Contacts of the strand formed by residues 48 - 54 (chain H) in PDB entry 1J5O
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 GLU 48 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H ILE* 2.9 23.2 - - - +
40H ARG* 2.9 60.7 + - + +
42H PRO* 4.8 9.0 - - + +
45H LYS* 4.3 20.4 + - - +
46H GLY 4.1 0.2 - - - -
47H LEU* 1.3 73.7 - - - +
49H TRP* 1.3 69.1 + - - +
50H LEU* 3.9 4.9 - - + -
62H ASN* 5.4 6.4 + - - +
64H SER* 6.0 1.2 - - - -
65H LEU* 5.6 3.1 - - + +
98L PHE* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR* 3.7 19.7 - - + -
38H TRP 4.0 1.8 - - - -
39H ILE* 4.3 3.4 - - + -
47H LEU 4.3 0.4 + - - -
48H GLU* 1.3 77.6 - - - +
50H LEU* 1.3 64.0 + - - +
51H ALA* 3.1 15.4 - - - -
52H THR* 2.9 19.5 + - - -
60H ARG 3.0 31.4 - - - -
61H TYR 3.4 10.5 - - - -
62H ASN* 3.3 39.8 - - + +
63H PRO* 4.6 4.7 - - + -
65H LEU* 5.2 0.2 - - - +
110H MET* 4.7 4.9 - - + -
94L PHE* 3.5 34.1 - + - -
95L PRO* 5.0 4.3 - - + -
96L TRP* 3.8 46.7 - + + +
97L THR* 5.8 0.2 - - - -
98L PHE* 4.4 10.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H TRP* 2.9 20.4 + - + +
39H ILE 3.5 17.3 - - - +
40H ARG* 3.4 52.7 - - + +
48H GLU* 4.5 6.1 - - + +
49H TRP* 1.3 76.8 - - - +
51H ALA* 1.3 68.7 + - + +
62H ASN* 3.1 26.9 + - - +
65H LEU* 3.7 20.6 - - + -
69H LEU* 3.8 17.7 - - + +
82H LEU* 4.9 8.1 - - + -
84H MET* 4.9 2.7 - - + -
95H TYR* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H THR* 3.1 2.9 - - - +
38H TRP* 2.7 36.6 + - + +
49H TRP* 3.1 13.8 - - - -
50H LEU* 1.3 87.7 - - + +
52H THR* 1.3 67.6 + - - +
60H ARG 3.2 14.6 - - - +
61H TYR* 3.7 11.0 - - + -
69H LEU* 4.3 9.4 - - + -
71H VAL* 4.5 16.4 - - + -
82H LEU* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLY 4.8 0.4 - - - -
36H VAL 3.3 13.5 - - - +
37H THR* 2.9 26.2 + - - +
49H TRP* 2.9 14.8 + - - -
51H ALA* 1.3 86.0 + - - +
53H ILE* 1.3 66.2 + - - +
54H TRP* 3.1 48.0 + - + +
59H ASN* 3.9 1.5 - - - -
60H ARG 3.3 19.9 + - - -
71H VAL* 5.6 0.4 - - - -
100H SER* 3.7 9.9 - - - +
94L PHE* 4.6 3.8 - - - -
96L TRP* 4.4 4.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H LEU* 4.7 2.2 - - + +
35H GLY* 3.3 4.3 - - - -
36H VAL* 2.7 45.6 + - + +
38H TRP* 3.8 11.2 - - + +
52H THR* 1.3 72.6 - - - +
54H TRP* 1.3 67.3 + - - +
57H ASP* 6.2 1.3 - - - +
59H ASN* 4.6 9.9 - - + +
71H VAL* 3.5 37.5 - - + -
72H SER* 3.0 29.8 - - - +
73H LYS* 3.6 29.2 - - + -
80H ALA* 3.6 17.3 - - + -
81H PHE 3.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLU* 3.0 30.1 - - + -
29H LEU* 5.2 1.3 - - - -
33H GLY 4.4 4.0 - - - -
34H ILE 3.8 20.6 - - - -
35H GLY* 4.9 2.0 - - - -
52H THR* 3.1 37.3 + - + +
53H ILE* 1.3 77.9 - - - +
55H TRP* 1.3 70.4 + + + +
56H ASP* 3.4 13.0 - - - +
57H ASP* 2.8 24.1 + - - -
58H ASP* 2.9 33.0 + - + +
59H ASN* 4.7 0.2 - - - +
60H ARG* 4.2 7.2 - - + +
73H LYS* 4.3 8.3 - - - -
100H SER* 5.3 6.3 - - - -
101H ALA* 5.7 0.4 - - - -
102H ILE* 3.2 29.4 - - + -
108H SER* 4.1 4.7 - - - -
94L PHE* 3.5 35.6 - + - -
96L TRP* 3.8 11.0 - + - -
----------------------------------------------------------
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