Contacts of the strand formed by residues 325 - 330 (chain B) in PDB entry 3MYV
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 LEU 325 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 3.7 36.1 - - + -
309B TYR* 3.9 19.1 - - + -
310B ALA* 3.9 33.4 - - + -
313B MSE 4.3 11.7 - - + -
314B LEU* 4.4 11.9 - - + -
321B ARG 4.7 1.1 - - - +
322B GLY* 3.1 22.5 + - - +
323B HIS 4.0 4.9 - - - +
324B LEU* 1.3 80.3 - - - +
326B GLU* 1.3 71.9 + - - +
327B GLU 4.2 0.6 + - - -
336B TRP* 4.2 12.1 - - + -
337B TRP 3.6 4.7 - - - +
338B LEU* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TRP* 5.0 9.9 + - - -
298A TYR* 4.8 15.9 - - - -
301A GLN* 5.3 5.0 + - - -
323B HIS 4.8 6.2 - - - +
324B LEU 5.5 0.2 - - - -
325B LEU* 1.3 82.0 - - - +
327B GLU* 1.3 68.7 + - - +
336B TRP* 3.2 4.6 - - - -
337B TRP* 2.9 68.6 + - + +
339B TYR* 4.0 33.2 - - + -
342B ARG* 5.1 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A TYR* 5.2 10.7 - - + -
347A LYS* 2.8 60.4 + - + +
325B LEU 4.2 0.4 + - - -
326B GLU* 1.3 79.6 + - - +
328B ASN* 1.3 71.8 + - - +
329B LYS* 3.7 10.2 + - - +
334B THR* 3.4 32.5 - - + +
335B VAL 3.4 7.0 - - - +
336B TRP* 3.5 27.8 + - - +
337B TRP* 5.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 5.7 5.1 + - - -
348A THR* 5.7 1.0 + - - -
297B TRP* 3.3 58.0 - - + +
298B TYR* 4.7 7.1 + - - -
326B GLU 3.7 0.4 + - - -
327B GLU* 1.3 79.6 + - - +
329B LYS* 1.3 80.2 + - - +
334B THR* 3.5 8.8 - - - +
335B VAL* 2.9 32.6 + - + +
337B TRP* 4.6 8.1 - - + +
501B PO4 4.8 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASP* 5.6 7.2 - - - +
297B TRP* 3.5 14.8 - - - -
327B GLU* 3.7 10.9 + - - +
328B ASN* 1.3 87.9 + - - +
330B TYR* 1.3 61.1 + - - +
332B GLY* 5.1 6.3 - - - +
333B LYS* 3.3 16.4 - - - +
334B THR* 2.6 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 3.6 7.7 + - - -
78B GLU* 3.0 59.7 + - + +
79B GLU* 4.1 9.0 + - - +
297B TRP* 4.4 2.9 - + + -
301B GLN* 3.7 37.9 - - - -
304B PHE* 3.7 22.0 - + + -
329B LYS* 1.3 75.7 - - - +
331B ALA* 1.3 77.2 + - + +
332B GLY 3.1 1.6 - - - -
333B LYS* 2.9 24.7 + - - +
335B VAL* 4.0 24.7 - - + +
442B LEU* 5.9 2.2 - - + -
----------------------------------------------------------
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