Contacts of the strand formed by residues 27 - 33 (chain O) in PDB entry 3K9Q
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 LEU 27 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O ALA* 4.3 0.4 - - - -
3O VAL* 3.6 32.5 - - + -
5O VAL* 4.1 11.0 - - + -
21O ILE* 3.6 24.8 - - + +
24O VAL* 3.7 38.6 - - + +
25O GLU* 3.2 3.1 - - - +
26O GLY* 1.3 80.6 + - - +
28O GLU* 1.3 66.3 + - - +
325O VAL* 4.1 20.4 - - + -
328O LEU* 4.2 19.7 - - + -
329O ALA* 4.3 21.8 - - + -
332O ALA* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O MET* 5.5 6.1 - - - +
2O ALA* 4.1 18.8 + - + +
3O VAL 3.0 11.3 + - - +
4O LYS* 3.8 2.6 - - + -
5O VAL* 2.9 27.2 + - - +
21O ILE* 4.4 0.9 - - - -
27O LEU* 1.3 78.3 - - - +
29O VAL* 1.3 64.9 + - - +
30O VAL* 3.5 18.9 + - + +
70O LYS* 4.5 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O VAL* 3.3 10.5 - - + +
7O ILE* 3.9 15.3 - - + -
18O PHE* 3.7 37.1 - - + -
21O ILE* 3.7 40.8 - - + +
22O GLN* 5.0 2.5 + - - +
28O GLU* 1.3 73.0 - - - +
30O VAL* 1.3 59.8 + - - +
31O ALA 3.4 24.7 - - - +
32O VAL* 4.0 9.6 - - + -
71O GLU 4.7 1.6 - - - +
72O VAL* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O LYS* 4.2 28.5 - - + -
5O VAL 2.9 10.3 + - - +
28O GLU* 4.2 25.6 - - + +
29O VAL* 1.3 76.7 - - - +
31O ALA* 1.3 63.7 + - + +
71O GLU 4.3 6.7 - - - +
72O VAL* 3.8 4.3 - - - -
73O LYS* 2.9 28.4 + - - +
88O LEU* 4.6 12.6 - - + +
90O ILE* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O VAL 3.7 0.8 + - - -
6O ALA* 3.2 7.7 - - + -
7O ILE 2.9 23.2 + - - -
29O VAL* 3.4 4.3 - - - +
30O VAL* 1.3 84.5 - - + +
32O VAL* 1.3 67.4 + - - +
72O VAL* 4.2 0.9 - - - -
73O LYS 3.1 11.2 - - - +
75O PHE* 4.3 3.8 - - + -
85O TRP* 3.8 18.6 - - + -
88O LEU* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O ILE* 3.4 11.0 - - + +
10O PHE* 3.6 54.3 - - + -
18O PHE* 4.8 0.9 - - + -
29O VAL* 4.0 15.0 - - + -
31O ALA* 1.3 79.6 - - - +
33O ASN* 1.3 65.0 + - - +
41O LEU* 4.1 19.7 - - + -
65O PHE* 4.6 5.2 - - + -
72O VAL* 4.0 14.6 - - + -
73O LYS 2.8 6.7 + - - +
74O SER* 3.2 5.3 - - - -
75O PHE* 2.9 27.7 + - - -
85O TRP* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0O NAD 3.4 13.3 - - - -
7O ILE 2.9 9.2 + - - +
8O ASN* 2.8 25.9 + - - +
9O GLY* 2.7 28.2 + - - -
10O PHE 3.7 2.3 + - - -
32O VAL* 1.3 76.7 - - - +
34O ASP* 1.3 63.9 + - - +
75O PHE* 3.0 20.8 - - + +
76O SER 3.2 0.2 + - - -
77O GLU 2.8 47.3 + - - -
83O LEU* 3.5 25.3 - - + +
85O TRP* 4.5 5.8 - - + -
----------------------------------------------------------
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