Contacts of the strand formed by residues 42 - 47 (chain T) in PDB entry 2BTO
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 ILE 42 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24T ILE* 5.3 4.3 - - + -
26T LEU* 5.7 0.4 - - + -
34T ASP* 3.8 20.9 - - + +
35T VAL* 4.0 23.8 - - + +
38T ALA* 4.7 4.3 - - + -
40T GLY 4.2 6.5 - - - +
41T ALA* 1.3 76.7 - - - +
43T LEU* 1.3 64.3 + - - +
44T VAL* 4.1 12.3 - - + -
72T LEU* 3.8 3.3 - - - +
73T THR* 3.3 32.5 - - + +
75T ALA* 3.9 20.2 - - + -
98T LEU 3.4 2.1 - - - +
99T LEU* 3.4 2.5 - - - +
100T PHE* 2.6 66.2 + - + +
101T LYS 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T ILE* 1.3 71.6 - - - +
44T VAL* 1.3 58.2 + - - +
45T ASP 4.0 0.2 + - - -
61T LEU* 4.3 23.1 - - + -
64T ILE* 5.2 2.7 - - + -
72T LEU* 3.8 21.0 - - + +
73T THR 3.0 8.7 + - - +
74T VAL* 3.6 10.7 - - + +
75T ALA 2.7 33.3 + - - +
97T LEU* 3.8 33.7 - - + -
98T LEU 3.2 21.8 - - - +
99T LEU* 4.0 14.4 - - + +
118T LEU* 4.5 7.9 - - + -
121T PHE* 4.4 11.0 - - + -
122T LEU* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T LEU* 3.9 20.2 - - + -
31T PHE* 4.2 3.4 - - + -
35T VAL* 4.0 22.2 - - + -
42T ILE* 4.3 4.5 - - + -
43T LEU* 1.3 76.3 - - - +
45T ASP* 1.3 64.7 + - - +
46T PHE* 4.0 26.4 - - + -
75T ALA* 3.2 11.9 - - + +
77T LEU* 4.4 5.6 - - + -
96T THR 3.1 6.9 - - - +
97T LEU* 3.2 4.1 - - - -
98T LEU 2.7 38.0 + - - +
100T PHE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T VAL* 1.3 72.2 - - - +
46T PHE* 1.3 68.9 + - - +
47T TRP* 3.3 21.9 - - - +
54T CYS 5.0 2.9 - - - +
57T ILE* 4.2 4.9 - - - +
58T ALA* 5.7 0.2 - - - -
61T LEU* 3.1 31.7 - - + +
74T VAL* 5.9 0.2 - - + -
75T ALA 2.8 15.3 + - - +
76T LYS* 3.7 17.8 - - + -
77T LEU 3.0 23.2 + - - -
95T PRO* 3.7 15.1 - - - +
96T THR 3.6 2.0 - - - +
97T LEU* 3.6 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T PHE* 4.3 13.9 - + - -
44T VAL* 4.0 20.2 - - + -
45T ASP* 1.3 71.4 - - - +
47T TRP* 1.3 60.4 + - - +
77T LEU* 3.5 37.5 - - + -
79T ILE* 4.0 14.1 - - + -
85T THR* 4.1 17.5 - - + -
86T ALA* 4.1 14.6 - - + -
89T TYR* 4.7 3.8 - + - -
91T ILE* 3.7 21.3 - - + -
94T ILE* 3.1 21.7 - - + +
95T PRO* 3.4 3.3 - - - +
96T THR* 3.0 37.7 + - + +
98T LEU* 3.4 32.3 - - + -
100T PHE* 5.2 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T HIS* 4.5 18.4 + + - -
45T ASP* 3.3 28.0 - - - +
46T PHE* 1.3 75.0 - - - +
48T ALA* 1.3 87.3 + - - +
49T GLU* 4.0 21.3 - - + -
54T CYS* 3.9 28.3 - - + -
55T LYS* 5.4 7.9 - - + -
58T ALA* 6.2 4.7 - - + -
76T LYS* 3.9 29.6 - - + +
77T LEU 3.2 19.4 + - - -
78T ASN* 3.5 33.7 - - + +
79T ILE* 3.0 30.7 + - - +
94T ILE* 3.9 5.9 - - - +
----------------------------------------------------------
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