Contacts of the strand formed by residues 64 - 67 (chain O) in PDB entry 2BDI
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 THR 64 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O ALA 3.7 0.5 - - - +
33O LEU* 4.9 0.9 - - - +
34O VAL* 3.2 55.4 + - + +
35O MET* 5.2 2.5 + - - -
62O SER 5.3 0.3 + - - -
63O TYR* 1.3 76.3 + - - +
65O ILE* 1.3 62.0 + - - +
66O GLY 3.8 0.2 + - - -
82O MET* 5.2 15.2 - - + +
83O VAL 3.8 10.8 - - - +
84O GLU* 4.6 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O ALA* 4.0 23.1 - - + -
32O ALA 3.3 9.2 - - - +
33O LEU* 4.2 12.3 - - + -
52O VAL* 4.2 15.0 - - + -
63O TYR* 3.8 13.0 - - + -
64O THR* 1.3 71.7 - - - +
66O GLY* 1.3 59.7 + - - +
67O LEU* 4.2 13.9 - - + -
81O GLN 3.6 0.7 - - - +
82O MET* 3.4 3.9 - - - -
83O VAL* 3.0 42.1 + - + +
85O ALA* 4.3 7.9 - - + -
106O ILE* 3.9 28.3 - - + -
108O LEU* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O GLN 4.1 1.6 - - - +
31O ALA* 3.7 3.6 - - - -
32O ALA* 2.9 36.3 + - - +
34O VAL* 5.8 0.4 - - - +
64O THR 3.8 1.6 + - - -
65O ILE* 1.3 74.3 - - - +
67O LEU* 1.3 61.7 + - - -
70O LEU* 3.6 17.6 - - - +
81O GLN 3.7 0.2 - - - -
82O MET* 3.5 24.9 - - - -
141O TRP* 5.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O PRO 5.2 1.6 - - - +
29O TRP 5.0 0.2 - - - +
30O GLN 3.9 16.6 - - - +
31O ALA* 4.0 19.7 - - + -
46O LEU* 4.3 29.6 - - + -
52O VAL* 5.1 0.9 - - + -
65O ILE* 4.2 9.4 - - + -
66O GLY* 1.3 71.4 - - - -
69O GLY* 1.3 66.0 + - - +
70O LEU* 3.1 5.3 + - - +
80O SER* 3.3 3.6 - - - -
81O GLN* 3.0 30.2 + - + +
83O VAL* 4.6 15.3 - - + -
108O LEU* 5.1 3.4 - - + -
112O VAL* 3.8 36.8 - - + -
118O ILE* 3.4 19.3 - - + -
----------------------------------------------------------
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