Contacts of the strand formed by residues 386 - 392 (chain A) in PDB entry 1SNU
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 ASP 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A TYR* 3.1 6.1 - - - -
382A TRP* 2.9 59.3 + - + +
383A LEU* 5.0 1.7 - - - +
384A ASN 2.5 11.3 + - - -
385A LYS* 1.3 97.7 - - - +
387A LYS* 1.3 60.3 + - - +
388A VAL* 3.1 12.5 + - + +
422A TYR* 3.3 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.3 22.2 - - + +
380A GLY 3.4 8.5 - - - +
381A TYR* 3.5 38.2 + - + +
386A ASP* 1.3 69.2 - - - +
388A VAL* 1.3 60.1 + - - +
422A TYR* 5.1 1.2 - - - -
436A GLU* 4.6 0.9 - - - -
437A PHE* 2.9 52.0 + - + +
439A GLU* 2.6 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.9 1.2 - - - +
380A GLY 2.9 42.6 + - - +
381A TYR* 3.6 7.6 - - - +
382A TRP* 3.9 8.7 - - + +
386A ASP* 3.3 17.9 - - + +
387A LYS* 1.3 75.4 - - - +
389A ALA* 1.3 60.8 + - - +
390A ILE* 3.9 17.9 - - + -
422A TYR* 3.4 36.3 - - + -
434A VAL* 3.8 14.8 - - + -
435A PHE 3.1 8.7 - - - +
437A PHE* 3.7 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A STU 3.2 51.1 - - + +
369A ILE* 4.9 0.7 - - + -
377A VAL* 4.5 5.4 - - + -
378A HIS 3.5 7.2 - - - +
388A VAL* 1.3 73.3 - - - +
390A ILE* 1.3 60.3 + - - +
433A LEU 3.5 2.4 - - - +
435A PHE* 2.7 41.5 + - + +
436A GLU 4.2 1.3 - - - +
437A PHE* 4.0 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 3.7 34.1 - - + -
364A THR 4.5 2.2 - - - +
365A PHE* 3.8 28.3 - - + -
376A LEU 3.7 1.0 - - - +
377A VAL* 3.1 4.1 - - - -
378A HIS* 2.6 45.0 + - - +
380A GLY* 4.1 14.6 - - - -
388A VAL* 3.9 24.9 - - + -
389A ALA* 1.3 74.4 - - - +
391A LYS* 1.3 60.5 + - - +
392A THR* 3.8 1.4 + - + -
432A CYS* 3.5 33.9 - - + -
433A LEU 3.5 5.6 - - - +
434A VAL* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A STU 3.5 37.6 - - + +
374A PHE* 3.1 39.6 + - - +
375A GLY 4.2 9.5 + - - -
376A LEU 3.5 4.5 - - - +
377A VAL* 3.9 16.8 - - + +
389A ALA 4.0 1.0 + - - -
390A ILE* 1.3 73.3 - - - +
392A THR* 1.3 66.4 + - - +
393A ILE* 4.6 6.2 - - + +
432A CYS* 3.3 2.6 - - - +
433A LEU* 2.9 38.8 + - + +
435A PHE* 4.0 20.9 - - + -
500A ASP* 4.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A PHE* 4.1 26.7 - - + -
374A PHE 3.1 6.4 - - - +
375A GLY* 2.7 23.1 - - - -
376A LEU* 2.9 32.1 + - - +
378A HIS* 4.3 8.6 + - + +
390A ILE* 4.5 1.6 - - + +
391A LYS* 1.3 81.6 - - - +
393A ILE* 1.3 58.1 + - - +
430A PRO* 4.4 20.2 - - + +
431A ILE 3.6 7.2 - - - -
432A CYS* 3.9 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