Contacts of the strand formed by residues 359 - 363 (chain B) in PDB entry 1BJW
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 HIS 359 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PRO* 4.6 19.5 - - + +
150B PHE* 4.6 10.6 - + - -
324B LEU* 4.0 38.1 - - + +
325B MET 3.3 7.0 - - - +
326B ASP* 3.6 36.2 + - + +
327B THR* 4.1 3.6 - - - -
334B GLU* 3.3 11.6 - - - +
351B GLY* 3.0 22.1 + - - -
356B ALA* 3.7 12.8 + - + +
357B PHE 3.0 24.3 + - - -
358B GLY* 1.3 82.3 - - - +
360B VAL* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL 3.7 0.2 - - - +
324B LEU* 3.5 5.1 - - - -
325B MET* 2.9 47.9 + - + +
327B THR* 3.8 18.4 - - + -
334B GLU 4.8 3.1 - - - +
338B ALA* 4.7 6.3 - - + -
341B LEU* 4.8 1.8 - - + -
348B VAL* 3.0 31.0 - - + -
349B VAL 3.0 23.3 - - - +
350B PRO* 3.8 7.0 - - + -
351B GLY 4.0 0.4 - - - +
359B HIS* 1.3 74.3 - - - +
361B ARG* 1.3 57.6 + - - +
362B LEU* 3.7 23.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 3.8 5.2 + - - +
37B THR 3.1 25.5 + - - -
38B ALA 3.8 2.8 + - - -
175B ASN* 3.1 19.4 + - - -
176B PRO* 3.6 28.9 - - + +
322B TYR* 3.4 45.3 - - + -
323B VAL 3.6 3.6 - - - +
324B LEU* 3.9 10.6 - - + +
349B VAL* 2.8 54.9 + - + +
351B GLY 4.7 1.2 - - - +
354B PHE* 3.9 22.7 - - + -
360B VAL* 1.3 71.2 - - - +
362B LEU* 1.3 65.9 + - - +
363B SER* 5.1 1.8 - - - -
414B PO4 3.0 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.8 17.9 - - + -
303B LEU* 4.0 30.7 - - + -
307B LEU* 4.6 5.6 - - + -
322B TYR* 3.2 5.9 - - - +
323B VAL* 2.8 45.0 + - + +
325B MET* 4.3 20.4 - - + -
348B VAL* 3.6 31.6 - - + -
360B VAL* 4.0 13.0 - - + -
361B ARG* 1.3 76.2 - - - +
363B SER* 1.3 60.6 + - - +
364B TYR* 4.3 0.6 + - - -
378B PHE* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.0 39.7 + - - +
37B THR 4.1 1.1 - - - -
38B ALA* 2.7 34.7 + - - +
303B LEU* 5.6 0.9 - - - -
321B PHE* 3.4 15.3 + - - -
322B TYR* 4.1 7.4 - - - -
361B ARG* 5.1 1.3 - - - -
362B LEU* 1.3 75.0 - - - +
364B TYR* 1.3 60.5 + - - +
365B ALA* 3.3 13.4 + - - +
366B THR* 3.8 9.9 + - - -
371B LEU* 4.5 1.3 - - - +
----------------------------------------------------------
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