Contacts of the strand formed by residues 21 - 28 (chain E) in PDB entry 3BZE
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 ARG 21 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E THR 3.5 1.0 - - - +
11E SER* 3.1 4.9 + - - -
12E VAL* 2.8 44.3 + - + +
14E ARG* 3.4 34.2 - - + +
20E PRO* 1.3 72.8 - - - +
22E PHE* 1.3 60.5 + - - +
23E ILE* 3.5 36.9 - - - +
37E ASP* 3.0 23.5 + - - -
38E ASN* 3.6 3.8 - - - -
39E ASP* 2.9 36.8 + - - +
51F HIS* 6.1 3.8 - - - -
54F LEU* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E HIS* 4.1 13.7 - - + -
10E THR 3.3 6.1 - - - -
11E SER* 3.9 19.5 - - - +
20E PRO 4.9 0.7 - - - +
21E ARG* 1.3 73.8 - - - +
23E ILE* 1.3 65.6 + - - +
24E SER* 2.8 28.9 - - - -
36E PHE* 3.9 15.3 - + - -
37E ASP* 3.6 1.6 - - - -
38E ASN* 2.8 50.3 + - - +
67E ALA* 3.8 13.0 - - - -
70E THR* 3.4 36.3 - - + -
71E ALA* 3.5 27.8 - - + -
74E PHE* 3.9 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PHE 3.9 1.4 - - - +
9E HIS* 3.4 1.0 - - - -
10E THR* 2.8 43.3 + - + +
21E ARG* 3.5 41.1 - - - +
22E PHE* 1.3 82.7 - - - +
24E SER* 1.3 75.6 + - - +
25E VAL* 4.5 4.5 - - + -
35E ARG* 5.5 1.1 - - - -
36E PHE 3.2 10.3 - - - +
37E ASP* 3.9 14.6 - - + +
53F ASP* 5.2 2.7 - - + -
54F LEU* 4.0 52.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E TYR* 5.7 1.6 - - - -
8E PHE 3.6 6.1 - - - -
9E HIS* 2.8 26.4 + - - -
22E PHE* 2.8 31.2 - - - -
23E ILE* 1.3 71.6 + - - +
25E VAL* 1.3 65.6 + - - +
35E ARG* 3.0 6.0 - - - +
36E PHE* 2.8 47.4 + - - +
45E MET* 5.1 9.6 - - - -
67E ALA* 4.8 2.1 - - - +
2R MET* 4.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LYS 4.1 0.2 - - - +
7E TYR* 3.2 7.7 - - - -
8E PHE* 3.0 43.9 + - + +
23E ILE* 4.5 3.1 - - + -
24E SER* 1.3 80.1 - - - +
26E GLY* 1.3 59.5 + - - +
27E TYR* 3.8 13.2 - - + -
32E GLN* 3.7 15.0 - - - +
34E VAL 3.6 3.4 - - - -
35E ARG* 4.0 2.0 - - + +
53F ASP* 3.5 34.1 - - + +
54F LEU 3.7 16.4 - - - +
55F SER* 3.7 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LYS 3.4 6.1 - - - -
7E TYR* 3.4 19.3 - - - -
25E VAL* 1.3 73.9 - - - +
27E TYR* 1.3 62.0 + - - -
32E GLN* 3.3 10.2 - - - +
33E PHE* 3.0 29.3 + - - -
34E VAL* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E SER 3.7 0.2 - - - +
5E LEU* 3.0 21.0 - - - +
6E LYS* 2.7 33.2 + - - +
8E PHE* 3.9 22.0 - + + -
25E VAL* 3.8 14.8 - - + +
26E GLY* 1.3 79.7 - - - -
28E VAL* 1.3 59.4 + - - +
29E ASP 3.8 18.4 - - - +
30E ASP* 4.2 7.4 - - - -
31E THR 3.4 8.7 - - - -
32E GLN* 3.7 43.6 + - + +
33E PHE* 3.4 5.7 - - - -
53F ASP 5.2 0.9 + - - -
55F SER* 3.7 23.9 + - - -
63F TYR* 3.1 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E SER 3.4 7.0 - - - +
5E LEU* 4.0 6.7 - - + -
27E TYR* 1.3 71.8 - - - +
29E ASP* 1.3 67.9 + - - +
31E THR* 2.9 33.9 + - - +
33E PHE* 3.5 26.5 - - + -
51E TRP* 3.6 21.3 - - + -
168E LEU* 4.4 6.1 - - + -
171E TYR* 4.0 14.6 - - + -
172E LEU* 4.0 20.4 - - + -
179E LEU* 4.0 24.1 - - + +
209E TYR* 4.0 0.7 + - - -
----------------------------------------------------------
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