Contacts of the helix formed by residues 26 - 37 (chain O) in PDB entry 3J9X
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 ASN 26 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N THR* 4.9 3.6 - - - +
32N THR* 4.0 19.6 + - + +
22O ASN 3.6 2.4 + - - +
23O ALA 3.1 15.6 + - - +
24O PHE 3.0 1.2 + - - -
25O SER* 1.3 78.8 + - - +
27O PRO* 1.4 66.9 - - - +
28O THR* 2.7 32.9 + - - +
29O VAL* 2.7 33.9 + - + -
30O ALA* 2.9 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O SER 3.2 6.2 - - - +
26O ASN* 1.4 92.5 - - - +
28O THR* 1.3 63.1 + - + +
30O ALA* 3.8 2.4 + - + +
31O SER* 2.8 30.0 + - - -
27P PRO* 3.5 32.6 - - + +
28P THR* 5.7 0.2 - - - -
31P SER* 3.5 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N THR* 3.1 30.3 - - + +
29N VAL* 4.8 1.1 - - - -
26O ASN* 2.7 19.7 + - - +
27O PRO* 1.3 79.6 - - + +
29O VAL* 1.3 58.8 + - - +
31O SER* 3.2 6.0 + - - -
32O THR* 2.4 39.7 + - - -
27P PRO* 5.5 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
28N THR 4.5 0.2 - - - +
29N VAL* 3.9 28.3 - - + -
32N THR* 3.7 24.2 - - - +
33N ILE* 4.9 7.2 - - + -
23O ALA 3.5 18.8 - - - +
24O PHE* 4.0 8.5 - - - -
26O ASN* 2.7 31.1 + - + +
28O THR* 1.3 75.5 - - - +
30O ALA* 1.3 65.5 + - - +
32O THR* 3.7 0.5 - - - -
33O ILE* 3.0 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O PHE* 3.3 39.1 + - + +
25O SER 5.0 0.4 - - - -
26O ASN 2.9 11.3 + - - +
27O PRO 4.1 2.0 - - - +
29O VAL* 1.3 78.4 - - - +
31O SER* 1.3 57.9 + - - +
33O ILE* 3.9 0.5 - - - +
34O LEU* 2.9 37.1 + - + +
30P ALA* 3.6 28.7 - - + -
34P LEU* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O PRO 2.8 21.7 + - - -
28O THR* 3.2 10.0 + - - -
30O ALA* 1.3 76.0 - - - +
32O THR* 1.3 59.3 + - - +
34O LEU* 4.5 0.7 - - - +
35O SER* 2.6 39.8 + - - -
25P SER 3.4 23.8 - - - -
27P PRO* 3.5 25.2 - - - +
30P ALA* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N ALA* 3.6 35.0 - - + +
26N ASN* 4.0 18.6 + - + +
29N VAL* 3.8 13.0 - - + +
28O THR* 2.4 26.3 + - - -
29O VAL 3.7 3.6 - - - -
31O SER* 1.3 78.7 + - - +
33O ILE* 1.3 63.4 + - - +
35O SER* 3.2 3.6 + - - -
36O ASN* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2577 A 3.6 42.6 - - - +
2587 T 4.7 8.5 - - - +
838 A 5.4 2.2 - - - +
20N LYS* 3.9 15.9 - - + -
23N ALA* 3.8 23.1 - - + -
29N VAL* 4.9 7.6 - - + -
33N ILE* 5.3 6.3 - - + -
24O PHE* 4.3 14.1 - - + -
29O VAL* 3.0 33.7 + - + +
30O ALA 3.9 2.2 - - - +
32O THR* 1.3 78.1 - - - +
34O LEU* 1.3 59.4 + - + +
36O ASN* 3.1 2.4 + - - +
37O VAL* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2567 T 4.6 6.3 - - + -
2577 A 4.2 24.2 - - - +
24O PHE* 4.0 13.5 - - + -
30O ALA* 2.9 30.1 + - + +
31O SER 4.3 0.2 - - - +
33O ILE* 1.3 78.1 - - - +
35O SER* 1.3 51.3 + - - +
37O VAL* 3.5 6.6 - - + +
38O SER* 2.6 37.1 + - - -
21P PHE* 3.9 23.9 - - + -
24P PHE* 3.5 39.0 - - + +
25P SER* 3.8 26.2 - - - -
30P ALA* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O SER* 2.6 25.9 + - - -
32O THR* 3.2 6.9 + - - -
34O LEU* 1.3 77.3 - - - +
36O ASN* 1.3 69.7 + - - +
38O SER* 3.3 20.3 + - - -
39O PRO* 4.0 3.6 - - - +
25P SER* 4.5 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ALA* 3.4 29.4 + - + +
22N ASN* 4.0 10.5 - - - +
23N ALA* 3.5 30.7 - - - +
32O THR* 3.0 27.6 + - - +
33O ILE* 3.1 4.0 + - - +
35O SER* 1.3 89.4 + - - +
37O VAL* 1.3 57.6 + - - +
38O SER 3.3 0.6 + - - -
39O PRO* 3.6 12.3 - - - +
40O VAL* 4.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2567 T 3.9 22.4 - - - +
2577 A 3.9 4.0 - - - +
16N LYS* 4.7 9.9 - - + -
19N ALA* 3.7 18.2 - - + -
20N LYS* 3.6 31.4 - - + -
33O ILE 3.0 20.7 + - - +
34O LEU* 3.5 15.9 - - + +
36O ASN* 1.3 75.0 - - - +
38O SER* 1.3 67.5 + - - +
39O PRO* 3.5 1.8 - - - -
40O VAL* 3.3 8.5 + - + +
41O ALA* 2.9 20.0 + - + +
21P PHE* 4.5 9.6 - - + -
----------------------------------------------------------
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