Contacts of the strand formed by residues 47 - 50 (chain E) in PDB entry 1N13
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 ASN 47 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 3.5 16.2 - - + +
52C SER* 4.1 3.4 - - - -
53D PYR 3.0 15.2 - - - +
54D ILE* 2.7 50.2 + - - +
162D LEU* 3.9 10.9 - - - +
46E VAL* 1.3 69.9 - - - +
48E LEU* 1.3 62.8 + - - +
49E ILE* 3.6 0.5 + - - +
70F GLY* 3.0 24.4 + - - -
71F ALA 2.7 12.8 + - - +
72F LEU* 3.6 17.6 - - + +
73F VAL* 2.8 29.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
51C ILE* 3.4 6.1 - - - -
52C SER* 2.9 50.6 + - - +
34E PHE* 4.9 0.9 - - + -
38E LEU* 3.7 27.4 - - + -
43E ILE* 3.6 30.7 - - + -
46E VAL* 4.0 10.5 - - + +
47E ASN* 1.3 72.9 - - - +
49E ILE* 1.3 60.3 + - - +
50E ARG 3.7 1.1 + - - -
73F VAL* 3.5 3.4 - - + +
75F THR* 3.4 23.6 - - + +
77F TYR* 4.1 21.3 - - + -
157F PHE* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.8 37.9 - - + -
49C ILE* 4.0 9.4 - - + -
50C ARG 4.4 4.3 - - - +
51C ILE* 4.5 8.5 - - + -
7E PRO* 5.1 4.3 - - + -
8E LEU* 3.8 31.4 - - + -
47E ASN 4.4 2.9 - - - +
48E LEU* 1.3 72.1 - - - +
50E ARG* 1.3 62.7 - - - +
51E ILE* 3.3 1.0 + - - +
72F LEU* 3.6 41.7 - - + +
73F VAL 2.9 13.0 + - - +
74F PRO* 3.4 11.3 - - + +
75F THR 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 4.1 5.9 - - - +
49A ILE* 4.2 10.7 - - - +
50A ARG* 4.6 3.5 + - - +
50C ARG 4.5 7.2 + - - +
52C SER* 4.9 2.0 + - - +
48E LEU 3.7 4.8 + - - -
49E ILE* 1.3 74.9 - - - +
51E ILE* 1.3 71.5 + - - +
52E SER* 5.1 2.9 + - - -
75F THR 3.3 7.9 - - - +
77F TYR* 2.8 74.8 + - + +
78F GLY* 4.5 2.4 - - - -
79F TYR* 4.0 20.0 + - - +
109F GLU* 4.6 8.1 + - - +
111F GLU* 5.3 2.2 + - - -
7005F MRD 5.2 1.8 - - - +
----------------------------------------------------------
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