Contacts of the helix formed by residues 397 - 409 (chain B) in PDB entry 2BAP
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 ALA 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B VAL* 5.7 5.8 - - + -
395B SER* 2.9 11.8 - - - +
396B LYS* 1.3 80.9 - - - +
398B GLU* 1.3 66.1 + - - +
399B PRO* 3.2 1.1 - - - +
400B HIS* 2.9 32.7 + - + +
401B PHE* 3.6 6.5 + - + -
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B VAL* 3.3 29.5 + - + +
393B LYS* 2.6 33.1 - - - +
394B ASP* 4.5 2.4 - - - +
395B SER 3.1 11.1 + - - +
397B ALA* 1.3 76.5 - - - +
399B PRO* 1.4 68.9 - - + +
400B HIS 3.0 1.9 + - - -
401B PHE* 3.2 2.1 + - - +
402B LEU* 3.1 30.2 + - + +
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Residues in contact with PRO 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B SER 4.6 0.4 - - - +
396B LYS 3.2 18.2 - - - +
397B ALA 3.2 2.9 - - - +
398B GLU* 1.4 95.9 - - + +
400B HIS* 1.3 70.1 + - + +
402B LEU* 4.1 10.3 + - + +
403B SER* 3.7 16.5 + - - -
406B GLN* 5.3 0.3 + - - -
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Residues in contact with HIS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B LYS 5.0 3.0 + - - -
397B ALA* 2.9 23.3 + - + +
399B PRO* 1.3 84.3 - - + +
401B PHE* 1.3 57.5 + - - +
403B SER* 2.8 27.7 + - - -
404B ILE* 2.9 20.7 + - + +
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Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ILE* 4.2 24.9 - - + -
392B VAL* 3.8 43.1 - - + -
397B ALA* 3.6 7.1 + - + +
398B GLU 3.2 3.2 + - - +
400B HIS* 1.3 76.7 - - - +
402B LEU* 1.3 62.5 + - - +
404B ILE* 3.4 22.9 + - + +
405B LEU* 3.0 51.3 + - + +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B GLU* 3.1 24.9 + - + +
399B PRO* 4.2 9.0 - - + +
401B PHE* 1.3 76.9 - - - +
403B SER* 1.3 57.4 + - - +
405B LEU* 3.5 14.5 + - + +
406B GLN* 2.9 60.8 + - + +
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Residues in contact with SER 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PRO 3.7 11.6 + - - -
400B HIS* 2.8 12.4 + - - -
402B LEU* 1.3 76.4 - - - +
404B ILE* 1.3 70.2 + - - +
406B GLN* 3.1 17.7 + - - +
407B HIS* 3.0 43.7 + - - -
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B HIS* 2.9 17.2 + - + +
401B PHE* 3.4 34.1 - - + +
403B SER* 1.3 76.6 - - - +
405B LEU* 1.3 66.6 + - + +
407B HIS* 3.1 7.3 + - - +
408B LEU* 3.0 41.4 + - + +
429B VAL* 6.5 1.1 - - + -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 4.7 16.8 - - + -
401B PHE* 3.0 43.3 + - + +
402B LEU* 3.6 17.9 - - + +
403B SER 3.2 0.2 - - - -
404B ILE* 1.3 79.1 - - + +
406B GLN* 1.3 63.3 + - - +
408B LEU* 3.0 24.6 + - + +
409B LEU* 2.9 39.6 + - + +
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PRO 5.3 0.2 + - - -
402B LEU* 2.9 53.5 + - + +
403B SER* 3.1 23.5 + - - +
405B LEU* 1.3 74.3 - - - +
407B HIS* 1.3 61.9 + - + +
409B LEU* 3.5 12.7 + - - +
410B LEU* 3.3 22.5 + - + +
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Residues in contact with HIS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 3.0 36.0 + - - +
404B ILE* 3.5 9.1 - - - +
406B GLN* 1.3 73.9 - - + +
408B LEU* 1.3 67.2 + - + +
409B LEU 3.1 2.9 + - - -
410B LEU* 3.3 38.1 + - + +
411B VAL* 4.9 2.4 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B ILE* 3.0 39.0 + - + +
405B LEU* 3.0 27.5 + - + +
407B HIS* 1.3 76.9 - - + +
409B LEU* 1.3 54.5 + - + +
410B LEU 3.6 2.1 + - - -
411B VAL* 4.0 4.7 - - - +
422B TYR* 2.6 42.8 + - + -
425B ILE* 4.4 23.1 - - + -
429B VAL* 6.1 6.7 - - + -
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B LEU* 2.9 33.7 + - + +
406B GLN* 3.5 10.5 + - - +
407B HIS 3.1 0.6 - - - -
408B LEU* 1.3 81.8 - - + +
410B LEU* 1.3 60.0 + - - +
411B VAL 3.6 3.9 - - - +
422B TYR* 4.0 9.6 - - + +
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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