Contacts of the helix formed by residues 388 - 401 (chain B) in PDB entry 4BEJ
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 ASN 388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B GLY 3.0 13.4 + - - +
387B LEU* 1.3 82.0 - - - +
389B THR* 1.3 66.3 + - + +
390B ILE* 3.5 30.1 - - + +
391B ASP* 3.1 25.3 + - - +
392B ILE* 3.5 6.1 + - - +
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Residues in contact with THR 389 (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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387B LEU 4.2 0.2 + - - -
388B ASN* 1.3 74.1 - - + +
390B ILE* 1.3 73.6 + - + +
392B ILE* 3.0 23.6 + - - +
393B LEU* 3.1 23.2 + - + +
618B CYS* 4.2 14.4 - - - -
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Residues in contact with ILE 390 (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 ASN* 3.5 27.4 - - + +
389B THR* 1.3 85.4 - - + +
391B ASP* 1.3 71.6 + - - +
393B LEU* 3.1 17.3 + - + +
394B THR* 2.9 32.9 + - - +
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY 3.6 9.4 - - - +
387B LEU* 3.6 15.8 - - + +
388B ASN* 3.1 35.0 + - - +
389B THR 3.2 0.4 - - - -
390B ILE* 1.3 89.2 - - - +
392B ILE* 1.3 62.4 + - - +
394B THR* 3.3 9.8 + - - -
395B ALA* 3.1 21.1 + - - +
416B LEU* 4.3 3.7 - - - +
419B ARG* 4.5 19.1 + - - +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 5.9 0.4 - - + -
387B LEU* 3.9 26.2 - - + -
388B ASN 3.5 6.0 + - - +
389B THR* 3.0 11.7 + - - +
391B ASP* 1.3 76.5 - - - +
393B LEU* 1.3 63.2 + - - +
395B ALA* 3.3 4.7 + - - +
396B ILE* 3.1 31.5 + - + +
416B LEU* 3.6 30.0 - - + +
618B CYS* 3.4 41.7 - - + -
621B ILE* 4.3 15.3 - - + -
622B GLU* 4.6 17.0 - - + -
625B ILE* 4.6 0.2 - - + -
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Residues in contact with LEU 393 (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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389B THR* 3.1 25.2 + - + +
390B ILE* 3.4 17.3 - - + +
392B ILE* 1.3 75.4 - - - +
394B THR* 1.3 58.8 + - - +
396B ILE* 3.4 14.7 + - + +
397B ARG* 3.0 28.7 + - - +
616B ARG* 6.2 3.8 - - - +
618B CYS* 4.5 20.0 - - + -
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 2.9 15.7 + - - +
391B ASP* 3.5 12.0 + - - -
393B LEU* 1.3 74.5 - - - +
395B ALA* 1.3 65.0 + - - +
397B ARG* 3.4 6.9 + - + +
398B ASN* 3.3 37.1 + - - +
419B ARG* 5.9 4.9 - - - +
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Residues in contact with ALA 395 (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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391B ASP 3.1 12.5 + - - +
392B ILE 3.3 9.6 + - - +
394B THR* 1.3 76.7 - - - +
396B ILE* 1.3 58.2 + - - +
398B ASN* 3.5 4.6 + - - +
399B ALA* 3.0 27.5 + - - +
412B SER* 4.0 21.9 - - - +
415B LEU* 4.4 16.6 - - + -
416B LEU* 4.0 20.6 - - + -
419B ARG* 5.4 2.2 - - - +
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Residues in contact with ILE 396 (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 ILE* 3.1 23.6 + - + +
393B LEU* 3.6 19.7 - - + +
394B THR 3.3 0.2 - - - -
395B ALA* 1.3 73.7 - - - +
397B ARG* 1.3 66.1 + - - +
399B ALA* 3.1 7.5 + - + +
400B THR* 3.0 33.5 + - + +
409B PRO* 6.0 1.8 - - + -
412B SER* 4.0 7.0 - - - -
617B ASP* 4.9 9.9 - - + -
618B CYS* 4.8 9.9 - - + +
621B ILE* 3.7 31.2 - - + -
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Residues in contact with ARG 397 (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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393B LEU 3.0 17.2 + - - +
394B THR* 3.7 8.1 - - - +
395B ALA 3.4 0.4 - - - -
396B ILE* 1.3 77.5 - - - +
398B ASN* 1.3 67.4 + - - +
400B THR* 2.7 22.7 + - - +
401B ALA* 3.2 11.1 + - - +
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Residues in contact with ASN 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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394B THR* 3.3 28.4 + - - +
395B ALA* 4.1 4.0 - - - +
396B ILE 3.3 0.2 - - - -
397B ARG* 1.3 84.8 + - - +
399B ALA* 1.3 65.4 + - - +
400B THR 3.3 0.2 - - - -
401B ALA* 3.1 26.8 + - - -
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Residues in contact with ALA 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 ALA 3.0 16.0 + - - +
396B ILE* 3.1 14.3 + - + +
398B ASN* 1.3 79.2 - - - +
400B THR* 1.3 61.2 + - + +
401B ALA 4.0 3.8 - - - +
408B VAL* 4.2 29.7 + - - +
411B VAL* 4.2 23.8 - - + +
412B SER* 4.4 5.4 - - - +
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 3.0 23.5 + - + +
397B ARG* 2.7 27.8 + - - +
399B ALA* 1.3 77.2 - - + +
401B ALA* 1.3 60.8 + - - +
408B VAL 5.5 9.2 - - - +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ARG 3.2 12.8 + - - +
398B ASN* 3.1 21.9 + - - +
399B ALA 4.0 3.8 - - - +
400B THR* 1.3 84.3 + - - +
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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