Contacts of the helix formed by residues 26 - 37 (chain s) 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 s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28r THR* 4.9 3.0 - - - +
32r THR* 4.0 19.4 + - + +
22s ASN 4.6 2.0 - - - +
23s ALA 3.1 15.3 + - - +
24s PHE 3.0 0.8 + - - -
25s SER* 1.3 79.2 + - - +
27s PRO* 1.4 66.9 - - - +
28s THR* 2.7 32.0 + - - +
29s VAL* 2.7 35.4 + - + -
30s ALA* 2.9 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25s SER 3.2 7.1 - - - +
26s ASN* 1.4 92.3 - - - +
28s THR* 1.3 63.1 + - + +
30s ALA* 4.1 2.0 - - + +
31s SER* 2.8 30.5 + - - -
27t PRO* 3.5 33.9 - - + +
28t THR* 5.7 0.2 - - - -
31t SER* 3.5 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28r THR* 3.1 28.8 - - + +
29r VAL* 4.8 0.9 - - - -
26s ASN* 2.7 21.2 + - - +
27s PRO* 1.3 79.5 - - + +
29s VAL* 1.3 57.8 + - - +
31s SER* 3.2 6.6 + - - -
32s THR* 2.4 40.9 + - - -
27t PRO* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28r THR 4.5 0.2 - - - +
29r VAL* 3.9 27.6 - - + -
32r THR* 3.7 24.9 - - - +
33r ILE* 4.9 7.4 - - + -
23s ALA 3.5 20.2 - - - +
24s PHE* 4.0 8.3 - - - -
26s ASN* 2.7 31.3 + - + +
28s THR* 1.3 74.7 - - - +
30s ALA* 1.3 65.0 + - - +
32s THR* 3.4 0.7 + - - -
33s ILE* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24s PHE* 3.3 40.2 + - + +
25s SER 5.0 0.9 - - - +
26s ASN 2.9 11.2 + - - +
27s PRO* 4.1 2.2 - - + +
29s VAL* 1.3 77.2 - - - +
31s SER* 1.3 56.6 + - - +
33s ILE* 3.9 0.3 - - - +
34s LEU* 2.9 38.2 + - + +
30t ALA* 3.6 28.3 - - + -
34t LEU* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27s PRO 2.8 21.8 + - - -
28s THR* 3.2 9.7 + - - -
30s ALA* 1.3 76.5 - - - +
32s THR* 1.3 60.3 + - - +
34s LEU* 4.6 0.4 - - - -
35s SER* 2.6 39.6 + - - -
25t SER 3.4 24.2 - - - -
27t PRO* 3.5 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23r ALA* 3.6 35.4 - - + +
26r ASN* 4.0 18.3 + - + +
29r VAL* 3.8 13.0 - - + +
28s THR* 2.4 26.7 + - - -
29s VAL 3.7 3.6 - - - -
30s ALA 3.3 0.2 - - - -
31s SER* 1.3 77.7 + - - +
33s ILE* 1.3 63.6 + - - +
35s SER* 3.2 3.4 + - - -
36s ASN* 3.0 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777 A 3.6 42.6 - - - +
787 T 4.7 7.9 - - - +
2638 A 5.4 2.0 - - - +
20r LYS* 3.9 16.6 - - + -
23r ALA* 3.8 22.7 - - + -
29r VAL* 4.9 7.6 - - + -
33r ILE* 5.3 5.8 - - + -
24s PHE* 4.3 14.6 - - + -
29s VAL* 3.0 34.1 + - + +
30s ALA 3.9 2.0 - - - +
32s THR* 1.3 78.3 - - - +
34s LEU* 1.3 59.7 + - + +
36s ASN* 3.1 2.9 + - - +
37s VAL* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 T 4.6 6.5 - - + -
777 A 4.2 24.0 - - - +
24s PHE* 4.0 15.5 - - + -
30s ALA* 2.9 28.9 + - + +
31s SER 4.3 0.2 - - - +
33s ILE* 1.3 77.2 - - - +
35s SER* 1.3 52.7 + - - +
37s VAL* 3.4 6.6 + - + +
38s SER* 2.6 37.2 + - - -
21t PHE* 3.9 23.6 - - + -
24t PHE* 3.5 39.0 - - + +
25t SER* 3.8 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31s SER* 2.6 25.9 + - - -
32s THR* 3.2 6.4 + - - -
34s LEU* 1.3 78.6 - - - +
36s ASN* 1.3 70.3 + - - +
38s SER* 3.3 20.4 + - - -
39s PRO* 4.0 3.8 - - - +
25t SER* 4.5 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19r ALA* 3.4 30.2 + - + +
22r ASN* 4.0 10.1 - - - +
23r ALA* 3.5 31.1 - - - +
32s THR* 3.0 27.2 + - - +
33s ILE* 3.1 4.2 + - - +
35s SER* 1.3 90.3 + - - +
37s VAL* 1.3 58.3 + - - +
38s SER 3.3 0.7 + - - -
39s PRO* 3.6 11.8 - - - +
40s VAL* 4.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767 T 3.9 22.2 - - - +
777 A 3.9 4.3 - - - +
16r LYS* 4.7 10.3 - - + -
19r ALA* 3.7 18.4 - - + -
20r LYS* 3.6 30.5 - - + -
33s ILE 3.0 20.9 + - - +
34s LEU* 3.5 15.7 - - + +
36s ASN* 1.3 76.3 - - - +
38s SER* 1.3 69.2 + - - +
39s PRO* 3.5 1.6 - - - -
40s VAL* 3.3 8.2 + - + +
41s ALA* 2.9 19.7 + - + +
21t PHE* 4.5 9.4 - - + -
----------------------------------------------------------
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