Contacts of the strand formed by residues 43 - 47 (chain A) in PDB entry 2LXU
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 ILE 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.5 39.0 - - + +
27A VAL* 4.2 14.6 - - + -
28A GLN* 3.6 33.9 - - + +
36A ILE* 4.1 7.9 - - + -
39A GLY 3.9 8.5 - - - +
40A ALA* 3.0 22.3 + - - +
41A GLN 4.2 0.5 - - - +
42A GLY* 1.3 78.7 - - - +
44A ARG* 1.3 70.1 + - - +
45A PHE* 4.4 11.2 - - + -
57A ALA* 4.5 6.1 - - + -
58A PHE 3.4 4.0 - - - -
59A VAL* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 6.0 0.2 - - - +
41A GLN 2.9 30.0 + - - -
42A GLY 3.2 12.3 + - - -
43A ILE* 1.3 81.1 - - - +
45A PHE* 1.3 65.3 + - - +
47A TYR* 5.8 0.7 - - - -
57A ALA* 3.3 2.0 - - - -
58A PHE 2.9 35.7 + - - +
60A GLU* 3.0 40.8 + - - +
93A MET* 3.0 34.7 - - - +
97A LEU* 3.5 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 9.9 - - + -
19A PRO 5.8 0.4 - - - -
22A CYS* 3.8 23.6 - - - -
23A SER* 3.5 23.6 - - - -
24A ALA* 3.5 25.6 - - + -
27A VAL* 3.5 26.7 - - + -
43A ILE* 4.4 7.2 - - + -
44A ARG* 1.3 75.0 - - - +
46A ILE* 1.3 58.8 + - - +
47A TYR* 2.9 54.4 + + + -
53A PRO* 4.0 19.5 - - + -
55A GLY* 5.7 0.4 - - - -
56A GLU 3.3 17.7 - - - +
57A ALA* 3.7 7.0 - - + -
97A LEU* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 4.6 3.6 - - - -
45A PHE* 1.3 66.1 - - - +
47A TYR* 1.3 60.5 + - - +
48A THR* 3.8 1.2 + - - +
53A PRO* 4.3 0.7 - - - -
54A SER* 3.0 32.2 + - - -
56A GLU* 2.9 51.8 + - + +
57A ALA* 4.3 2.2 - - - +
58A PHE* 3.6 40.4 - - + -
96A VAL* 3.6 28.5 - - + +
97A LEU* 4.2 8.5 - - + +
100A THR* 3.5 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 5.8 0.4 - - - -
45A PHE* 2.9 59.6 + + + -
46A ILE* 1.3 75.7 - - - +
48A THR* 1.3 68.1 + - - +
51A GLY* 4.1 13.7 - - - -
52A ARG 3.6 7.2 - - - +
53A PRO* 3.6 33.6 - - + +
97A LEU 4.7 10.0 + - - +
100A THR* 5.1 3.6 - - - +
----------------------------------------------------------
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