Contacts of the helix formed by residues 364 - 376 (chain A) in PDB entry 2B9S
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 LEU 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A MET* 4.5 19.5 - - + -
291A PHE* 4.0 21.8 - - + -
306A TYR* 3.4 28.8 + - + +
363A VAL* 1.3 77.5 - - - +
365A PRO* 1.4 75.5 - - + +
366A GLU* 4.2 5.6 - - + +
367A VAL* 3.0 14.9 + - + +
368A TYR 3.0 19.2 + - - -
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Residues in contact with PRO 365 (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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343A ASN* 3.7 30.9 - - - +
363A VAL 3.4 4.4 - - - +
364A LEU* 1.4 88.1 - - + +
366A GLU* 1.3 56.3 + - - +
368A TYR* 3.5 2.0 + - + +
369A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 366 (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 PHE* 4.5 22.9 - - + -
364A LEU* 3.2 6.0 - - + -
365A PRO* 1.3 81.1 - - - +
367A VAL* 1.3 59.2 + - - +
369A ALA* 4.1 5.1 - - - +
370A LEU* 3.2 30.5 + - - +
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Residues in contact with VAL 367 (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 PHE* 3.3 42.8 - - + -
303A VAL* 4.1 17.9 - - + +
306A TYR* 3.8 34.3 - - + -
307A PHE* 4.3 2.5 - - + -
363A VAL* 4.0 11.7 - - + -
364A LEU* 3.0 16.5 + - + +
366A GLU* 1.3 74.6 - - - +
368A TYR* 1.3 61.8 + - - +
369A ALA 3.3 0.2 - - - -
370A LEU* 3.3 6.9 + - - +
371A LEU* 2.9 36.8 + - + +
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Residues in contact with TYR 368 (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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339A LEU* 3.5 29.0 + - + +
340A MET 2.7 30.3 + - - -
341A PRO* 4.5 4.2 + - - +
343A ASN* 3.5 43.5 - - - +
344A ILE 3.6 13.9 - - - -
345A VAL* 4.3 6.7 - - + -
363A VAL* 3.6 16.6 - - + -
364A LEU 3.0 10.4 + - - +
365A PRO 3.8 4.3 - - - +
367A VAL* 1.3 78.4 - - - +
369A ALA* 1.3 60.7 + - + +
371A LEU* 3.4 8.5 + - - +
372A GLN* 3.2 49.5 + - + +
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Residues in contact with ALA 369 (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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365A PRO 3.0 18.8 + - - +
366A GLU* 4.2 6.1 - - - +
368A TYR* 1.3 75.8 - - + +
370A LEU* 1.3 63.8 + - - +
372A GLN* 3.3 20.9 + - - +
373A ARG* 3.2 19.6 + - - +
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Residues in contact with LEU 370 (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 PHE* 3.7 44.4 - - + +
299A ALA* 4.3 8.5 - - + +
303A VAL* 3.5 29.4 - - + -
366A GLU 3.2 22.1 + - - +
367A VAL 3.3 5.8 + - - +
369A ALA* 1.3 77.0 - - - +
371A LEU* 1.3 56.0 + - - +
373A ARG* 3.1 38.0 + - - +
374A PHE* 2.8 46.3 + - + -
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Residues in contact with LEU 371 (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 VAL* 4.0 21.5 - - + -
307A PHE* 3.9 22.7 - - + -
337A ILE* 4.0 18.6 - - + -
339A LEU* 4.2 13.8 - - + +
345A VAL* 3.7 36.3 - - + -
367A VAL* 2.9 26.0 + - + +
368A TYR* 3.5 10.8 - - - +
369A ALA 3.3 0.2 - - - -
370A LEU* 1.3 72.4 - - - +
372A GLN* 1.3 62.2 + - - +
374A PHE* 3.9 13.2 - - + +
375A THR* 2.9 32.4 + - - +
384A ILE* 4.5 9.4 - - + -
385A PHE* 4.8 0.2 - - + -
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Residues in contact with GLN 372 (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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339A LEU* 3.6 21.9 - - + +
368A TYR* 3.2 37.5 + - + +
369A ALA* 3.5 22.6 - - - +
370A LEU 3.3 0.4 - - - -
371A LEU* 1.3 72.6 - - - +
373A ARG* 1.3 65.7 + - - +
375A THR* 3.5 1.9 + - - -
376A ARG* 3.1 30.1 + - - +
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Residues in contact with ARG 373 (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 PHE 5.4 0.6 + - - -
293A SER 4.3 12.9 + - - -
294A ASN* 5.1 4.9 + - - +
296A LEU* 3.6 35.5 - - + +
299A ALA* 4.1 17.6 - - - +
369A ALA 3.2 11.3 + - - +
370A LEU* 3.1 34.3 + - - +
372A GLN* 1.3 78.8 - - - +
374A PHE* 1.3 64.9 + - + +
375A THR 3.1 1.6 + - - -
376A ARG* 3.7 17.7 + - + +
378A LYS* 5.8 0.7 - - - -
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Residues in contact with PHE 374 (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 LEU* 4.1 17.9 - - + -
299A ALA 3.9 6.1 - - - -
300A GLN* 3.6 45.3 - - + +
303A VAL* 3.8 22.2 - - + -
370A LEU* 2.8 41.0 + - + +
371A LEU* 3.4 13.0 + - + +
372A GLN 3.3 0.4 - - - -
373A ARG* 1.3 85.8 - - + +
375A THR* 1.3 60.6 + - - +
378A LYS* 3.2 30.5 + - - +
384A ILE* 3.9 26.7 - - + +
385A PHE* 3.9 22.7 - + - -
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Residues in contact with THR 375 (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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334A VAL* 4.1 33.4 - - + +
337A ILE* 4.2 23.6 - - + -
339A LEU* 4.1 9.9 - - + +
371A LEU 2.9 22.2 + - - +
372A GLN* 3.7 5.7 + - - -
373A ARG 3.1 0.4 - - - -
374A PHE* 1.3 85.5 - - + +
376A ARG* 1.3 68.0 + - - +
377A ARG 3.2 2.8 + - - -
378A LYS* 3.3 20.3 + - - +
384A ILE* 4.3 9.2 - - + -
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Residues in contact with ARG 376 (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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372A GLN 3.1 18.3 + - - +
373A ARG* 3.7 14.3 + - - +
374A PHE 3.9 0.2 - - - -
375A THR* 1.3 80.0 - - - +
377A ARG* 1.3 73.7 + - + +
378A LYS* 3.7 1.3 + - - +
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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