Contacts of the helix formed by residues 42 - 51 (chain J) in PDB entry 6A5T
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 ARG 42 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B GLU* 4.1 33.0 + - + +
1006B ILE* 4.2 30.1 - - + +
174C SER* 4.2 1.8 + - - -
175C ALA* 3.1 40.0 + - - +
233C GLU* 3.8 19.1 + - - +
10J CYS* 3.6 18.2 - - - +
12J LYS* 4.4 9.3 - - - +
40J LEU 3.7 1.7 - - - +
41J LYS* 1.3 101.3 - - + +
43J TYR* 1.3 62.9 + - - +
44J CYS* 3.9 22.5 - - - +
45J CYS* 4.4 7.7 + - - +
46J ARG* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B ILE* 3.7 27.8 - - + -
1004B GLU* 5.1 0.2 - - - -
1006B ILE* 3.3 32.7 - - + +
1033B LYS* 4.7 14.1 - - + -
1036B SER* 3.3 30.1 - - - +
1037B ILE* 4.5 15.7 - - + -
1064B TYR* 4.5 16.8 - + - -
1070B GLU* 4.2 10.9 + - - -
1087B PHE* 3.3 27.5 + - - -
1088B GLY* 4.7 0.2 - - - -
1089B PRO* 4.3 15.7 - - + -
42J ARG* 1.3 73.6 - - - +
44J CYS* 1.3 59.0 + - - +
46J ARG* 2.4 34.3 + - + +
47J ARG* 2.7 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B ILE* 5.2 4.0 - - + -
1006B ILE* 5.2 11.8 - - + +
7J CYS* 3.3 6.2 - - - -
9J SER* 3.7 26.2 - - - +
10J CYS* 3.2 24.5 - - - -
42J ARG* 3.9 15.7 - - + +
43J TYR* 1.3 85.5 - - + +
45J CYS* 1.3 69.5 + - - +
47J ARG* 3.1 28.4 + - - +
48J MET* 3.1 4.5 + - - +
101J ZN 2.2 36.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J CYS* 3.5 9.9 - - + -
10J CYS* 3.2 15.9 - - - -
12J LYS* 3.9 20.2 - - - -
14J VAL* 4.6 2.5 - - + -
40J LEU* 3.6 38.7 - - + +
42J ARG* 4.4 12.8 - - + +
43J TYR 3.3 0.4 - - - -
44J CYS* 1.3 77.3 - - - +
46J ARG* 1.3 58.5 + - - +
48J MET* 2.9 19.6 + - - +
49J VAL* 3.3 8.5 + - - +
101J ZN 2.0 43.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B SER* 3.2 20.4 + - - +
1037B ILE* 2.2 36.3 + - - +
1038B ARG 4.0 6.3 - - - -
1039B GLY* 4.1 2.0 - - - +
32J GLY* 4.0 14.8 - - - -
35J LEU* 4.0 28.1 - - + +
36J ASP* 2.8 30.1 + - - -
40J LEU* 3.3 27.3 + - + +
41J LYS* 3.9 6.5 + - - +
42J ARG 2.9 26.9 + - - +
43J TYR* 2.4 30.4 + - + +
45J CYS* 1.3 70.3 - - - +
47J ARG* 1.3 55.4 + - - -
50J LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLN* 4.1 4.6 + - - +
803B LEU* 5.1 6.3 - - + -
822B ASN* 2.8 39.6 + - - -
823B ALA* 4.3 0.4 - - - +
824B ILE* 4.5 8.9 - - - +
850B LEU* 6.0 0.2 - - - +
1009B ASP* 3.2 11.7 + - - -
1036B SER* 5.0 12.0 - - - -
1089B PRO* 4.3 14.9 - - + +
8J PHE* 3.6 20.8 - - - +
9J SER* 2.7 31.7 + - - +
43J TYR* 2.7 15.9 + - + +
44J CYS* 3.1 20.1 + - - +
46J ARG* 1.3 70.7 - - - +
48J MET* 1.3 89.2 + - - +
49J VAL 2.7 12.7 + - - -
50J LEU* 4.1 3.4 - - - +
51J THR* 3.0 41.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLN* 3.4 20.2 - - - +
3J ILE* 3.7 14.6 - - - +
4J PRO* 3.6 31.2 - - + +
6J ARG 4.5 1.3 - - - +
7J CYS* 3.3 38.4 - - + -
8J PHE* 3.3 32.5 - - + +
14J VAL* 4.7 8.3 - - + +
44J CYS 3.1 2.0 + - - +
45J CYS* 2.9 11.3 + - - +
47J ARG* 1.3 107.1 - - - +
49J VAL* 1.3 63.7 + - - +
51J THR* 4.8 0.9 - - - -
52J HIS* 4.1 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J ILE* 4.5 9.0 - - + -
14J VAL* 4.4 23.8 - - + +
17J LYS* 5.4 8.3 - - + +
18J TRP* 4.7 8.6 - - + -
21J TYR* 3.7 40.3 - - + -
35J LEU* 4.3 20.6 - - + -
38J LEU* 5.7 1.3 - - + -
40J LEU* 4.4 10.3 - - + -
45J CYS 3.3 10.2 + - - +
47J ARG 2.7 4.4 + - - -
48J MET* 1.3 83.4 - - - +
50J LEU* 1.3 66.8 + - - +
51J THR 3.2 1.9 + - - -
52J HIS* 3.5 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B LYS* 4.2 9.2 - - - -
803B LEU* 5.2 12.0 - - + +
1035B GLY 3.9 7.9 - - - +
1036B SER* 4.5 9.6 - - - +
1039B GLY* 3.4 36.6 - - - +
1040B TYR* 3.8 8.3 - - - +
1041B GLU* 4.8 6.3 - - + +
21J TYR* 4.4 8.4 + - - +
31J GLU* 3.9 30.3 - - + -
35J LEU* 4.4 11.4 - - + +
46J ARG 2.9 21.6 + - - +
47J ARG* 4.4 2.7 - - - -
49J VAL* 1.3 80.4 - - - +
51J THR* 1.3 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLN* 3.4 26.6 - - - +
801B LYS* 3.1 49.5 - - - +
803B LEU* 4.3 17.7 - - + -
822B ASN* 3.9 22.2 - - - +
1041B GLU* 5.5 0.4 - - - -
47J ARG* 3.0 29.2 + - + +
48J MET* 4.8 0.2 - - - -
50J LEU* 1.3 81.2 - - + +
52J HIS* 1.3 72.6 + - - +
53J VAL 3.7 0.2 - - - -
----------------------------------------------------------
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