Contacts of the strand formed by residues 419 - 425 (chain A) in PDB entry 5H65
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 TYR 419 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 2.6 30.8 + - - +
415A ASN* 3.4 3.3 - - - -
416A THR* 3.0 55.7 + - + +
418A LEU* 1.3 98.5 - - + +
420A ASP* 1.3 59.8 + - - +
421A SER* 3.5 13.5 - - - -
437A HIS* 3.5 28.7 - - + -
438A PHE 3.2 21.1 - - - +
439A VAL* 4.0 4.7 - - + -
440A LYS* 3.7 9.2 - - - +
454A LEU* 3.9 13.7 - - + -
482A ASP* 4.4 8.2 + - - -
483A LEU* 3.2 28.2 - - + +
512A ILE* 4.4 4.3 - - + -
513A GLN* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 3.6 9.5 - - - +
419A TYR* 1.3 73.1 - - - +
421A SER* 1.3 61.5 + - - +
437A HIS* 3.2 2.4 - - - -
438A PHE* 2.7 50.3 + - + +
440A LYS* 3.2 30.3 + - - +
445A LEU* 3.5 23.5 - - + +
268B GLN* 3.3 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLN* 3.3 29.0 - - - -
415A ASN* 2.8 41.9 + - - +
419A TYR* 3.5 2.6 - - - -
420A ASP* 1.3 75.1 - - - +
422A LYS* 1.3 75.0 + - - +
423A ILE* 5.5 0.4 - - - -
436A VAL 3.5 4.5 - - - -
437A HIS* 2.9 26.3 + - - -
438A PHE* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A SER* 1.3 80.5 + - - +
423A ILE* 1.3 68.6 + - - +
424A TRP* 3.4 26.7 - - + -
435A ALA* 3.4 2.6 - - - -
436A VAL 2.9 35.1 + - - +
437A HIS* 5.7 0.2 - - - -
438A PHE* 4.4 5.2 - - + -
268B GLN* 4.8 15.7 + - - +
272B VAL* 4.0 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PRO* 4.1 7.6 - - + -
411A VAL* 6.2 0.7 - - + -
414A GLN* 3.4 39.3 - - + +
422A LYS* 1.3 80.3 - - - +
424A TRP* 1.3 74.3 + - - +
425A THR* 4.2 5.5 + - + +
433A LYS* 4.3 23.8 - - + -
434A VAL 3.3 5.4 - - - +
435A ALA* 3.2 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 3.4 36.3 - - + -
423A ILE* 1.3 76.4 - - - +
425A THR* 1.3 61.4 + - - +
426A THR* 4.6 0.7 - - - +
433A LYS* 3.4 7.4 - - - +
434A VAL* 2.8 38.2 + - + +
436A VAL* 3.4 25.4 - - + -
438A PHE* 4.4 4.3 - + - -
272B VAL* 3.7 31.6 - - + +
275B ALA* 4.0 18.2 - - + -
276B GLU* 3.2 32.3 + - + +
279B LEU* 3.6 16.4 - - + -
281B LEU* 3.5 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 4.2 5.6 + - + +
424A TRP* 1.3 78.9 - - - +
426A THR* 1.3 69.9 + - - +
432A ARG 4.3 3.8 - - - -
433A LYS* 4.7 20.9 - - + -
281B LEU* 3.9 14.0 - - - +
----------------------------------------------------------
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