Contacts of the strand formed by residues 43 - 47 (chain T) in PDB entry 5EF3
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 VAL 43 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11T VAL* 4.0 23.1 - - + -
12T ILE 3.2 7.2 - - - +
13T LYS* 3.8 20.6 - - + -
38T LEU* 4.9 1.1 - - - -
41T GLY 3.7 0.2 + - - -
42T GLU* 1.4 79.2 - - - +
44T LEU* 1.3 62.8 + - - +
45T ILE* 4.0 15.0 - - + -
55U ILE 3.9 0.9 - - - +
56U LYS* 3.3 6.3 - - - +
57U VAL* 2.9 37.7 + - + +
63U ILE* 4.1 23.1 - - + -
70U ILE* 4.6 5.8 - - + -
71U GLU 4.3 2.2 - - - +
72U SER* 3.7 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10T VAL 3.7 1.7 - - - +
11T VAL* 3.6 1.2 - - - -
12T ILE* 2.8 41.6 + - + +
21T VAL* 3.8 37.0 - - + -
36T GLU* 4.3 19.3 - - + -
38T LEU* 4.1 16.8 - - + +
43T VAL* 1.3 75.2 - - - +
45T ILE* 1.3 61.4 + - - +
46T ALA* 4.0 16.5 + - + -
24U LEU* 4.0 22.7 - - + -
54U ALA* 4.4 6.7 - - + -
55U ILE 3.5 14.6 - - - +
56U LYS* 4.0 17.0 - - + -
101U TRP* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T PHE* 3.4 36.3 - - + -
10T VAL 3.3 3.6 - - - +
11T VAL* 4.2 11.9 - - + -
43T VAL* 4.0 15.7 - - + -
44T LEU* 1.3 74.8 - - - +
46T ALA* 1.3 57.5 + - - +
10U VAL* 4.0 25.1 - - + -
12U ILE* 5.5 0.2 - - + -
48U PHE* 3.5 21.6 - - + -
54U ALA* 3.2 4.5 - - - +
55U ILE* 2.8 50.0 + - + +
57U VAL* 4.8 7.2 - - + -
63U ILE* 4.3 20.0 - - + -
65U THR* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9T PHE* 3.1 4.5 - - - -
10T VAL* 2.9 44.6 + - + +
12T ILE* 5.2 2.2 - - + -
21T VAL* 5.2 0.4 - - + -
44T LEU* 3.9 20.1 - - + +
45T ILE* 1.3 74.1 - - - +
47T GLN* 1.3 60.7 + - - +
55T ILE* 4.3 8.0 - - + +
54U ALA* 4.1 7.6 - - + -
101U TRP* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5T THR* 3.1 24.4 + - - -
6T ASN 4.4 0.4 - - - -
7T SER* 3.3 23.7 + - - +
8T ASP 3.2 11.9 - - - +
9T PHE* 3.8 5.4 - - + +
45T ILE 4.3 0.4 + - - -
46T ALA* 1.3 72.3 - - - +
48T PHE* 1.3 72.8 + - - +
49T THR* 3.6 5.6 + - + +
52T THR* 4.5 2.3 - - - -
55T ILE* 4.4 3.7 - - - +
7U SER* 5.5 0.2 - - - -
8U ASP* 5.9 1.6 - - - +
26U ARG* 2.6 32.0 + - - -
48U PHE* 3.5 31.6 - - + +
53U SER* 3.1 25.2 + - - +
101U TRP* 2.9 24.3 + - - -
----------------------------------------------------------
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