Contacts of the strand formed by residues 120 - 127 (chain B) in PDB entry 1E50
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 120 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 5.5 6.7 - - + +
27B ILE 3.5 11.7 - - - +
28B LYS* 3.1 36.0 - - + +
114B ILE* 3.4 5.7 - - - -
115B ASP* 2.8 28.9 + - - +
118B ARG* 2.9 53.0 + - + +
119B LEU* 1.3 78.4 - - - +
121B GLY* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 3.4 9.8 - - - +
27B ILE* 2.8 37.3 + - - +
113B TRP* 3.3 26.0 - - - -
120B ASP* 1.3 78.0 - - - +
122B MET* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.6 52.0 - - + +
25B CYS* 3.5 5.8 - - - -
26B GLU* 3.6 17.3 - - - +
27B ILE* 3.3 5.3 - - - +
112B GLY* 3.1 1.9 - - - -
113B TRP* 2.8 65.1 + - + +
121B GLY* 1.3 83.0 - - - +
123B GLY* 1.3 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 4.3 4.9 - - - +
25B CYS* 3.1 31.9 + - - +
27B ILE* 3.5 9.9 - - - +
57B PHE* 3.6 12.8 - - - -
110B TRP* 4.9 1.6 - - - -
111B LYS 3.0 13.5 - - - -
112B GLY* 3.5 4.5 - - - -
122B MET* 1.3 75.1 - - - +
124B CYS* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 3.4 13.9 - - - +
22B SER 3.9 12.1 - - - -
23B ARG 3.8 16.8 - - - -
24B GLU* 4.3 14.8 - - - -
57B PHE* 4.0 8.1 - - - -
109B ILE 3.7 0.2 - - - +
110B TRP* 3.4 6.3 - - - +
111B LYS* 2.7 43.0 + - - +
123B GLY* 1.3 77.4 - - - +
125B LEU* 1.3 69.5 + - - +
126B GLU* 5.0 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.4 24.0 - - + -
18B PHE* 4.7 6.1 - - + -
21B LEU* 2.9 42.7 + - + +
22B SER* 3.6 15.2 - - - +
57B PHE* 4.2 4.9 - - + -
64B LEU* 4.5 5.2 - - + -
101B MET* 5.4 0.7 - - - -
103B LEU* 3.5 26.5 - - + -
108B VAL* 4.1 20.4 - - + -
109B ILE 3.5 1.3 - - - +
110B TRP* 3.5 41.3 - - + +
124B CYS* 1.3 78.8 - - - +
126B GLU* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.9 5.2 - - - -
108B VAL* 3.0 7.2 - - - -
109B ILE* 2.7 51.7 + - + +
111B LYS* 2.8 52.0 + - + +
124B CYS* 5.0 10.7 - - - -
125B LEU* 1.3 77.9 - - - +
127B PHE* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.4 25.8 - - + -
9B ARG* 3.4 66.9 - - + +
12B PHE* 3.5 43.7 - + + -
106B VAL* 4.7 2.2 - - + -
107B CYS 3.6 15.9 - - - -
108B VAL* 4.5 0.7 - - - +
109B ILE* 5.4 0.7 - - - +
126B GLU* 1.3 75.8 - - - +
128B ASP* 1.3 56.5 + - - +
129B GLU* 3.3 25.2 + - + +
132B ALA* 3.6 25.1 - - + -
----------------------------------------------------------
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