Contacts of the strand formed by residues 23 - 28 (chain A) in PDB entry 1L2B
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 23 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 1.3 73.4 - - - +
24A GLU* 1.3 61.4 + - - +
25A ASP 3.9 20.6 - - - +
26A VAL* 4.1 14.8 - - + -
47A MET* 3.8 35.4 - - + +
48A ILE* 4.3 2.0 - - - +
49A GLY* 2.9 28.8 + - - -
50A GLN 2.9 19.2 + - - +
52A VAL* 4.9 3.1 - - + -
66A LEU* 4.2 31.6 - - + -
98A PHE* 4.9 12.1 - - + -
99A CYS 3.7 4.9 - - - +
100A PHE* 3.7 22.7 - - + -
101A THR* 4.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR 3.5 0.6 + - - -
23A ILE* 1.3 72.6 - - - +
25A ASP* 1.3 62.0 + - + +
48A ILE* 3.7 23.7 - - - +
99A CYS* 2.7 19.3 + - + +
100A PHE 4.2 3.1 - - - +
101A THR* 3.8 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.8 3.7 - - - +
24A GLU* 1.3 83.2 - - + +
26A VAL* 1.3 92.0 + - - +
27A ARG* 3.6 30.0 + - - +
44A ALA* 5.8 0.5 - - - +
48A ILE* 4.2 15.7 - - - +
98A PHE* 3.6 0.5 - - - -
99A CYS* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.1 13.5 - - + -
25A ASP* 1.3 93.5 + - - +
27A ARG* 1.3 65.8 + - - +
28A ILE* 4.0 20.0 + - + -
43A PHE* 4.4 9.0 - - + -
44A ALA* 3.8 41.0 + - + +
47A MET* 4.4 9.9 - - + -
48A ILE* 4.9 1.8 - - + +
96A VAL* 4.7 1.3 - - + -
97A VAL 3.4 10.1 - - - +
98A PHE* 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 3.6 24.6 + - - +
26A VAL* 1.3 79.3 - - - +
28A ILE* 1.3 64.6 + - - +
29A PHE* 3.8 28.3 - - + -
95A HIS 3.9 0.5 - - - +
96A VAL* 3.3 6.2 - - - -
97A VAL* 2.9 41.1 + - + +
99A CYS* 3.0 36.3 - - - +
105A GLU* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.0 15.9 - - + +
27A ARG* 1.3 83.6 - - - +
29A PHE* 1.3 69.3 + - - +
30A TRP 3.9 6.7 - - - +
31A PRO* 3.8 29.5 - - + +
34A ILE* 3.4 36.3 - - + -
40A SER* 4.5 17.0 - - - +
43A PHE* 4.4 4.5 - - + -
44A ALA* 5.3 2.0 - - + -
95A HIS 3.6 4.5 - - - +
96A VAL* 3.7 25.8 - - + -
----------------------------------------------------------
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