A LEU* 2.8 19.8 + - - +
300A LYS* 3.5 11.3 - - - -
302A ALA* 1.3 75.9 - - - +
304A LEU* 1.3 64.3 + - - +
306A GLU* 3.4 7.3 + - - +
307A HIS* 3.1 24.4 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 4.7 11.0 - - + +
273A HIS* 5.5 0.4 - - + -
274A GLY* 4.2 24.2 - - - +
277A ILE* 3.8 16.4 - - + +
300A LYS* 3.1 16.0 + - + +
301A ILE* 3.1 11.6 + - - +
303A SER* 1.3 82.7 - - - +
305A ALA* 1.3 61.4 + - - +
307A HIS* 3.4 8.0 + - + +
308A ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 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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277A ILE* 3.8 7.1 - - + +
285A LEU* 3.8 25.6 - - + -
301A ILE 2.9 15.8 + - - +
302A ALA* 3.8 6.7 - - - +
304A LEU* 1.3 73.2 - - - +
306A GLU* 1.3 66.1 - - - +
308A ALA* 3.3 1.4 + - - -
309A GLY 3.2 3.6 + - - -
310A LEU* 3.0 40.0 + - + +
311A MSE 5.4 0.2 - - - +
312A LEU* 4.9 4.3 - - + -
328A TYR* 3.3 14.1 - - + +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 2.8 19.2 + - - +
303A SER* 3.6 8.8 - - - +
305A ALA* 1.3 76.3 - - - +
307A HIS* 1.3 63.7 + - - +
309A GLY* 3.0 8.5 + - - -
328A TYR* 3.2 12.1 + - + -
329A PRO* 3.6 36.3 - - + +
330A ARG* 2.9 37.4 + - - +
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Residues in contact with HIS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER 3.1 14.9 + - - +
304A LEU* 3.8 8.5 - - + +
306A GLU* 1.3 86.8 + - - +
308A ALA* 1.3 62.5 + - + +
309A GLY* 3.1 1.8 + - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.8 24.9 - - + +
304A LEU 3.0 17.9 + - - +
305A ALA 3.8 4.7 - - - +
306A GLU 3.2 0.4 - - - -
307A HIS* 1.3 76.9 - - + +
309A GLY* 1.3 61.6 + - - +
310A LEU* 3.5 18.1 + - + +
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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