Contacts of the strand formed by residues 26 - 33 (chain D) in PDB entry 1JB0
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 LYS 26 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 3.9 24.4 - - + +
21D ALA* 3.6 27.6 - - + +
22D ASP* 5.2 5.8 + - - +
25D GLU* 1.3 76.4 - - - +
27D TYR* 1.3 89.7 + - - +
57D TYR* 4.0 27.1 - - + -
58D PHE 3.8 10.3 - - - +
59D ALA* 4.7 1.3 - - - +
84D ARG* 3.6 3.1 - - - +
85D ILE* 2.9 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ARG* 3.9 2.4 + - - +
25D GLU* 2.5 36.1 + - + -
26D LYS* 1.3 80.9 - - - +
28D ALA* 1.3 62.1 + - - +
57D TYR* 3.1 12.1 - - - +
58D PHE 2.8 35.1 + - - +
59D ALA 3.5 23.1 - - - -
60D ARG* 3.7 2.5 - - - +
61D LYS* 3.7 46.7 - - + +
64D CYS* 3.5 18.4 - - - -
82D ILE* 4.6 2.5 - - + -
83D TYR 3.2 16.2 - - - -
84D ARG* 2.9 37.2 + - + -
85D ILE* 4.6 1.3 - - - +
94D ILE* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 3.6 31.6 - - + -
27D TYR* 1.3 76.3 - - - +
29D ILE* 1.3 61.6 + - - +
30D THR 4.3 0.4 - - - -
55D LEU* 3.9 5.2 - - + -
56D VAL 3.2 11.0 - - - +
57D TYR* 3.8 8.1 - - + -
64D CYS* 4.1 2.7 - - - -
81D LYS 4.3 0.2 - - - -
82D ILE* 3.3 6.6 - - - +
83D TYR* 2.8 37.3 + - + +
85D ILE* 3.8 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ALA* 1.3 75.6 - - - +
30D THR* 1.3 72.2 + - - +
31D TRP* 3.9 7.5 - - + -
55D LEU* 3.7 1.4 - - - -
56D VAL* 2.9 39.5 + - + +
58D PHE* 4.1 11.7 - - + -
64D CYS* 3.7 25.8 - - - +
67D LEU* 3.8 24.2 - - + -
68D ALA* 4.3 6.3 - - + -
72D LEU* 3.9 25.4 - - + -
80D TYR* 4.2 7.6 - - + -
81D LYS 3.1 10.8 - - - +
82D ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.5 7.4 - - + -
4D THR 3.9 14.1 - - - +
29D ILE* 1.3 73.5 - - - +
31D TRP* 1.3 62.4 + - - +
53D GLU* 4.4 10.9 + - - +
54D ASN 3.2 11.7 - - - +
55D LEU* 3.7 26.5 - - + -
79D ASP 4.0 1.0 + - - +
80D TYR* 2.9 6.9 - - - +
81D LYS* 2.8 52.9 + - - +
83D TYR* 3.9 17.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.9 15.7 - - + -
29D ILE* 3.9 17.5 - - + -
30D THR* 1.3 79.7 - - - +
32D THR* 1.3 80.5 + - - +
33D SER* 4.0 0.4 - - - -
39D PHE* 4.1 13.2 - + - -
49D MET* 3.4 39.9 - - + -
53D GLU* 3.4 5.0 - - - +
54D ASN* 2.8 58.3 + - + -
56D VAL* 3.9 16.4 - - + -
67D LEU* 3.8 21.8 - - + -
72D LEU* 3.7 25.0 - - + +
77D ILE* 3.6 16.2 - - + -
79D ASP* 3.8 12.8 - - - +
80D TYR* 3.8 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TRP* 1.3 89.3 - - - +
33D SER* 1.3 60.5 + - - +
34D PRO* 4.5 1.2 - - - +
52D GLY* 2.9 15.7 - - - +
53D GLU* 4.0 17.9 - - + -
77D ILE* 3.5 14.6 - - - +
79D ASP* 2.5 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TRP* 4.0 4.3 - - - -
32D THR* 1.3 77.7 - - - +
34D PRO* 1.3 66.7 - - - +
35D LYS 2.7 24.4 + - - -
37D GLN* 3.0 17.0 + - - -
49D MET* 3.4 22.8 - - - -
50D ARG 3.6 14.1 - - - -
51D GLU* 3.6 0.7 - - - +
52D GLY* 2.9 29.7 + - - -
77D ILE* 4.0 2.2 - - - -
----------------------------------------------------------
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