Contacts of the strand formed by residues 571 - 579 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PHE* 3.1 31.6 + - - -
425A LYS* 4.9 0.8 - - - +
426A ASP* 2.8 37.5 + - - +
569A LEU* 2.8 26.0 + - + +
570A PRO* 1.3 77.0 - - - +
572A ALA* 1.3 62.2 + - - +
633A GLY* 3.1 25.8 - - - +
634A TYR* 4.0 18.7 + - + +
635A ASN* 3.8 3.6 - - - +
731A GLY* 3.8 2.4 - - - -
732A ASN* 3.0 23.0 + - - +
900A LEU* 4.1 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LYS* 1.3 77.5 - - - +
573A ASN* 1.3 62.6 + - - +
574A LEU* 4.3 10.1 - - + -
633A GLY 2.8 19.6 + - - -
635A ASN* 4.2 9.6 - - + +
638A GLN* 2.8 38.9 + - - +
730A HIS 3.6 12.1 - - - +
731A GLY* 4.1 6.3 - - - -
732A ASN 4.2 2.7 - - - +
733A ILE* 4.6 8.7 - - + -
900A LEU* 3.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ALA* 1.3 75.7 - - - +
574A LEU* 1.3 64.8 + - - +
575A ASN* 4.1 14.1 - - - +
631A VAL 3.6 2.9 - - - -
632A LYS* 3.3 34.4 - - + +
633A GLY 4.5 1.0 + - - -
728A LEU* 3.9 1.5 - - + +
729A LEU* 3.7 1.4 - - - -
730A HIS* 2.9 35.2 + - + +
900A LEU* 3.5 18.0 - - - +
901A SER* 3.6 19.5 + - - +
904A SER* 2.6 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ALA* 4.3 8.1 - - + -
573A ASN* 1.3 81.7 - - - +
575A ASN* 1.3 62.1 + - - +
576A PHE* 4.0 12.2 - - + -
629A LEU 3.8 1.4 - - - +
630A SER* 3.3 1.7 - - - -
631A VAL* 2.8 47.0 + - + +
638A GLN* 3.8 36.1 - - + +
639A PRO 5.6 0.4 - - - -
642A LEU* 3.9 28.0 - - + -
728A LEU 3.7 3.8 - - - -
729A LEU* 3.8 23.6 - - + -
733A ILE* 4.5 9.4 - - + -
741A ILE* 4.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ASN* 4.1 12.0 - - - +
574A LEU* 1.3 82.3 + - - +
576A PHE* 1.3 63.1 + - - +
628A TYR* 3.6 15.5 + - - -
629A LEU 3.6 2.2 - - - -
630A SER* 3.0 24.7 + - - -
632A LYS* 4.3 7.2 + - - +
727A ALA* 3.0 9.0 - - - +
728A LEU* 2.8 49.2 + - + +
729A LEU* 4.1 1.6 - - - +
904A SER* 5.4 4.4 - - - -
908A TRP* 3.8 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 4.0 21.1 - - + -
575A ASN* 1.3 73.0 - - - +
577A GLU* 1.3 59.0 + - - +
578A PHE* 3.6 23.3 + + + -
628A TYR* 3.5 5.7 - - - -
629A LEU* 2.8 55.4 + - + +
631A VAL* 5.1 1.1 - - + -
642A LEU* 3.9 34.3 - - + -
725A ILE* 4.1 15.5 - - + -
726A GLU 3.5 3.4 - - - -
727A ALA* 3.7 22.9 - - + -
729A LEU* 4.1 18.6 - - + -
741A ILE* 4.5 4.9 - - + -
742A MET* 4.3 11.0 - - + -
745A VAL* 4.1 17.7 - - + -
908A TRP* 4.1 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PHE* 1.3 69.3 - - - +
578A PHE* 1.3 70.6 + - - +
579A PHE* 3.7 25.6 - - + -
623A THR* 3.6 32.6 + - - +
625A TYR* 3.9 16.5 - - - +
627A MET 3.6 10.9 - - - +
628A TYR* 4.1 8.0 - - + +
724A HIS 3.6 1.4 - - - +
725A ILE* 3.3 6.0 - - - -
726A GLU* 2.6 41.8 + - + +
908A TRP* 3.7 22.9 - - + -
911A ILE* 6.5 0.2 - - + -
912A ILE* 4.0 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PHE* 3.9 26.7 - + + -
577A GLU* 1.3 76.1 - - - +
579A PHE* 1.3 59.8 + - - +
620A LEU* 5.4 1.8 - - + -
625A TYR 3.7 0.7 - - - +
626A GLY* 3.4 4.4 - - - -
627A MET* 2.8 77.9 + - + +
629A LEU* 3.9 17.5 - - + -
646A ILE* 4.3 21.1 - - + -
649A MET* 5.1 10.1 - - + -
723A LEU* 4.3 17.7 - - + -
724A HIS 3.6 1.8 - - - -
725A ILE* 3.9 33.4 - - + -
745A VAL* 4.4 5.8 - - + -
749A LEU* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLU* 3.7 34.1 - - + -
578A PHE* 1.3 74.7 - - - +
580A SER* 1.3 61.5 + - - +
625A TYR* 3.4 40.8 - + + -
723A LEU* 3.3 29.5 - - - +
724A HIS* 2.8 37.3 + + + +
726A GLU* 4.5 19.3 - - + -
758A LEU* 3.3 16.0 - - + +
763A LEU* 4.3 20.2 - - + -
764A VAL 6.2 0.2 - - - -
765A ARG* 5.0 13.2 - - - -
912A ILE* 6.2 1.3 - - - -
914A GLN* 5.2 9.9 - - - -
----------------------------------------------------------
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