Contacts of the strand formed by residues 40 - 48 (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 LEU 40 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O ALA* 3.8 16.8 - - + -
33O LEU 3.2 20.4 - - - +
34O VAL* 3.7 8.4 - - + +
38O GLU* 1.3 97.2 - - + +
41O PHE* 1.3 64.1 + - - +
42O CYS 3.2 32.1 - - - +
43O SER* 5.1 1.6 - - - +
73O LEU* 4.1 25.0 - - + +
141O TRP* 4.3 24.7 - - + -
151O MET* 4.3 15.4 - - + +
193O GLY* 3.7 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 3.0 41.4 + - + -
34O VAL 3.7 12.3 - - - -
35O MET* 3.4 39.3 - - + -
38O GLU* 4.9 0.7 - - - +
40O LEU* 1.3 79.9 - - - +
42O CYS* 1.3 91.3 + - + +
58O CYS* 3.5 22.7 - - - -
60O GLN* 3.8 24.7 - - + -
63O TYR* 4.6 5.8 - + + -
193O GLY* 4.3 14.2 - - - -
195O SER* 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 2.9 37.9 + - + -
40O LEU* 3.2 16.3 - - - +
41O PHE* 1.3 104.7 - - + +
43O SER* 1.3 67.7 + - - +
57O HIS* 5.3 0.2 - - - -
58O CYS* 2.1 48.9 - - - -
193O GLY 4.4 3.8 - - - -
195O SER* 3.6 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O GLN* 3.6 17.0 + - - -
31O ALA 3.0 12.9 + - - -
33O LEU* 3.9 6.4 - - - +
40O LEU* 5.1 0.3 - - - +
42O CYS* 1.3 82.5 + - - +
44O GLY* 1.3 60.5 + - - +
54O SER* 2.9 19.9 + - - -
140O GLY* 4.5 5.5 - - - -
141O TRP* 4.0 13.7 - - - -
193O GLY 4.5 7.8 + - - -
194O ASP 4.6 0.9 + - - -
195O SER 3.0 5.2 + - - +
196O GLY* 3.2 9.8 - - - +
197O GLY* 3.8 24.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O TRP 3.6 0.5 - - - +
30O GLN* 3.8 2.3 - - - -
31O ALA* 2.7 39.5 + - - +
33O LEU* 4.1 0.9 - - - +
43O SER* 1.3 75.8 - - - +
45O VAL* 1.3 69.5 + - - +
52O VAL* 3.9 7.4 - - - -
53O LEU 3.0 13.7 - - - -
54O SER* 4.1 2.0 - - - -
196O GLY 3.6 4.7 - - - -
198O PRO* 4.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O TRP* 3.4 10.3 - - + +
44O GLY* 1.3 80.9 - - - +
46O LEU* 1.3 60.4 + - - +
47O VAL* 3.0 9.3 + - + -
52O VAL* 4.0 2.4 - - - +
53O LEU* 2.6 43.0 + - + +
121O ILE* 3.4 31.6 - - + -
198O PRO* 3.5 35.4 - - + -
209O LEU* 3.6 27.4 - - + -
212O LEU* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O PRO 5.0 0.4 - - - +
29O TRP* 2.9 19.9 + - - +
31O ALA* 4.8 0.6 - - - +
44O GLY 4.1 0.2 - - - -
45O VAL* 1.3 68.1 - - - +
47O VAL* 1.3 59.5 + - - +
48O HIS 2.9 26.2 - - - +
49O PRO* 4.2 3.4 - - + +
51O TRP 3.4 10.1 - - - +
52O VAL* 3.9 16.9 - - + +
67O LEU* 4.3 15.7 - - + -
108O LEU* 4.2 12.3 - - + -
112O VAL* 4.1 13.2 - - + -
114O GLU* 5.7 2.9 - - + -
118O ILE* 4.0 27.4 - - + +
119O ARG 4.3 12.6 - - - +
120O SER* 3.2 12.6 - - - -
121O ILE* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O VAL* 3.0 16.8 + - + +
46O LEU* 1.3 74.3 - - - +
48O HIS* 1.3 64.4 + - + +
51O TRP* 3.2 16.1 + - + +
53O LEU* 3.7 23.3 - - + +
105O LEU* 4.3 14.1 - - + -
120O SER* 4.1 6.4 + - - -
121O ILE 3.7 13.0 - - - +
122O SER* 5.7 0.3 - - - -
123O ILE* 3.7 32.5 - - + -
209O LEU* 3.8 17.0 - - + -
238O ILE* 5.2 1.3 - - + -
242O VAL* 5.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O LEU* 2.9 28.1 + - - +
47O VAL* 1.3 81.3 - - + +
49O PRO* 1.3 94.0 - - + +
50O GLN* 2.7 27.7 + - + -
51O TRP* 3.2 32.6 + + + +
120O SER* 3.8 7.0 - - - -
242O VAL* 3.6 23.3 + - + +
243O GLN* 5.5 5.2 + - - -
----------------------------------------------------------
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