Contacts of the strand formed by residues 41 - 49 (chain O) in PDB entry 4PJO
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 CYS 41 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LEU* 4.5 7.4 - - - -
20O CYS* 6.0 0.4 - - - -
32O LEU* 3.9 23.8 - - + -
34O GLU 3.6 2.9 - - - -
35O ALA* 4.1 10.3 - - - -
39O MET 3.3 17.5 + - - -
40O ASN* 1.3 77.0 - - - +
42O GLN* 1.3 59.5 + - - +
43O MET* 4.5 11.0 - - + -
62O TYR* 3.2 5.7 - - - -
63O ILE* 2.7 47.9 + - + +
68O ILE* 4.3 10.8 - - + -
71O LEU* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O LEU* 3.5 5.7 - - - +
33O ILE* 3.0 51.7 + - - +
34O GLU* 2.9 24.0 + - + +
40O ASN 4.3 0.2 - - - -
41O CYS* 1.3 74.4 - - - +
43O MET* 1.3 63.4 + - - +
60O GLN* 3.3 30.5 + - - +
61O VAL 3.3 14.6 - - - +
62O TYR* 3.8 15.7 - - + -
8U GLU 5.6 1.9 - - - +
11U LYS* 4.3 20.9 - - - +
12U PHE* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O VAL* 3.4 42.4 - - + +
20O CYS* 4.5 9.2 - - + -
28O TYR* 3.7 13.7 - - - +
30O GLY 3.6 18.8 - - - +
31O LYS 3.2 9.0 - - - +
32O LEU* 4.2 11.9 - - + -
33O ILE* 4.3 2.2 - - - +
41O CYS* 4.1 10.7 + - + +
42O GLN* 1.3 80.3 - - - +
44O SER* 1.3 62.5 + - - +
46O ILE* 3.3 22.7 - - + -
60O GLN* 3.3 7.6 - - - +
61O VAL* 2.8 37.1 + - + +
63O ILE* 4.1 23.6 - - - -
71O LEU* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O LYS* 2.9 32.0 + - - +
33O ILE* 3.5 26.1 - - - +
43O MET* 1.3 71.1 - - - +
45O ASN* 1.3 84.3 + - - +
46O ILE* 3.5 4.4 - - - +
59O GLU 3.2 6.7 - - - -
60O GLN* 2.7 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O ARG 3.6 1.2 - - - +
30O GLY* 3.6 11.1 - - - -
31O LYS* 4.2 21.1 - - + +
44O SER* 1.3 84.7 + - - +
46O ILE* 1.3 61.7 + - - +
47O THR* 4.0 1.7 + - - -
57O GLN* 4.9 6.5 + - - +
58O LEU 3.5 5.2 - - - -
59O GLU* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O TYR* 3.9 27.6 - - + -
29O ARG 3.1 4.7 - - - +
30O GLY* 3.8 3.8 - - - -
43O MET* 3.3 47.8 - - + -
44O SER* 3.7 15.0 - - - +
45O ASN* 1.3 75.1 - - - +
47O THR* 1.3 65.3 + - - +
48O VAL* 3.5 15.5 - - + +
56O ALA 3.7 0.2 - - - +
57O GLN* 3.2 12.2 + - - -
58O LEU* 2.8 44.1 + - + +
59O GLU 4.9 0.4 - - - +
61O VAL* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O VAL 3.4 3.8 - - - +
29O ARG* 2.8 40.4 + - - +
45O ASN 4.8 1.7 + - - -
46O ILE* 1.3 73.9 - - - +
48O VAL* 1.3 70.6 + - - +
49O THR* 3.7 6.8 + - - +
55O VAL* 4.2 18.4 - - + -
56O ALA 3.4 8.3 - - - +
57O GLN* 3.5 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O GLU* 4.3 2.2 - - + -
27O VAL 3.3 6.1 - - - +
28O TYR* 3.6 38.6 - - + +
46O ILE* 3.5 8.5 + - - +
47O THR* 1.3 76.4 - - - +
49O THR* 1.3 66.3 + - - +
50O TYR* 3.6 37.9 - - + +
55O VAL* 3.3 5.9 - - - +
56O ALA* 3.2 48.7 + - + +
58O LEU* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 49 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N TYR* 4.0 22.9 - - + -
25O GLY 4.3 0.9 - - - +
26O GLU* 3.5 2.6 - - - -
27O VAL* 2.8 49.3 + - + +
47O THR* 3.8 9.2 + - - +
48O VAL* 1.3 78.8 + - - +
50O TYR* 1.3 73.7 + - - +
53O GLY 3.9 20.6 - - - +
54O ARG 3.5 3.1 - - - +
55O VAL* 4.0 12.3 - - + +
----------------------------------------------------------
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