Contacts of the helix formed by residues 290 - 298 (chain D) in PDB entry 4BGG
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 SER 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289D GLY* 1.3 75.6 - - - -
291D LEU* 1.3 60.5 + - - +
292D TYR* 3.4 10.3 + - - +
293D ASP* 2.6 40.3 + - - +
294D TYR* 2.9 27.5 + - - +
339D SER 3.9 6.1 - - - -
340D LYS* 3.9 19.0 - - - +
342D ILE 3.2 12.8 - - - -
343D LEU* 3.9 7.6 - - - +
344D VAL* 4.0 1.3 - - - -
1000D 844 4.6 3.0 - - - -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER* 1.3 71.8 - - - +
292D TYR* 1.3 56.8 + - - +
294D TYR* 4.2 2.7 - - + -
295D LEU* 3.0 63.7 + - + +
308D ILE* 4.1 22.9 - - + -
312D ILE* 4.0 23.1 - - + -
339D SER* 3.6 14.1 - - - +
342D ILE* 2.8 28.0 + - + +
344D VAL* 3.7 21.9 - - + +
350D CYS* 4.5 1.1 - - - -
410D VAL* 4.1 12.1 - - + -
413D GLU* 6.4 0.2 - - + -
414D VAL* 3.9 18.2 - - + -
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Residues in contact with TYR 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER* 3.1 8.0 + - - +
291D LEU* 1.3 80.2 - - - +
293D ASP* 1.3 74.1 + - - +
295D LEU* 3.9 4.8 + - - +
296D GLN* 3.0 48.6 + - - +
339D SER* 3.5 22.2 + - - +
340D LYS* 3.8 47.8 + - + +
427D TYR* 3.2 41.1 - + - -
429D PRO* 5.2 6.2 - - + +
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Residues in contact with ASP 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D MET 4.8 5.6 - - - +
289D GLY 4.9 0.2 - - - -
290D SER* 2.6 35.7 + - - +
292D TYR* 1.3 84.0 - - - +
294D TYR* 1.3 66.4 + - - +
296D GLN* 3.2 22.1 + - - +
297D LEU* 3.7 7.8 + - - +
1000D 844 4.0 42.0 + - - +
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Residues in contact with TYR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D MET* 3.6 40.6 + - + +
290D SER 2.9 16.8 + - - +
291D LEU* 3.8 12.3 - - + +
293D ASP* 1.3 77.3 - - - +
295D LEU* 1.3 64.1 + - + +
296D GLN 3.1 1.5 + - - -
297D LEU* 3.2 8.0 + - - +
298D THR* 2.8 51.1 + - + +
300D LEU* 4.2 23.0 - - + +
304D SER* 5.9 1.7 - - - -
308D ILE* 4.4 8.9 - - + +
344D VAL* 3.9 35.2 - - + -
348D GLY* 6.0 1.7 - - - -
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D LEU* 3.0 53.7 + - + +
292D TYR* 4.4 1.8 - - - +
293D ASP 3.3 0.2 - - - -
294D TYR* 1.3 80.7 - - + +
296D GLN* 1.3 63.0 + - - +
297D LEU 3.4 0.2 - - - -
298D THR 4.0 4.5 - - - +
300D LEU* 4.1 25.8 - - + -
339D SER* 5.2 0.2 - - - -
413D GLU* 4.2 13.0 - - + +
414D VAL* 4.0 17.5 - - + -
417D ARG* 2.7 49.2 + - + -
427D TYR* 3.7 32.3 - - + +
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Residues in contact with GLN 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D TYR* 3.0 49.6 + - - +
293D ASP* 3.2 12.0 + - - +
294D TYR 3.1 1.4 - - - -
295D LEU* 1.3 80.9 - - - +
297D LEU* 1.3 58.3 + - - +
298D THR 3.5 0.4 + - - -
417D ARG* 3.9 7.1 + - - -
427D TYR* 3.8 32.4 - - + -
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Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D ASP 3.7 6.7 + - - +
294D TYR* 3.2 5.2 + - - +
296D GLN* 1.3 77.7 - - - +
298D THR* 1.3 64.6 + - - +
417D ARG* 4.5 2.0 - - - -
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Residues in contact with THR 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D TYR* 2.8 53.1 + - + +
295D LEU* 3.5 8.5 - - - +
296D GLN 3.5 1.6 - - - -
297D LEU* 1.3 85.5 + - - +
299D THR* 1.3 75.4 + - - +
300D LEU* 4.9 1.6 - - + +
417D ARG* 3.0 27.8 + - - +
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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