Contacts of the helix formed by residues 295 - 307 (chain A) in PDB entry 6BCH
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A THR* 3.8 5.5 - - - +
291A LYS 4.5 7.2 - - - +
292A GLU* 3.1 13.4 + - - +
293A HIS 3.2 0.4 - - - -
294A LEU* 1.3 85.9 - - + +
296A SER* 1.3 59.7 + - - +
297A GLU* 3.9 5.2 + - - +
298A GLY* 3.1 17.8 + - - -
299A LEU* 2.8 30.8 + - - +
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Residues in contact with SER 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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199A THR* 4.2 7.7 - - - +
295A THR* 1.3 72.2 - - - +
297A GLU* 1.3 65.8 + - - +
299A LEU* 3.2 9.6 + - - +
300A GLU* 2.9 29.5 + - - +
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Residues in contact with GLU 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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295A THR* 3.4 5.5 + - - +
296A SER* 1.3 82.7 + - - +
298A GLY* 1.3 57.1 + - - +
300A GLU* 3.2 9.2 + - - +
301A LYS* 2.9 26.4 + - - +
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Residues in contact with GLY 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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287A LEU* 5.7 0.2 - - - +
292A GLU* 3.3 27.1 - - - -
295A THR* 3.1 11.0 + - - -
297A GLU* 1.3 76.4 - - - +
299A LEU* 1.3 57.0 + - - +
301A LYS* 3.2 10.0 + - - +
302A ILE* 2.9 34.9 + - - +
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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
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191A ILE* 4.9 10.8 - - + -
199A THR* 3.8 22.9 - - - +
201A TYR* 3.5 38.6 - - + -
203A VAL* 3.8 28.3 - - + -
292A GLU 4.1 1.0 + - - -
293A HIS 4.4 7.6 + - - +
295A THR 2.8 18.5 + - - +
296A SER* 3.2 8.3 + - - +
298A GLY* 1.3 74.9 - - - +
300A GLU* 1.3 57.5 + - - +
302A ILE* 3.3 8.1 + - + +
303A GLN* 2.9 30.4 + - + +
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Residues in contact with GLU 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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296A SER 2.9 13.1 + - - +
297A GLU* 3.4 11.4 - - - +
299A LEU* 1.3 73.1 - - - +
301A LYS* 1.3 67.1 + - - +
303A GLN* 3.4 7.4 + - - +
304A LYS* 2.9 24.7 + - - +
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Residues in contact with LYS 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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287A LEU* 5.2 6.7 - - + -
297A GLU 2.9 13.0 + - - +
298A GLY* 3.2 13.9 - - - +
300A GLU* 1.3 76.9 - - - +
302A ILE* 1.3 59.5 + - + +
304A LYS* 3.1 8.7 + - - +
305A ILE* 2.9 38.6 + - + +
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Residues in contact with ILE 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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189A ILE* 3.9 28.5 - - + -
191A ILE* 4.9 7.2 - - + -
203A VAL* 4.1 16.4 - - + -
284A VAL* 4.0 22.9 - - + -
287A LEU* 4.4 19.7 - - + -
288A ILE* 4.4 4.5 - - + -
292A GLU 5.3 0.2 - - - -
293A HIS* 3.7 33.9 - - + +
298A GLY 2.9 19.4 + - - +
299A LEU* 3.7 6.5 - - + +
300A GLU 3.3 0.2 - - - -
301A LYS* 1.3 73.5 - - - +
303A GLN* 1.3 62.3 + - - +
305A ILE* 3.1 8.6 + - - +
306A LYS* 2.8 28.3 + - + +
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Residues in contact with GLN 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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191A ILE* 3.9 31.4 - - + +
299A LEU* 2.9 20.5 + - + +
300A GLU* 3.6 7.6 - - - +
302A ILE* 1.3 77.3 - - - +
304A LYS* 1.3 59.3 + - - +
306A LYS* 3.6 7.2 - - - +
307A GLU* 2.9 38.8 + - + +
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Residues in contact with LYS 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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300A GLU 2.9 13.8 + - - +
301A LYS* 3.2 12.3 - - - +
303A GLN* 1.3 78.7 - - - +
305A ILE* 1.3 63.4 + - + +
307A GLU* 3.4 14.2 + - - +
308A GLY* 3.6 7.3 + - - -
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Residues in contact with ILE 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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280A ASP* 4.3 19.6 - - + +
283A LYS* 5.6 5.4 - - + -
284A VAL* 3.7 32.3 - - + +
287A LEU* 3.9 22.4 - - + -
301A LYS* 2.9 25.0 + - + +
302A ILE* 3.1 5.8 + - - +
304A LYS* 1.3 73.7 - - + +
306A LYS* 1.3 61.1 + - - +
308A GLY* 2.9 19.8 + - - -
309A MET* 3.3 21.0 + - - +
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Residues in contact with LYS 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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189A ILE* 4.7 25.1 - - + +
191A ILE* 5.9 3.6 - - + -
284A VAL* 5.5 0.6 - - - +
302A ILE* 2.8 16.5 + - + +
303A GLN* 3.6 13.5 - - - +
305A ILE* 1.3 75.7 - - - +
307A GLU* 1.3 61.9 + - - +
308A GLY 3.0 0.2 - - - -
309A MET* 3.0 32.4 + - - +
18C C 5.2 2.9 + - - -
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Residues in contact with GLU 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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303A GLN* 2.9 27.7 + - + +
304A LYS* 3.7 9.4 - - - +
305A ILE 3.2 0.6 - - - -
306A LYS* 1.3 75.3 - - - +
308A GLY* 1.3 55.9 + - - +
309A MET 3.4 1.3 - - - -
312A GLY* 3.7 21.9 - - - +
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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
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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