Contacts of the strand formed by residues 68 - 73 (chain E) in PDB entry 6DDE
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 PHE 68 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ARG* 4.0 9.6 - - - -
48E VAL* 3.7 24.9 - - + -
60E TYR* 3.4 25.8 - - + -
64E VAL* 3.1 31.8 + - + +
66E GLY 4.7 4.5 + - - -
67E ARG* 1.3 108.6 + - + +
69E THR* 1.3 63.1 + - - +
81E LEU* 4.3 15.0 - - + -
82E GLN 3.7 3.4 - - - -
83E MET* 3.5 43.1 - - + -
84E THR 4.7 1.1 - - - -
86E LEU* 4.1 6.3 - - + -
90E ASP* 3.9 23.8 - - - -
94E TYR* 4.1 6.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E TYR* 3.3 9.0 - - - +
66E GLY 5.6 0.9 + - - -
67E ARG 4.8 2.4 + - - -
68E PHE* 1.3 76.5 + - - +
70E ILE* 1.3 70.3 + - - +
71E SER* 4.1 6.7 + - - +
81E LEU* 3.3 5.9 - - - -
82E GLN* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E MET 4.6 3.4 - - - +
36E TRP* 3.4 31.2 - - + +
49E ALA* 3.7 25.4 - - + +
50E TYR* 4.0 3.4 - - - +
51E ILE* 3.5 35.0 - - + +
58E ILE* 3.8 21.2 - - + +
60E TYR* 2.8 32.3 + - + +
69E THR* 1.3 78.2 - - - +
71E SER* 1.3 66.3 + - - +
79E LEU* 4.1 6.7 - - + -
80E PHE 3.6 11.9 - - - +
81E LEU* 3.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ILE* 3.8 8.7 - - - -
58E ILE* 5.9 0.4 - - - -
69E THR* 4.9 7.3 + - - +
70E ILE* 1.3 76.8 - - - +
72E ARG* 1.3 64.9 + - - +
79E LEU* 3.3 6.4 - - - +
80E PHE* 2.8 51.4 + - - +
82E GLN* 5.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PHE* 3.2 52.1 + - + -
30E SER* 3.7 7.6 - - - +
32E PHE 3.2 19.6 + - - -
34E MET* 4.1 6.6 - - - +
51E ILE* 3.6 22.8 + - + +
52E SER 3.4 19.4 + - - -
53E SER* 4.5 1.5 - - - +
54E GLY 5.4 1.1 - - - +
55E SER* 3.3 27.8 - - - +
71E SER* 1.3 81.0 - - - +
73E ASP* 1.3 58.6 + - - +
74E ASP* 2.6 30.6 + - - +
78E THR 3.5 11.0 - - - +
79E LEU* 4.1 9.6 - - + +
80E PHE* 4.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 1.3 70.1 - - - +
74E ASP* 1.3 60.2 + - - +
75E PRO* 3.5 4.9 - - + -
76E LYS* 3.3 36.5 + - + +
77E ASN 3.0 22.0 + - - -
78E THR* 2.8 20.8 + - - +
80E PHE* 4.4 18.0 - - + -
----------------------------------------------------------
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