Contacts of the strand formed by residues 45 - 50 (chain E) in PDB entry 5X6E
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 45 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLY* 1.3 82.5 - - - +
46E THR* 1.3 70.1 + - - +
62E TYR* 4.7 8.3 - - + -
63E TYR 3.3 6.1 - - - +
64E LYS* 4.4 15.5 - - + -
65E GLY 5.8 0.2 - - - +
87E VAL* 4.0 3.2 - - - +
88E ILE* 3.0 31.3 + - + -
89E SER* 3.1 31.3 + - - +
92E ALA* 4.7 0.9 - - - +
154E TYR* 3.3 44.6 - - + +
166E LEU* 5.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ILE* 5.0 2.5 - - + -
41E LEU* 3.6 33.4 - - + -
45E ILE* 1.3 74.3 - - - +
47E LYS* 1.3 58.3 + - - +
62E TYR* 3.3 3.3 - - - +
63E TYR* 2.4 48.1 + - + +
69E ILE* 4.9 0.2 - - + -
85E LEU* 3.3 35.3 + - + +
86E GLU 2.4 34.1 + - - -
87E VAL* 3.7 9.5 + - - +
88E ILE* 4.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR* 1.3 74.4 + - - +
48E LEU* 1.3 59.8 + - - +
49E THR* 3.8 13.4 + - + +
57E ILE* 6.0 0.8 - - - +
59E ASN* 3.3 33.3 + - + +
61E GLN 3.4 4.0 - - - +
62E TYR* 3.5 22.0 - - + +
84E ASN 3.5 0.9 - - - +
85E LEU* 3.3 8.4 - - - +
86E GLU* 2.7 76.6 + - + +
88E ILE* 3.6 22.6 - - + +
173E GLU* 3.7 23.5 + - - +
176E TYR* 5.4 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PHE* 4.1 17.9 - - + -
47E LYS* 1.3 71.2 - - - +
49E THR* 1.3 58.7 + - - +
59E ASN* 3.9 2.6 - - - +
60E LEU* 3.0 45.8 + - + +
61E GLN* 2.7 15.8 + - - +
63E TYR* 3.6 32.5 - - + +
69E ILE* 4.9 5.4 - - + -
83E TYR* 3.6 23.3 - - + -
84E ASN 3.3 13.5 - - - +
85E LEU* 4.1 6.0 - - + +
128F LEU* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LYS* 3.8 41.3 - - + +
48E LEU* 1.3 79.0 - - - +
50E SER* 1.3 62.6 + - - +
51E ILE* 4.7 6.3 - - - +
57E ILE* 5.5 5.2 - - + -
58E MET 3.5 9.0 - - - -
59E ASN* 4.2 9.2 - - - +
60E LEU* 5.0 0.9 - - - -
83E TYR* 3.5 9.3 - - - +
84E ASN* 2.8 53.8 + - - +
86E GLU* 4.3 11.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLN* 4.5 2.5 - - - -
49E THR* 1.3 76.8 - - - +
51E ILE* 1.3 65.3 + - - +
52E SER* 5.6 0.7 - - - -
56E THR 3.9 1.9 - - - +
57E ILE* 3.9 0.9 - - - -
58E MET* 2.9 38.5 + - - +
60E LEU* 4.7 6.1 - - - -
82E TYR 4.7 2.5 - - - -
83E TYR* 3.8 23.6 - - - -
84E ASN* 4.7 0.2 - - - +
132F ASN* 3.6 22.9 + - - +
220F LYS* 4.2 16.1 - - - +
----------------------------------------------------------
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