Contacts of the helix formed by residues 26 - 37 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 4.9 2.8 - - - +
32H THR* 4.0 19.4 + - + +
22I ASN 4.6 1.8 - - - +
23I ALA 3.1 16.2 + - - +
24I PHE 3.0 1.0 + - - -
25I SER* 1.3 77.9 + - - +
27I PRO* 1.4 66.9 - - - +
28I THR* 2.7 31.9 + - - +
29I VAL* 2.7 35.5 + - + -
30I ALA* 2.9 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER 3.2 6.8 - - - +
26I ASN* 1.4 92.8 - - - +
28I THR* 1.3 63.9 + - + +
30I ALA* 4.1 2.2 - - + +
31I SER* 2.8 30.3 + - - -
27J PRO* 3.5 33.4 - - + +
28J THR* 5.7 0.2 - - - -
31J SER* 3.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 3.1 30.3 - - + +
29H VAL* 4.8 1.1 - - - -
26I ASN* 2.7 20.3 + - - +
27I PRO* 1.3 80.4 - - + +
29I VAL* 1.3 58.5 + - - +
31I SER* 3.2 6.1 + - - -
32I THR* 2.4 40.3 + - - -
27J PRO* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR 4.5 0.2 - - - +
29H VAL* 3.9 27.8 - - + -
32H THR* 3.7 24.9 - - - +
33H ILE* 4.9 7.6 - - + -
23I ALA 3.5 19.5 - - - +
24I PHE* 4.0 8.3 - - - -
26I ASN* 2.7 30.8 + - + +
28I THR* 1.3 75.5 - - - +
30I ALA* 1.3 65.0 + - - +
32I THR* 3.4 0.7 + - - -
33I ILE* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I PHE* 3.3 39.6 + - + +
25I SER 5.0 0.7 - - - -
26I ASN 2.9 10.6 + - - +
27I PRO* 4.1 2.9 - - + +
29I VAL* 1.3 78.2 - - - +
31I SER* 1.3 58.0 + - - +
33I ILE* 3.9 0.5 - - - +
34I LEU* 2.9 36.7 + - + +
30J ALA* 3.6 27.8 - - + -
34J LEU* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PRO 2.8 21.4 + - - -
28I THR* 3.2 10.0 + - - -
30I ALA* 1.3 76.8 - - - +
32I THR* 1.3 60.0 + - - +
34I LEU 4.5 0.2 - - - +
35I SER* 2.6 39.9 + - - -
25J SER 3.4 23.8 - - - -
27J PRO* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ASN 5.2 0.2 - - - +
23H ALA* 3.6 34.1 - - + +
26H ASN* 4.0 18.2 + - + +
29H VAL* 3.8 13.8 - - + +
28I THR* 2.4 25.9 + - - -
29I VAL 3.7 4.0 - - - -
30I ALA 3.3 0.2 - - - -
31I SER* 1.3 77.8 + - - +
33I ILE* 1.3 63.7 + - - +
35I SER* 3.2 3.2 + - - -
36I ASN* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2937 A 3.6 42.6 - - - +
2947 T 4.7 8.5 - - - +
478 A 5.4 2.2 - - - +
20H LYS* 3.9 17.3 - - + -
23H ALA* 3.8 22.7 - - + -
29H VAL* 4.9 7.4 - - + -
33H ILE* 5.3 5.8 - - + -
24I PHE* 4.3 14.1 - - + -
29I VAL* 3.0 34.6 + - + +
30I ALA 3.9 2.0 - - - +
32I THR* 1.3 77.9 - - - +
34I LEU* 1.3 58.2 - - + +
36I ASN* 3.1 2.9 + - - +
37I VAL* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2927 T 4.6 6.3 - - + -
2937 A 4.2 23.6 - - - +
24I PHE* 4.0 14.6 - - + -
30I ALA* 2.9 31.0 + - + +
31I SER 4.3 0.4 - - - +
33I ILE* 1.3 77.9 - - + +
35I SER* 1.3 51.8 + - - +
37I VAL* 3.4 6.5 + - + +
38I SER* 2.6 36.7 + - - -
21J PHE* 3.9 23.6 - - + -
24J PHE* 3.5 38.8 - - + +
25J SER* 3.8 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I SER* 2.6 26.7 + - - -
32I THR* 3.2 6.4 + - - -
34I LEU* 1.3 77.3 - - - +
36I ASN* 1.3 69.3 + - - +
38I SER* 3.3 19.9 + - - -
39I PRO* 4.0 3.6 - - - +
25J SER* 4.5 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ALA* 3.4 30.1 + - + +
22H ASN* 4.0 10.7 - - - +
23H ALA* 3.5 29.9 - - - +
32I THR* 3.1 27.5 + - - +
33I ILE* 3.6 4.5 - - - +
35I SER* 1.3 89.8 + - - +
37I VAL* 1.3 58.7 - - - +
38I SER 3.3 0.8 + - - -
39I PRO* 3.6 11.8 - - - +
40I VAL* 4.3 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2927 T 3.9 22.2 - - - +
2937 A 3.9 4.5 - - - +
16H LYS* 4.7 9.9 - - + -
19H ALA* 3.7 18.4 - - + -
20H LYS* 3.6 30.7 - - + -
33I ILE 3.0 20.3 + - - +
34I LEU* 3.5 16.2 - - + +
36I ASN* 1.3 76.3 - - + +
38I SER* 1.3 69.6 + - - +
39I PRO* 3.5 1.3 - - - -
40I VAL* 3.3 8.0 + - + +
41I ALA* 2.9 20.1 + - + +
21J PHE* 4.5 8.7 - - + -
----------------------------------------------------------
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