Contacts of the strand formed by residues 333 - 338 (chain B) in PDB entry 3B6R
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 VAL 333 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.0 24.2 - - + -
296B HIS* 4.0 28.9 - - + +
297B ILE 3.5 9.0 - - - +
298B LYS* 4.2 13.2 - - + -
322B THR* 2.9 47.0 + - + +
329B ALA* 3.6 9.8 - - - +
330B VAL 3.2 12.0 + - - +
331B GLY* 3.1 12.3 - - - +
332B GLY* 1.3 75.8 - - - +
334B PHE* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B VAL 3.2 3.6 - - - +
296B HIS* 3.4 3.6 - - - -
297B ILE* 2.8 41.7 + - + +
299B LEU* 3.1 38.8 - - + -
300B PRO* 5.1 0.4 - - + -
303B GLY* 3.3 27.6 - - - -
308B PHE* 4.6 16.2 - + + -
319B LYS* 4.7 15.3 - - + -
320B ARG 4.1 6.7 - - - +
329B ALA* 3.5 26.0 - - + -
332B GLY* 3.3 27.8 - - - -
333B VAL* 1.3 73.9 - - - +
335B ASP* 1.3 60.7 + - - +
336B VAL* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 3.1 42.8 + - - -
294B GLY* 4.9 0.9 - - - -
295B VAL 3.4 8.4 + - - +
296B HIS* 4.2 9.8 - - - +
318B GLN 3.5 1.4 - - - +
319B LYS* 3.2 6.4 - - - -
320B ARG* 2.8 55.1 + - + +
321B GLY 3.5 15.6 + - - +
324B GLY* 5.0 0.2 - - - -
333B VAL 4.2 0.6 + - - -
334B PHE* 1.3 70.5 - - - +
336B VAL* 1.3 65.8 + - - +
337B SER* 4.2 0.3 - - - -
601B ADP 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLY* 2.9 20.7 - - - -
295B VAL* 2.9 18.7 + - + +
297B ILE* 4.1 23.8 - - + -
299B LEU* 5.1 0.9 - - + -
308B PHE* 4.9 5.6 - - + -
312B LEU* 4.4 10.8 - - + -
317B LEU* 4.0 24.7 - - + -
318B GLN 3.5 4.7 - - - +
319B LYS* 4.8 5.4 - - + -
334B PHE* 4.3 10.8 - - + -
335B ASP* 1.3 75.0 - - - +
337B SER* 1.3 64.3 + - - +
353B VAL* 4.6 2.9 - - + +
357B VAL* 5.0 8.3 - - + -
360B LEU* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 2.8 46.5 + - - +
293B ALA 3.0 22.9 - - - -
294B GLY* 3.8 1.1 - - - -
317B LEU* 3.2 11.2 - - - -
318B GLN* 2.7 48.0 + - - +
320B ARG* 4.9 0.3 + - - -
335B ASP* 4.1 0.4 + - - -
336B VAL* 1.3 74.7 - - - +
338B ASN* 1.3 58.8 + - - +
353B VAL* 4.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.0 20.8 + - - +
292B ARG* 3.5 2.2 - - - +
293B ALA* 2.7 45.7 + - - +
316B ARG 3.7 7.2 - - - +
317B LEU* 3.9 6.1 - - + -
318B GLN* 4.9 0.6 - - - +
337B SER* 1.3 76.9 + - - +
339B ALA* 1.3 59.5 + - - +
340B ASP 3.0 20.5 - - - +
341B ARG* 2.9 24.1 + - - -
349B LEU* 3.4 23.5 - - + +
352B MET* 4.4 9.2 - - + -
353B VAL* 3.5 13.5 - - + +
----------------------------------------------------------
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