Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 2PY5
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 SER 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 5.3 1.5 - - - +
27A TYR* 3.4 13.7 - - - -
41A GLY 3.6 2.2 - - - -
42A ASN* 1.3 85.7 - - - +
44A LEU* 1.3 61.9 + - - +
45A ASP 3.3 4.9 + - - -
46A GLU* 3.1 21.8 + - - -
47A PHE 3.1 16.3 + - - -
9001A EDO 2.8 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.6 36.3 - - + -
24A VAL* 4.1 37.6 + - + +
42A ASN 4.4 0.6 - - - -
43A SER* 1.3 68.0 - - - +
45A ASP* 1.3 61.0 + - - +
47A PHE* 3.1 6.1 + - + -
48A MET* 2.8 43.8 + - + +
69A PHE* 3.9 24.7 - - + +
70A ILE* 5.4 0.4 - - + -
73A TRP* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.2 8.9 + - - +
44A LEU* 1.3 78.8 - - - +
46A GLU* 1.3 61.8 + - - +
48A MET* 3.5 1.2 + - - +
49A ALA* 3.0 24.8 + - - +
73A TRP* 2.9 32.6 + - + +
77A ASN* 4.7 4.6 + - - +
9001A EDO 2.6 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 2.6 29.8 + - + +
39A LYS* 3.9 14.6 + - - -
41A GLY* 4.3 6.4 - - - -
42A ASN* 4.9 2.0 + - - +
43A SER* 3.1 24.9 + - - +
45A ASP* 1.3 77.4 - - - +
47A PHE* 1.3 62.3 + - - +
49A ALA* 3.4 8.1 + - - +
50A TRP* 3.3 19.6 + - - +
9001A EDO 4.1 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS* 4.0 12.3 - - - -
13A PHE* 3.6 29.6 - + - -
27A TYR* 3.4 49.3 - + + -
28A GLY 4.5 4.3 - - - -
29A TYR* 4.3 5.2 - + + -
43A SER 3.1 7.1 + - - +
44A LEU* 3.5 10.3 - - + +
46A GLU* 1.3 77.6 - - - +
48A MET* 1.3 69.1 + - - +
50A TRP* 3.1 36.9 + + - +
51A VAL* 2.9 51.2 + - + +
58A LEU* 4.3 1.3 - - + -
60A PHE* 3.6 24.9 - + - -
70A ILE* 5.1 2.2 - - + -
119A ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.8 38.2 + - + +
45A ASP 4.1 0.4 - - - +
47A PHE* 1.3 90.4 - - - +
49A ALA* 1.3 65.4 + - - +
51A VAL* 3.2 14.2 + - + +
52A LEU* 2.9 31.0 + - + +
70A ILE* 4.2 28.3 - - + +
73A TRP* 3.6 54.7 - - + -
74A LEU* 4.1 15.0 - - + -
105A ILE* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP 3.0 17.9 + - - +
46A GLU* 3.6 8.3 - - - +
47A PHE 3.3 0.2 - - - -
48A MET* 1.3 76.8 - - - +
50A TRP* 1.3 61.8 + - - +
52A LEU* 3.3 16.2 + - - +
53A LYS* 3.4 20.6 + - + +
73A TRP* 5.0 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.7 28.3 + + + -
11A CYS* 4.4 0.4 - - - -
29A TYR* 3.6 63.7 + + + -
37A GLU* 5.4 0.8 + - - -
46A GLU 3.3 8.7 + - - +
47A PHE* 3.1 40.2 + + - +
49A ALA* 1.3 75.9 - - - +
51A VAL* 1.3 78.2 + - + +
53A LYS* 3.0 6.7 + - + +
54A VAL* 2.8 57.4 + - + +
58A LEU* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 2.9 53.2 + - + +
48A MET* 3.4 20.2 - - + +
50A TRP* 1.3 82.2 - - + +
52A LEU* 1.3 62.4 + - + +
53A LYS 3.3 0.7 + - - -
54A VAL* 3.6 6.6 + - - +
58A LEU* 3.8 11.7 - - + -
105A ILE* 3.8 25.4 - - + -
117A THR* 2.6 48.6 + - + -
119A ILE* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 2.9 23.0 + - + +
49A ALA* 3.8 7.6 - - - +
50A TRP 3.2 0.4 - - - -
51A VAL* 1.3 83.5 - - + +
53A LYS* 1.3 61.6 + - + +
55A GLN 4.9 0.9 + - - -
73A TRP* 4.1 19.5 - - + -
74A LEU* 5.0 0.2 - - + -
79A PHE* 3.8 31.4 - - + -
105A ILE* 3.6 31.6 - - + -
107A LEU* 3.6 35.9 - - + +
115A ILE* 4.6 7.4 - - - +
116A HIS 5.9 0.2 - - - -
117A THR* 4.7 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.4 14.9 + - + +
50A TRP* 3.0 6.7 + - + +
52A LEU* 1.3 81.4 - - + +
54A VAL* 1.3 63.4 + - - +
55A GLN* 3.3 18.0 + - - +
115A ILE* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 5.5 5.1 - - + +
9A TYR* 3.7 32.5 - - + +
50A TRP* 2.8 50.0 + - + +
51A VAL* 3.6 16.1 + - - +
53A LYS* 1.3 75.2 - - - +
55A GLN* 1.3 75.9 + - - +
56A ALA* 3.8 13.4 - - + +
58A LEU* 4.4 0.9 - - + -
117A THR* 3.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.6 30.5 + - - +
7A LYS* 4.8 1.4 + - - +
52A LEU 4.9 1.1 + - - +
53A LYS 3.3 14.8 + - - +
54A VAL* 1.3 78.3 - - - +
56A ALA* 1.3 56.8 + - - +
110A LYS* 6.2 0.8 - - - +
113A ARG* 5.0 3.1 - - - +
114A LYS 4.2 8.1 - - - +
115A ILE* 3.5 49.2 - - + +
116A HIS 3.3 17.0 - - - +
117A THR* 3.3 8.2 + - - -
----------------------------------------------------------
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