Contacts of the helix formed by residues 68 - 83 (chain A) in PDB entry 5B82
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 CYS 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.3 17.9 + - - +
67A VAL* 1.3 78.2 - - - +
69A ALA* 1.3 67.5 + - - +
70A PRO 3.4 0.7 - - - -
71A VAL* 3.0 24.4 + - - +
72A GLY* 3.2 5.0 + - - -
88A GLN* 4.7 2.1 + - - -
501A HEC 2.1 97.3 - - + +
502A CL 3.2 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 5.2 3.1 - - + -
68A CYS* 1.3 76.3 - - - +
70A PRO* 1.4 69.8 - - + +
72A GLY* 3.1 4.2 + - - -
73A LYS* 3.0 21.8 + - - +
158A LYS* 6.5 0.7 - - - -
159A TYR* 5.5 2.7 - - - +
501A HEC 4.0 19.1 - - + +
502A CL 3.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.5 16.2 - - + +
48A LEU* 3.8 15.0 - - + -
66A ALA* 4.0 21.1 - - + +
67A VAL 3.5 20.0 - - - +
68A CYS 3.6 0.9 - - - -
69A ALA* 1.4 95.6 - - + +
71A VAL* 1.3 53.8 + - - +
73A LYS* 3.7 16.2 - - + +
74A GLN* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.6 34.9 - - + +
44A MET* 4.1 9.2 - - + -
45A ARG* 3.7 46.7 - - + +
67A VAL 3.7 15.5 - - - +
68A CYS 3.0 10.1 + - - +
70A PRO* 1.3 78.2 - - - +
72A GLY* 1.3 56.7 + - - +
74A GLN 3.3 1.0 + - - -
75A ALA* 2.9 27.7 + - - +
88A GLN* 3.6 25.6 - - - +
176A TYR* 4.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A CYS 3.2 4.8 + - - -
69A ALA 3.1 6.9 + - - -
71A VAL* 1.3 75.5 - - - +
73A LYS* 1.3 65.0 + - - +
75A ALA* 3.2 5.9 + - - +
76A LYS* 3.0 31.8 + - - +
88A GLN* 3.7 17.8 - - - +
98A HIS* 5.3 4.3 - - - -
501A HEC 5.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 3.0 12.9 + - - +
70A PRO* 3.7 15.7 - - + +
71A VAL 3.3 0.2 - - - -
72A GLY* 1.3 76.4 - - - +
74A GLN* 1.3 62.5 + - - +
76A LYS* 3.1 12.3 + - + +
77A GLU* 3.0 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 18.4 - - + -
44A MET* 3.7 19.5 - - + +
70A PRO 2.9 19.0 + - - +
71A VAL 3.6 4.3 - - - +
73A LYS* 1.3 76.4 - - - +
75A ALA* 1.3 57.6 + - - +
77A GLU* 3.1 27.7 + - - +
78A ILE* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.2 12.8 - - + +
71A VAL 2.9 14.1 + - - +
72A GLY* 3.3 12.8 - - - +
74A GLN* 1.3 77.7 - - - +
76A LYS* 1.3 62.8 + - + +
78A ILE* 3.3 5.5 + - - +
79A ALA* 2.9 25.2 + - - +
86A VAL* 3.7 35.3 - - + +
87A ARG* 5.1 3.4 - - - +
88A GLN* 5.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.0 19.9 + - - +
73A LYS* 3.5 11.7 - - + +
75A ALA* 1.3 75.9 - - + +
77A GLU* 1.3 58.9 + - + +
79A ALA* 3.4 7.5 + - - +
80A ALA* 2.9 31.4 + - - +
86A VAL 5.4 2.9 - - - +
97A ASN* 5.0 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.0 40.2 + - + +
74A GLN* 3.1 31.9 + - - +
76A LYS* 1.3 77.9 - - + +
78A ILE* 1.3 57.9 + - + +
80A ALA* 3.4 4.5 + - - +
81A ALA* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.4 31.0 - - + +
38A ILE* 5.7 2.5 - - + -
41A LEU* 4.9 9.6 - - + -
74A GLN* 2.9 46.5 + - + +
75A ALA* 3.7 8.1 - - - +
77A GLU* 1.3 73.2 - - - +
79A ALA* 1.3 67.0 + - - +
81A ALA* 3.3 1.7 + - - -
82A ASN* 3.0 40.2 + - - +
84A TRP* 3.7 30.5 - - + -
86A VAL* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.9 17.6 + - - +
76A LYS* 3.5 8.3 - - - +
78A ILE* 1.3 76.6 - - - +
80A ALA* 1.3 56.4 + - - +
83A GLY* 3.0 26.2 + - - -
84A TRP* 3.1 28.8 + - - +
85A GLN* 4.4 0.9 - - - -
86A VAL* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS 2.9 17.6 + - - +
77A GLU* 3.9 4.5 - - - +
79A ALA* 1.3 74.9 - - - +
81A ALA* 1.3 64.8 + - - +
82A ASN 3.3 0.7 + - - -
83A GLY* 3.8 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 2.9 19.1 + - - +
78A ILE* 3.9 3.6 - - - +
80A ALA* 1.3 78.6 - - - +
82A ASN* 1.3 68.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.5 3.6 - - - +
33A LYS* 3.2 34.4 + - - +
78A ILE* 3.0 39.1 + - - +
81A ALA* 1.3 90.1 - - - +
83A GLY* 1.3 60.4 + - - +
84A TRP* 3.3 47.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA 3.0 7.7 + - - -
80A ALA* 3.8 5.8 + - - -
81A ALA 3.7 1.6 - - - -
82A ASN* 1.3 80.1 - - - +
84A TRP* 1.3 62.2 + - - +
181A PRO* 3.4 25.3 - - - +
184A GLN* 5.0 3.3 + - - +
----------------------------------------------------------
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