Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 3BPT
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 46 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 3.4 8.9 - - - +
43A LYS 2.9 30.6 + - - -
44A GLY 3.3 1.0 + - - -
45A CYS* 1.3 82.9 + - - +
47A GLY* 1.3 75.2 + - - +
48A VAL* 3.9 2.2 + - + +
83A LEU* 3.3 40.6 - - + +
85A ILE* 4.0 8.5 - - + -
229A LEU 4.0 2.4 + - - -
230A LEU* 3.4 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 3.4 2.0 - - - -
42A LYS* 4.4 0.7 - - - -
46A THR* 1.3 74.1 - - - +
48A VAL* 1.3 61.2 + - - -
75A TRP* 3.4 38.8 - - - -
81A THR* 3.9 3.8 - - - +
83A LEU 2.9 11.4 + - - -
84A ILE* 3.3 5.0 - - - +
85A ILE 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.6 1.4 - - - +
40A LEU* 3.5 5.0 - - - -
41A GLY* 2.8 40.4 + - - +
43A LYS* 4.4 16.8 - - + -
46A THR* 4.0 8.7 - - + +
47A GLY* 1.3 76.4 - - - +
49A ILE* 1.3 63.3 + - - +
50A THR* 3.8 19.8 + - - +
75A TRP* 3.5 2.1 - - - -
85A ILE* 3.5 12.6 - - + +
87A LYS* 4.2 18.4 - - + -
226A GLU* 5.3 4.7 - - - +
230A LEU* 4.0 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.6 23.3 - - + -
39A LEU 3.5 3.6 - - - -
40A LEU* 4.0 8.1 - - + -
48A VAL* 1.3 72.5 - - - +
50A THR* 1.3 60.9 + - - +
51A LEU* 4.2 2.7 - - + -
68A ILE* 4.0 32.1 - - + +
71A GLN* 6.4 0.2 - - + -
72A LEU* 5.6 4.3 - - + -
75A TRP* 3.6 23.1 - - + -
84A ILE* 3.9 20.4 - - + -
85A ILE 2.8 11.7 + - - +
86A ILE* 3.4 30.8 - - + -
87A LYS* 2.9 29.5 + - - +
135A TYR* 4.7 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.4 3.1 - - - -
39A LEU* 2.8 62.9 + - + +
48A VAL* 3.8 16.3 + - - +
49A ILE* 1.3 71.8 - - - +
51A LEU* 1.3 75.3 + - - +
52A ASN* 3.3 2.6 + - - +
87A LYS* 3.4 18.2 - - + +
88A GLY 4.3 3.1 - - - -
89A ALA* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 4.3 0.4 - - - -
38A VAL* 4.2 5.4 - - + -
49A ILE* 4.2 6.3 - - + -
50A THR* 1.3 70.3 - - - +
52A ASN* 1.3 58.5 + - - +
58A ASN* 3.4 19.9 - - + +
64A MSE 3.7 22.9 - - + -
68A ILE* 3.9 25.8 - - + -
86A ILE* 4.2 7.6 - - + -
87A LYS 2.8 18.5 + - - +
88A GLY* 4.3 0.2 - - - -
89A ALA* 2.9 28.1 + - - +
94A PHE* 3.5 33.2 - - + +
95A CYS* 3.7 18.4 - - + -
150A LEU* 3.8 19.1 - - + -
----------------------------------------------------------
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