Contacts of the strand formed by residues 395 - 399 (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 GLN 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B THR* 4.5 16.1 - - - +
362B LYS* 3.0 26.2 + - - +
363B LYS* 3.9 9.2 - - - +
364B VAL 4.2 2.7 - - - +
389B PHE* 3.1 12.6 - - - -
390B ASP* 2.8 42.2 + - + +
393B ARG* 3.4 42.7 + - + +
394B LYS* 1.3 75.1 - - - +
396B CYS* 1.3 56.4 + - - +
397B LEU* 4.4 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS 4.5 0.2 - - - -
361B THR* 3.3 5.5 - - - -
362B LYS 2.9 28.9 + - - -
364B VAL* 3.8 20.4 - - - -
370B CYS* 2.0 48.9 - - + -
387B PHE* 5.2 0.4 - - + -
388B VAL 3.6 5.6 - - - +
395B GLN* 1.3 74.3 - - - +
397B LEU* 1.3 66.7 + - - +
398B TRP* 3.3 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 5.5 4.0 - - - +
350B LEU 5.8 1.6 - - - +
359B ILE* 4.2 11.9 - - + -
360B LYS 3.5 4.5 - - - -
361B THR* 3.9 15.5 - - + -
387B PHE* 3.4 3.2 - - - +
388B VAL* 2.9 42.3 + - + +
390B ASP* 4.7 13.0 - - + +
395B GLN* 4.4 15.7 - - + +
396B CYS* 1.3 79.2 - - - +
398B TRP* 1.3 65.0 + - - +
399B PHE* 3.4 35.0 + - + -
416B PHE* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 3.5 8.3 - - - -
360B LYS* 2.7 62.9 + - + +
362B LYS* 3.2 43.3 - - + -
364B VAL* 4.8 2.2 - - + -
369B GLN 4.6 1.3 - - - -
370B CYS* 3.1 25.3 + - - +
373B ARG* 3.1 39.8 - - + +
374B CYS* 4.0 3.6 - - + -
380B LEU* 3.8 25.8 - - + -
382B PHE* 3.7 6.0 - - + -
384B CYS* 3.8 22.7 - - - -
386B ALA 4.0 1.1 - - - -
387B PHE* 3.9 11.7 - - + -
396B CYS* 3.3 34.4 - - + +
397B LEU* 1.3 69.4 - - - +
399B PHE* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 4.7 0.4 - - - -
350B LEU* 3.9 39.9 - - + -
359B ILE* 3.8 26.9 - - + -
382B PHE* 4.1 3.4 - - - -
384B CYS* 3.7 5.6 - - - -
385B LYS 3.0 22.7 + - - -
386B ALA* 2.9 26.1 + - + +
387B PHE 4.2 0.2 - - - -
388B VAL* 3.3 34.8 - - + -
397B LEU* 3.6 38.8 - - + -
398B TRP* 1.3 78.3 - - - +
400B PRO* 1.3 66.2 - - + +
401B PHE* 3.2 35.4 - + + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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