Contacts of the helix formed by residues 51 - 63 (chain A) in PDB entry 2AY6
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 ARG 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE 3.7 2.5 + - - +
50A MET* 1.3 71.4 - - - +
52A ALA* 1.3 61.9 + - - +
54A HIS* 3.3 7.8 + - - +
55A ALA* 3.1 23.6 + - - +
318A ASP* 3.2 45.3 + - - +
321A ALA* 4.6 5.5 - - - +
322A GLU* 3.0 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.3 1.7 - - + -
51A ARG* 1.3 78.2 - - - +
53A VAL* 1.3 57.3 + - + +
55A ALA* 3.4 7.5 + - - +
56A ALA* 3.1 27.0 + - - +
309A VAL* 3.8 14.2 - - + +
315A LEU* 3.8 22.2 - - + +
318A ASP* 3.7 8.5 + - + +
319A TRP* 3.8 38.1 - - + +
322A GLU* 4.5 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.1 15.5 - - + -
50A MET* 3.0 22.6 + - + +
52A ALA* 1.3 77.5 - - + +
54A HIS* 1.3 65.6 + - - +
56A ALA* 3.1 13.0 + - - +
57A GLU* 3.2 13.9 + - - +
260A PHE* 3.3 38.1 - - + +
261A GLY 5.6 0.2 - - - +
262A ILE* 3.8 18.4 - - + -
305A ILE* 3.7 28.9 - - + -
309A VAL* 4.7 2.0 - - + -
319A TRP* 5.4 1.3 - - + -
68B LYS* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.1 21.3 - - + +
50A MET 3.0 11.8 + - - +
51A ARG* 3.3 10.3 + - - +
53A VAL* 1.3 75.7 - - - +
55A ALA* 1.3 60.5 + - - +
57A GLU* 3.7 13.4 + - - +
58A GLN* 3.4 43.5 + - - +
61B LEU* 3.5 40.9 + - + +
64B GLU 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG 3.1 15.8 + - - +
52A ALA* 3.6 6.3 - - - +
54A HIS* 1.3 75.5 - - - +
56A ALA* 1.3 65.8 + - - +
58A GLN* 3.2 10.4 + - - +
59A ARG* 2.9 55.3 + - - +
315A LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA 3.1 13.9 + - - +
53A VAL 3.1 9.6 + - - +
55A ALA* 1.3 77.0 - - - +
57A GLU* 1.3 56.2 + - - +
59A ARG* 3.2 5.4 + - - +
60A MET* 2.9 35.2 + - - +
305A ILE* 3.8 28.0 - - + +
308A THR* 3.9 27.5 - - + +
309A VAL* 4.1 2.9 - - + -
315A LEU* 4.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 5.0 2.8 - - - +
53A VAL 3.2 10.9 + - - +
54A HIS* 4.0 9.1 - - - +
55A ALA 3.3 0.2 - - - -
56A ALA* 1.3 74.8 - - - +
58A GLN* 1.3 60.7 + - - +
60A MET* 3.8 7.7 - - - +
61A LEU* 3.0 27.9 + - - +
265A GLU* 4.1 0.2 - - - +
301A HIS* 2.8 30.2 + - + +
305A ILE* 3.3 24.6 - - + +
61B LEU* 4.0 25.0 - - + +
68B LYS* 2.8 36.4 + - - -
301B HIS* 4.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.4 41.3 + - + +
55A ALA* 3.2 11.7 + - - +
57A GLU* 1.3 75.5 - - - +
59A ARG* 1.3 88.8 + - - +
61A LEU* 3.0 19.2 + - + +
62A GLU* 3.2 23.6 + - - +
61B LEU* 4.1 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 2.9 45.3 + - - +
56A ALA* 3.5 10.1 - - - +
58A GLN* 1.3 110.4 + - - +
60A MET* 1.3 57.5 + - + +
62A GLU* 3.1 14.3 + - - +
63A THR* 2.8 37.6 + - + +
308A THR* 5.0 9.9 - - + -
315A LEU* 4.5 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 2.9 27.8 + - - +
57A GLU* 3.8 8.1 - - - +
58A GLN 3.2 0.2 - - - -
59A ARG* 1.3 77.0 - - + +
61A LEU* 1.3 57.9 + - - +
63A THR* 3.7 0.4 - - - -
64A GLU* 2.9 56.2 + - + +
300A PHE* 4.6 7.9 - - + -
301A HIS* 3.6 34.3 - - + +
304A LYS* 3.5 40.2 - - + -
305A ILE* 3.5 27.8 - - - -
308A THR* 4.4 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU 3.0 15.0 + - - +
58A GLN* 3.0 13.7 + - + +
60A MET* 1.3 75.8 - - - +
62A GLU* 1.3 62.5 + - + +
64A GLU* 4.8 4.7 - - - +
54B HIS* 3.8 26.4 + - + +
57B GLU* 3.7 38.4 - - + +
58B GLN* 3.5 40.4 - - + +
61B LEU* 4.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 3.6 22.4 - - - +
59A ARG* 3.1 14.9 + - - +
60A MET 3.1 0.6 - - - -
61A LEU* 1.3 83.7 - - + +
63A THR* 1.3 64.2 + - + +
64A GLU 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.8 24.1 + - + +
60A MET* 3.7 0.2 - - - -
62A GLU* 1.3 84.4 - - + +
64A GLU* 1.3 81.2 + - - +
66A THR* 3.1 16.4 + - - +
----------------------------------------------------------
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