Contacts of the strand formed by residues 26 - 31 (chain E) in PDB entry 5A15
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 26 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ALA* 4.7 4.9 - - + -
67D LYS 3.2 35.8 + - - +
68D ASP* 4.1 10.9 - - + -
69D SER 5.4 2.0 + - - +
74D PHE* 3.8 53.4 - - + -
24E PRO* 3.4 16.9 - - - +
25E GLU* 1.3 80.9 - - + +
27E VAL* 1.3 63.9 + - - +
28E GLU* 3.9 1.7 + - - +
37E PHE* 4.1 17.5 - - + -
38E THR 3.8 3.4 - - - +
39E ARG* 4.5 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E PHE* 5.2 0.9 - - + -
24E PRO* 4.1 16.4 - - + +
26E VAL* 1.3 74.8 - - - +
28E GLU* 1.3 62.7 + - - +
29E LEU* 3.8 12.0 + - + -
36E TYR 3.8 0.5 - - - +
37E PHE* 3.4 5.5 - - - +
38E THR* 2.7 39.5 + - + +
40E HIS* 3.8 39.9 - - + -
43E LEU* 4.1 12.3 - - + -
55E PHE* 3.9 15.7 - - + -
73E PHE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER* 4.7 9.7 + - - -
24E PRO* 5.5 0.8 - - - +
26E VAL 3.9 2.5 + - - +
27E VAL* 1.3 73.4 - - - +
29E LEU* 1.3 61.0 + - - +
35E VAL* 4.3 1.3 - - + +
36E TYR 3.8 2.7 - - - -
37E PHE* 3.2 45.9 - - + -
70E LYS 5.7 0.2 - - - +
72E ARG* 3.2 44.1 + - + +
73E PHE* 3.5 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E VAL* 4.1 13.0 - - + +
28E GLU* 1.3 73.9 - - - +
30E ASN* 1.3 58.9 + - - +
31E VAL* 4.3 10.8 - - + -
35E VAL* 3.3 11.3 - - - +
36E TYR* 2.7 43.3 + - + +
38E THR* 4.4 10.8 - - + -
43E LEU* 3.9 27.1 - - + -
51E LEU* 5.3 2.2 - - + -
55E PHE* 3.5 30.5 - - + -
72E ARG* 4.3 2.9 - - - -
73E PHE* 3.6 18.6 - - + +
75E ILE* 4.9 9.6 - - + -
82E PHE* 4.1 24.2 - - + -
86E LEU* 5.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 1.3 72.5 - - - +
31E VAL* 1.3 58.1 + - - +
33E GLY* 3.3 28.9 + - - -
34E GLN 3.9 2.5 - - - -
35E VAL* 4.6 3.1 - - - +
68E ASP* 2.9 39.3 + - - +
72E ARG* 4.0 18.4 - - + +
73E PHE 2.6 17.5 + - - +
74E PHE* 3.2 17.7 - - + -
75E ILE 2.7 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 4.3 9.4 - - + -
30E ASN* 1.3 75.6 + - - +
32E GLY* 1.3 60.0 + - - +
33E GLY 3.0 3.1 - - - -
34E GLN 2.8 31.1 + - - +
36E TYR* 4.2 6.7 - - + -
75E ILE* 3.5 30.1 - - + +
77E ARG* 3.9 15.7 - - + +
78E ASP 4.0 4.5 - - - +
79E GLY* 3.0 12.1 - - - -
82E PHE* 3.7 58.6 - - + -
----------------------------------------------------------
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