Contacts of the strand formed by residues 342 - 346 (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 PHE 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B THR* 3.0 33.2 - - - -
339B ILE* 2.8 23.4 + - - +
340B HIS* 4.3 5.4 - - - +
341B GLU* 1.3 83.1 - - + +
343B LYS* 1.3 63.2 + - - +
344B LYS* 3.4 5.2 + - - +
371B ALA* 3.7 18.2 - - + -
374B CYS* 3.9 24.2 - - + -
375B THR* 3.1 28.0 - - - -
387B PHE* 3.9 8.1 - + - -
419B TYR* 3.7 32.3 - - + -
420B GLU 3.4 3.4 - - - -
421B ASN* 3.7 32.8 - - + -
422B LYS* 4.5 3.4 - - - -
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Residues in contact with LYS 343 (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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342B PHE* 1.3 70.1 - - - +
344B LYS* 1.3 62.7 + - - +
345B SER* 3.8 11.2 + - - +
404B MET* 5.9 2.2 - - - +
418B LEU 3.8 1.2 - - - +
419B TYR* 3.5 1.8 - - - -
420B GLU* 2.8 45.5 + - + +
422B LYS* 4.1 3.7 - - + +
425B ILE* 3.8 31.2 - - + +
437B LYS* 3.0 28.5 + - - +
439B THR* 3.8 25.1 - - + -
471B ASP* 2.8 32.1 + - - -
473B GLN* 6.2 0.4 - - - -
476B TYR* 3.9 26.2 - - - +
478B ARG* 3.9 1.0 - - - +
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Residues in contact with LYS 344 (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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342B PHE 3.4 5.5 + - - +
343B LYS* 1.3 75.4 - - - +
345B SER* 1.3 72.8 + - - +
346B ALA* 4.1 10.1 + - - +
417B ASP* 3.9 16.4 + - + +
418B LEU 3.3 11.9 - - - +
419B TYR* 3.3 42.7 + - + +
474B GLU* 5.5 5.7 - - - +
476B TYR* 4.6 11.2 + - - -
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Residues in contact with SER 345 (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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343B LYS* 3.8 11.9 + - - -
344B LYS* 1.3 74.3 + - - +
346B ALA* 1.3 64.6 + - - +
348B THR* 3.9 16.1 + - - -
410B LYS* 4.4 12.8 + - - -
417B ASP* 3.6 0.2 - - - -
418B LEU* 2.7 56.1 + - - +
420B GLU* 4.7 8.6 + - - -
471B ASP* 5.3 3.8 + - - -
473B GLN* 6.1 0.7 - - - +
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Residues in contact with ALA 346 (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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344B LYS* 3.9 12.9 + - + +
345B SER* 1.3 70.4 - - - +
347B LYS* 1.3 91.2 + - + +
348B THR* 2.8 15.2 + - - -
417B ASP* 3.5 13.5 - - - +
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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