Contacts of the helix formed by residues 570 - 577 (chain A) in PDB entry 3A1B
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 GLY 570 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 3.7 7.6 + - - -
568A GLY 3.3 0.6 + - - -
569A PRO* 1.3 71.8 - - - +
571A ALA* 1.3 57.3 + - - +
572A ALA 3.3 2.2 - - - -
573A GLN* 3.3 11.7 + - - +
574A ALA* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A VAL* 3.7 13.4 - - + +
567A VAL* 3.6 31.0 - - + -
568A GLY* 3.0 19.7 + - - +
569A PRO 3.3 2.0 + - - -
570A GLY* 1.3 76.5 - - - +
572A ALA* 1.3 56.4 + - - +
574A ALA* 3.5 6.9 + - - +
575A ALA* 3.0 28.6 + - - +
584A TYR* 4.5 2.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
547A LEU* 4.0 8.2 - - + +
560A VAL* 3.9 29.8 - - + -
563A VAL* 3.5 16.7 - - + +
564A ASP* 3.3 22.6 + - - +
571A ALA* 1.3 74.7 - - - +
573A GLN* 1.3 58.1 + - - +
575A ALA* 3.0 3.8 + - - +
576A ILE* 2.8 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 4.7 0.2 + - - -
570A GLY* 3.3 11.7 + - - +
572A ALA* 1.3 78.5 - - - +
574A ALA* 1.3 61.6 + - - +
576A ILE* 3.4 29.7 + - - +
577A LYS* 3.1 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A GLY 3.0 17.2 + - - +
571A ALA* 3.7 8.3 - - - +
573A GLN* 1.3 77.6 - - - +
575A ALA* 1.3 57.4 + - - +
577A LYS* 3.4 15.1 + - - +
578A GLU* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A EDO 5.3 0.2 - - - +
456A ALA* 2.9 20.9 + - - +
547A LEU* 3.5 21.5 - - + -
571A ALA 3.0 14.5 + - - +
572A ALA 3.4 7.0 - - - +
574A ALA* 1.3 74.1 - - - +
576A ILE* 1.3 66.3 + - - +
578A GLU* 3.0 13.8 + - - +
581A TRP* 3.4 33.4 - - + +
584A TYR* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ALA* 3.2 31.6 + - - +
458A THR* 3.9 12.3 - - + -
545A GLU* 4.2 17.3 - - - +
547A LEU* 3.5 25.6 - - + -
560A VAL* 5.7 1.6 - - + -
572A ALA* 2.8 28.7 + - + +
573A GLN* 3.6 34.3 - - - +
575A ALA* 1.3 70.9 - - - +
577A LYS* 1.3 59.5 + - + +
579A ASP* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLN* 3.1 43.2 + - - +
574A ALA* 3.6 12.8 - - - +
576A ILE* 1.3 74.4 - - + +
578A GLU* 1.3 58.9 + - - +
579A ASP* 4.0 3.0 + - - +
----------------------------------------------------------
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