Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 2AVA
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 ASP 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 5.3 1.1 - - - -
38A SER 3.4 3.9 + - - +
39A LEU* 1.3 79.8 - - + +
41A THR* 1.3 64.7 + - - +
42A VAL* 3.5 19.5 + - - +
43A GLU* 3.3 41.8 + - + +
44A ILE* 3.5 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 5.0 15.9 - - + -
32A SER* 5.9 1.4 - - - -
39A LEU* 3.5 10.1 + - - +
40A ASP* 1.3 70.6 + - - +
42A VAL* 1.3 63.6 + - - +
43A GLU 3.1 2.5 - - - -
44A ILE* 2.8 12.1 + - + +
45A VAL* 2.8 36.2 + - + +
61A ALA* 2.9 28.9 - - + +
62A GLN* 4.7 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.7 13.7 - - - +
41A THR* 1.3 79.2 - - - +
43A GLU* 1.3 59.2 + - + +
45A VAL* 3.0 25.0 - - + +
46A MET* 3.1 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 2.9 32.1 + - - -
40A ASP* 3.3 34.7 + - + +
41A THR 3.1 0.6 - - - -
42A VAL* 1.3 78.5 - - + +
44A ILE* 1.3 64.8 + - - +
46A MET* 3.6 5.4 + - - +
47A ASN* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 6.1 0.2 - - + -
12A ILE* 4.4 11.7 - - + -
13A VAL* 4.7 15.0 - - + -
16A LYS* 3.4 42.2 - - + -
31A PHE* 4.7 26.0 - - + -
39A LEU* 5.0 10.1 - - + -
40A ASP 3.5 15.9 - - - +
41A THR* 2.8 13.4 + - + +
43A GLU* 1.3 73.4 - - - +
45A VAL* 1.3 65.1 - - - +
46A MET 3.1 1.1 - - - -
47A ASN* 3.0 15.2 + - - +
48A LEU* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.8 22.4 + - + +
42A VAL* 3.0 29.2 - - + +
44A ILE* 1.3 75.2 - - - +
46A MET* 1.3 58.0 + - + +
48A LEU* 4.1 7.5 - - - +
49A GLU* 2.9 38.8 + - - +
56A VAL* 3.4 22.6 - - + +
57A ASP 5.0 3.4 - - - +
58A GLU* 5.5 4.7 - - + -
61A ALA* 3.2 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.1 24.2 + - + +
43A GLU* 3.7 7.2 - - - +
44A ILE 3.1 0.4 - - - -
45A VAL* 1.3 82.4 - - + +
47A ASN* 1.3 55.9 + - - +
49A GLU* 4.5 18.4 - - + +
50A GLU* 2.7 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.2 38.8 - - + +
15A GLU* 4.3 13.9 + - - +
16A LYS* 4.3 13.5 + - - +
43A GLU* 3.2 17.8 + - - +
44A ILE 3.0 4.3 + - - +
46A MET* 1.3 78.2 - - - +
48A LEU* 1.3 53.6 + - - +
50A GLU* 3.1 4.9 + - - +
51A GLU* 2.7 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.6 39.0 - - + -
12A ILE* 3.4 34.1 - - + -
44A ILE* 3.1 29.8 + - + +
45A VAL* 4.1 5.8 - - - +
47A ASN* 1.3 74.5 - - - +
49A GLU* 1.3 59.4 + - - +
51A GLU* 4.8 0.4 - - - -
52A PHE* 2.8 54.0 + - + +
54A ILE* 4.8 1.1 - - + -
70A ALA* 5.5 2.9 - - + -
74A ILE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 2.9 25.7 + - - +
46A MET* 3.9 18.2 - - + +
48A LEU* 1.3 77.7 - - - +
50A GLU* 1.3 56.6 + - - +
53A GLY* 3.0 6.1 + - - -
54A ILE* 2.9 63.7 + - + +
55A ASN* 3.4 4.0 - - - -
56A VAL* 2.9 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 2.7 35.1 + - + +
47A ASN* 3.4 5.6 - - - +
49A GLU* 1.3 74.7 - - - +
51A GLU* 1.3 74.3 + - - +
53A GLY* 2.9 14.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.9 28.9 + - - +
12A ILE* 4.4 19.7 - - + +
15A GLU* 4.6 12.6 - - - +
47A ASN* 2.7 27.0 + - - +
48A LEU* 4.1 1.8 - - - +
50A GLU* 1.3 79.6 - - - +
52A PHE* 1.3 63.2 + - + +
53A GLY* 4.3 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 4.7 2.9 - - - -
5A THR* 3.6 27.4 - - + -
8A LYS* 3.3 51.1 - - + +
9A VAL* 3.7 22.7 - - + -
12A ILE* 5.1 1.8 - - + -
48A LEU* 2.8 46.4 + - + +
51A GLU* 1.3 77.0 - - + +
53A GLY* 1.3 64.0 + - - +
54A ILE* 4.2 10.3 - - + -
74A ILE* 3.6 21.5 - - + -
78A LEU* 3.5 32.4 - - + +
81A LYS* 5.5 0.2 - - - +
----------------------------------------------------------
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