Contacts of the strand formed by residues 34 - 39 (chain J) in PDB entry 4R2G
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 TRP 34 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J VAL* 4.8 7.9 - - + -
4J LEU* 3.4 30.1 - - + -
24J VAL* 3.9 21.3 - - + -
28J SER 4.1 0.7 - - - -
29J ILE* 2.6 50.5 + - + +
32J TYR* 3.4 39.8 + + + +
33J TYR* 1.3 72.3 - - - +
35J THR* 1.3 61.0 + - - +
50J TYR* 3.3 3.0 - - - -
51J ILE* 2.9 48.4 + - + +
52J SER 5.6 0.2 - - - -
69J ILE* 5.1 1.4 - - - +
71J ARG* 4.8 5.6 - - - -
78J LEU* 3.4 41.6 - - + +
93J ALA 3.7 9.4 - - - -
94J THR* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J TYR 4.4 0.2 + - - -
34J TRP* 1.3 75.6 - - - +
36J TRP* 1.3 67.1 + - - +
37J ILE* 4.3 7.0 - - + -
47J TRP* 2.6 23.4 + - - +
49J GLY 2.5 23.1 + - - -
50J TYR* 3.5 7.9 - - - +
78J LEU* 4.6 0.3 - - - +
92J CYS* 3.2 8.5 - - - +
93J ALA* 2.9 41.9 + - + +
95J ALA* 4.3 7.9 - - + -
100J MET* 3.5 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J GLU* 4.2 8.5 - - + -
20J VAL* 3.6 24.0 - - + -
21J THR 3.8 20.6 - - - -
22J CYS* 4.1 0.7 - - + -
35J THR* 1.3 79.7 + - - +
37J ILE* 1.3 62.2 + - - +
47J TRP* 3.5 6.6 - - - -
48J ILE* 3.0 43.6 + - + +
49J GLY 3.0 5.4 + - - +
69J ILE* 3.5 27.0 - - + +
78J LEU* 3.8 29.9 - - + +
79J SER 4.0 5.3 + - - -
80J LEU* 3.4 47.9 - - + +
90J TYR* 4.5 6.7 - + + -
91J PHE 3.1 28.7 - - - -
92J CYS* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I PHE* 3.5 27.8 - - + -
35J THR* 4.3 13.2 - - + -
36J TRP* 1.3 74.5 - - - +
38J ARG* 1.3 66.7 + - - +
45J LEU* 3.8 28.0 - - + -
46J GLU 3.2 10.3 - - - +
47J TRP* 3.2 34.8 - - + +
48J ILE* 3.6 2.7 - - - +
90J TYR* 3.8 0.7 - - - -
91J PHE* 2.9 33.2 + - + +
93J ALA* 5.5 1.6 - - + -
100J MET* 4.6 3.4 - - - +
103J TRP* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ILE* 1.3 78.4 - - - +
39J GLN* 1.3 59.9 + - - +
40J SER* 4.7 4.1 + - - +
44J GLY 3.9 0.2 - - - +
45J LEU* 3.6 1.9 - - - -
46J GLU* 2.7 83.8 + - + +
48J ILE* 3.6 19.1 - - + +
63J LEU* 4.0 17.5 - - - +
66J ARG* 4.6 2.0 - - - +
82J LEU* 3.6 6.2 - - - +
85J ALA* 4.0 15.5 + - - +
86J ASP* 2.8 35.6 + - - +
88J ALA* 4.2 10.8 - - + -
89J ILE 3.2 9.4 - - - +
90J TYR* 3.0 41.2 + - + -
91J PHE* 4.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 5.3 4.2 + - - -
38I HIS* 3.2 36.2 + - - +
40I PRO* 4.0 22.2 - - - +
41I GLY 4.4 4.5 + - - -
85I ASP* 5.2 1.6 + - - -
87I TYR* 5.5 2.2 + - - -
38J ARG* 1.3 74.5 - - - +
40J SER* 1.3 70.3 + - - +
41J PRO* 4.7 0.2 - - - +
43J LYS 4.4 9.8 + - - +
44J GLY 4.1 7.2 - - - +
45J LEU* 4.3 9.6 - - + -
88J ALA* 3.1 4.3 - - - +
89J ILE* 2.9 44.7 + - + +
91J PHE* 4.3 16.9 - - + -
----------------------------------------------------------
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