Contacts of the helix formed by residues 569 - 577 (chain A) in PDB entry 1N54
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 PHE 569 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A PHE* 3.4 34.8 - + - -
512A ALA 3.4 23.8 - - - -
513A THR 4.6 1.8 - - - -
514A ASN* 3.5 12.3 - - - +
517A ILE* 3.9 15.9 - - + -
547A PHE* 3.7 18.2 - + + -
551A LEU* 3.5 27.6 - - + -
565A ALA* 3.1 19.8 + - - +
566A LEU 3.8 3.4 - - - -
568A LYS* 1.3 104.8 - - + +
570A HIS* 1.3 63.2 + - - +
571A GLU 3.2 2.9 - - - -
572A VAL* 2.9 21.1 + - + +
573A PHE* 3.1 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A LEU 3.1 15.4 + - - +
567A ALA* 2.9 22.9 - - - +
568A LYS 3.0 2.7 - - - +
569A PHE* 1.3 76.1 - - - +
571A GLU* 1.3 62.6 + - - +
573A PHE* 3.1 7.3 + - - +
574A LYS* 2.9 55.7 + - + +
611A THR* 3.4 32.4 + - - -
613A ILE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 3.3 22.7 - - - +
515A ASP* 5.1 5.4 - - - +
518A PHE* 3.8 24.1 - - + -
568A LYS 4.4 0.8 + - - +
569A PHE 3.2 0.8 - - - -
570A HIS* 1.3 83.4 + - - +
572A VAL* 1.3 64.6 + - - +
574A LYS* 4.0 5.1 - - + +
575A THR* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 3.4 35.0 - - + +
517A ILE* 4.3 9.9 - - + -
518A PHE* 3.9 14.6 - - + -
521A LEU* 3.9 14.8 - - + -
547A PHE* 3.3 21.3 - - + -
569A PHE* 2.9 18.8 + - + +
571A GLU* 1.3 74.0 - - - +
573A PHE* 1.3 61.0 + - - +
575A THR* 2.4 29.4 - - - +
576A LEU* 2.8 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PHE* 3.6 24.9 - + - -
548A VAL* 3.8 33.9 - - + -
551A LEU* 4.1 16.8 - - + -
552A LEU* 6.0 2.5 - - + -
566A LEU* 3.2 52.0 - - + -
569A PHE 3.1 17.1 + - - -
570A HIS 3.1 7.1 + - - +
572A VAL* 1.3 79.6 - - - +
574A LYS* 1.3 58.1 + - - +
575A THR 3.0 0.3 + - - -
576A LEU* 3.1 5.6 + - + +
577A ALA* 2.8 35.3 + - - +
586A VAL* 4.6 15.9 - - + -
613A ILE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A HIS* 2.9 50.0 + - + +
571A GLU* 4.2 6.1 - - - +
573A PHE* 1.3 73.6 - - - +
575A THR* 1.3 60.0 + - - +
577A ALA 3.8 17.1 - - - +
578A GLU* 4.0 13.7 - - - +
583A LYS* 5.4 4.5 - - - +
612A GLN* 3.5 33.5 - - + +
613A ILE* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 3.3 28.5 - - + -
543A LYS* 5.9 3.0 + - - +
571A GLU* 3.1 13.7 + - - +
572A VAL 2.4 38.1 - - - +
574A LYS* 1.3 78.6 - - - +
576A LEU* 1.3 75.0 + - + +
577A ALA 3.6 0.2 + - - -
578A GLU* 3.9 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A PHE* 6.0 0.2 - - + -
521A LEU* 4.3 2.0 - - + -
539A PHE* 5.0 9.7 + - - -
540A ASN* 5.4 2.3 + - + +
543A LYS* 3.7 44.6 - - + +
544A ILE* 3.9 39.4 - - + +
547A PHE* 3.4 27.4 - - + -
572A VAL* 2.8 45.7 + - + +
573A PHE* 3.7 5.2 - - + +
575A THR* 1.3 86.0 - - + +
577A ALA* 1.3 57.2 + - + +
578A GLU 3.4 4.0 + - - -
579A SER* 4.9 4.2 + - - -
582A GLY* 5.0 0.7 - - - -
586A VAL* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 5.4 0.7 - - + -
573A PHE 2.8 17.4 + - - +
574A LYS* 3.8 11.7 - - - +
576A LEU* 1.3 69.9 - - - +
578A GLU* 1.3 54.9 + - - +
579A SER 3.4 3.1 - - - +
582A GLY* 3.9 7.2 - - - -
583A LYS* 2.6 48.4 + - + +
586A VAL* 3.8 28.3 - - + -
613A ILE* 4.3 9.1 - - + +
----------------------------------------------------------
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