Contacts of the strand formed by residues 571 - 579 (chain B) in PDB entry 3H44
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 LYS 571 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B PHE* 2.8 29.0 + - - +
425B LYS* 4.6 1.0 - - - +
426B ASP* 2.8 32.2 + - - +
564B ASP* 5.7 0.3 - - - +
569B LEU* 2.6 29.5 + - + +
570B PRO* 1.3 76.2 - - + +
572B ALA* 1.3 61.0 + - - +
573B ASN* 6.0 0.2 - - - +
633B GLY* 3.1 28.3 - - - +
634B TYR* 3.8 26.3 + - + +
635B ASN* 3.2 5.5 + - - +
731B GLY* 3.8 3.1 - - - -
732B ASN* 3.1 21.0 + - - +
900B LEU* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LYS* 1.3 75.8 - - - +
573B ASN* 1.3 70.8 + - - +
574B LEU* 4.5 5.2 - - + -
632B LYS* 3.5 0.9 - - - -
633B GLY 2.9 13.1 + - - -
635B ASN* 3.8 11.3 - - + +
638B GLN* 2.9 39.0 + - - +
730B HIS 3.7 9.0 - - - +
732B ASN 4.3 7.9 - - - +
733B ILE* 4.3 16.2 - - + -
900B LEU* 4.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LYS* 6.0 0.2 - - - +
572B ALA* 1.3 80.9 - - - +
574B LEU* 1.3 65.2 + - - +
575B ASN* 4.0 8.1 - - - +
631B VAL 3.4 2.5 - - - +
632B LYS* 3.4 30.5 - - + +
633B GLY 4.1 1.4 + - - -
728B LEU* 3.9 1.4 - - + +
729B LEU* 3.5 2.3 - - - -
730B HIS* 2.7 41.2 + - + +
900B LEU* 3.6 15.1 - - - +
901B SER* 3.3 29.8 - - - +
904B SER* 3.1 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ALA* 4.5 7.0 - - + -
573B ASN* 1.3 82.7 - - - +
575B ASN* 1.3 62.6 + - - +
576B PHE* 3.4 20.6 - - + -
630B SER* 3.4 2.9 - - - -
631B VAL* 2.8 41.9 + - + +
638B GLN* 3.6 39.5 - - + +
639B PRO* 6.2 0.2 - - + -
642B LEU* 4.7 12.1 - - + -
728B LEU 3.6 3.4 - - - -
729B LEU* 3.7 23.1 - - + -
733B ILE* 4.9 5.2 - - + -
741B ILE* 4.2 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASN* 4.4 4.8 - - - +
574B LEU* 1.3 81.7 - - - +
576B PHE* 1.3 65.8 + - - +
628B TYR* 4.2 11.4 + - + -
629B LEU 3.6 2.9 - - - +
630B SER* 2.8 27.8 + - - -
632B LYS* 4.1 13.9 + - - +
727B ALA* 3.0 9.5 - - - +
728B LEU* 2.7 45.0 + - + +
904B SER* 4.7 6.9 - - - -
908B TRP* 3.6 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B LEU* 3.4 32.3 - - + -
575B ASN* 1.3 86.6 - - - +
577B GLU* 1.3 61.7 + - - +
578B PHE* 3.7 25.5 - + + -
627B MET 3.6 0.9 - - - +
628B TYR* 3.5 4.9 - - - -
629B LEU* 2.9 53.0 + - + +
631B VAL* 5.5 0.4 - - + -
642B LEU* 4.6 12.1 - - + -
725B ILE* 3.9 15.3 - - + -
726B GLU 3.2 6.7 - - - +
727B ALA* 3.8 20.6 - - + -
729B LEU* 3.7 15.9 - - + -
741B ILE* 4.6 4.5 - - + -
742B MET* 4.3 12.8 - - + -
745B VAL* 4.1 28.3 - - + -
908B TRP* 3.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B PHE* 1.3 70.5 - - - +
578B PHE* 1.3 60.9 + - - +
579B PHE* 3.8 35.9 - - + -
623B THR* 3.4 39.6 + - - +
625B TYR* 4.2 8.1 - - - +
627B MET 3.5 7.0 - - - +
628B TYR* 4.0 10.0 - - + +
724B HIS 3.6 0.3 - - - +
725B ILE* 3.4 5.5 - - - +
726B GLU* 2.8 39.8 + - + +
908B TRP* 3.5 26.0 + - + -
912B ILE* 4.1 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B PHE* 3.7 33.7 - + + -
577B GLU* 1.3 75.2 - - - +
579B PHE* 1.3 63.0 + - - +
620B LEU* 5.8 1.1 - - + -
625B TYR 4.2 0.3 - - - -
626B GLY* 3.1 5.5 + - - -
627B MET* 2.8 74.0 + - + +
629B LEU* 3.9 17.9 - - + -
646B ILE* 4.3 20.4 - - + -
649B MET* 5.5 7.4 - - - -
723B LEU* 4.5 15.3 - - + -
724B HIS 3.4 5.8 - - - +
725B ILE* 3.5 36.1 - - + -
745B VAL* 4.6 2.2 - - + -
749B LEU* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLU* 3.8 32.8 - - + -
578B PHE* 1.3 74.2 - - - +
580B SER* 1.3 62.2 + - - +
625B TYR* 3.4 20.6 - + + +
723B LEU* 3.4 27.7 - - - +
724B HIS* 2.9 50.7 + + + +
726B GLU* 4.1 26.5 - - + -
758B LEU* 3.6 5.4 - - + +
763B LEU* 4.1 21.1 - - + -
765B ARG* 2.9 36.1 - - - -
912B ILE* 6.5 1.3 - - - -
914B GLN* 5.6 1.1 - - - -
----------------------------------------------------------
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