Contacts of the strand formed by residues 386 - 390 (chain B) in PDB entry 1BHT
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 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B PHE* 5.6 0.2 - - - -
374B CYS* 4.9 1.3 - - - -
384B CYS* 3.7 7.1 - - - -
385B LYS* 1.3 78.1 - - - +
387B PHE* 1.3 67.4 + - - +
399B PHE* 2.9 36.5 + - + +
401B PHE 3.2 20.9 - - - +
402B ASN* 3.9 14.1 - - + -
418B LEU* 4.2 5.4 - - + -
419B TYR 3.1 13.2 - - - +
420B GLU* 4.0 7.6 - - + -
421B ASN 4.4 0.9 - - - +
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 4.2 2.7 - - + -
342B PHE* 3.9 20.9 - + - -
367B ALA 3.5 19.3 - - - -
370B CYS* 3.3 24.7 - - + -
371B ALA* 3.4 26.5 - - + -
374B CYS* 4.2 9.6 - - + -
386B ALA* 1.3 76.8 - - - +
388B VAL* 1.3 72.0 + - - +
389B PHE* 4.1 7.6 - - + -
397B LEU 3.4 8.7 - - - +
398B TRP* 3.9 20.9 - - + -
399B PHE* 4.2 0.7 - - - -
418B LEU* 4.4 0.7 - - - -
419B TYR* 2.8 83.7 + + + +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 3.7 30.5 - - - +
387B PHE* 1.3 75.6 - - - +
389B PHE* 1.3 64.9 + - - +
390B ASP 3.9 1.3 + - - +
396B CYS* 3.6 2.1 - - - -
397B LEU* 2.9 40.5 + - + +
399B PHE* 3.3 29.8 - - + -
416B PHE* 3.6 34.3 - - + -
417B ASP 3.3 8.1 - - - +
418B LEU* 3.6 20.9 - - + -
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Residues in contact with PHE 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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364B VAL* 4.5 4.0 - - + -
365B ASN 3.5 24.0 - - - -
366B THR* 4.0 7.2 - - - -
367B ALA* 3.6 26.9 - - + -
370B CYS* 3.4 19.5 - - - -
387B PHE* 3.9 18.4 + - + -
388B VAL* 1.3 74.9 - - - +
390B ASP* 1.3 60.6 + - - +
391B LYS* 3.3 29.0 + - + +
394B LYS* 3.7 17.7 - - + -
395B GLN* 3.1 39.3 - - - -
396B CYS* 4.6 0.7 - - - +
416B PHE* 3.7 3.3 - - - -
417B ASP* 3.0 32.8 + - + +
419B TYR* 4.7 3.8 - - + -
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Residues in contact with ASP 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 VAL* 3.9 2.0 + - - +
389B PHE* 1.3 71.2 - - - +
391B LYS* 1.3 59.2 + - - +
392B ALA 3.1 8.7 + - - -
393B ARG* 3.0 40.9 + - - +
394B LYS* 2.9 27.0 + - - -
395B GLN* 2.8 27.7 + - + +
397B LEU* 4.7 8.2 - - + +
415B GLU* 3.1 27.4 - - - +
416B PHE* 4.0 19.6 - - + -
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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