Contacts of the strand formed by residues 38 - 43 (chain A) in PDB entry 1IL8
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 GLU 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A CYS* 3.2 2.8 - - - +
8A GLN* 3.2 15.2 + - - +
9A CYS* 2.8 61.0 + - + +
27A VAL* 3.8 1.2 - - - +
28A ILE* 3.1 38.4 + - + +
33A HIS* 4.6 0.5 + - - -
34A CYS* 3.1 32.4 - - + +
36A ASN* 5.5 0.6 - - + +
37A THR* 1.3 86.2 - - - +
39A ILE* 1.3 65.2 + - - +
40A ILE* 3.5 4.6 + - + +
51A LEU 5.2 1.6 - - - +
53A PRO* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A CYS* 5.2 0.4 - - - -
25A LEU* 4.8 6.3 - - + -
26A ARG 3.7 4.9 - - - +
27A VAL* 4.1 25.6 - - + +
37A THR* 4.9 4.9 - - + -
38A GLU* 1.3 73.1 - - - +
40A ILE* 1.3 71.0 + - - +
50A CYS* 5.0 0.2 - - - -
51A LEU* 3.1 44.3 + - + +
53A PRO* 3.9 31.9 - - + +
58A VAL* 4.9 7.6 - - + -
62A VAL* 4.6 28.0 - - + -
66B LEU* 5.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 4.1 15.3 - - + +
9A CYS* 3.1 33.4 - - - -
25A LEU* 4.1 1.4 - - - +
26A ARG* 2.5 71.4 + - + +
28A ILE* 3.5 35.9 - - + -
38A GLU* 3.5 3.9 + - + +
39A ILE* 1.3 79.5 - - - +
41A VAL* 1.3 83.8 + - - +
48A GLU* 5.2 6.7 - - + -
49A LEU 3.5 13.7 - - - +
50A CYS* 3.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 5.1 0.9 - - + -
22A ILE* 3.5 40.6 - - + -
24A GLU 3.4 13.7 - - - +
25A LEU* 4.4 8.3 - - + -
26A ARG* 4.3 2.7 - - - +
40A ILE* 1.3 86.1 - - - +
42A LYS* 1.3 74.3 + - - +
43A LEU* 4.3 11.0 - - + -
48A GLU* 3.4 3.6 - - - -
49A LEU* 3.2 38.7 + - + +
51A LEU* 4.0 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.9 1.9 - - - -
23A LYS* 3.3 22.0 + - - +
24A GLU* 2.8 53.6 + - + +
26A ARG* 4.3 20.3 - - - +
40A ILE* 6.1 0.2 - - + -
41A VAL* 1.3 77.1 - - - +
43A LEU* 1.3 67.6 + - - +
46A GLY* 5.0 13.0 - - - -
47A ARG 3.3 16.6 - - - +
48A GLU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 6.0 0.7 - - + -
21A PHE* 3.2 25.8 - - + +
22A ILE* 3.7 22.0 - - + -
23A LYS* 5.0 0.9 - - - -
41A VAL* 4.4 6.1 - - + -
42A LYS* 1.3 87.5 - - - +
44A SER* 1.3 54.4 + - - +
45A ASP* 2.9 30.9 - - - +
46A GLY* 2.7 28.2 + - - -
47A ARG* 2.9 13.8 + - + +
49A LEU* 3.7 33.9 - - + -
----------------------------------------------------------
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