Contacts of the helix formed by residues 81 - 94 (chain C) in PDB entry 1DXO
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 SER 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS 4.1 6.9 + - - -
54C ASP* 2.6 32.9 + - - -
56C THR* 3.8 6.8 - - - +
80C LEU* 1.3 71.1 - - - +
82C PRO* 1.3 76.2 - - - +
83C ASP* 2.7 24.1 + - - -
84C ILE* 3.0 13.5 + - - +
85C VAL* 3.0 22.0 + - - +
118C ARG* 4.4 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 4.0 14.4 - - + -
80C LEU 3.5 2.0 - - - +
81C SER* 1.3 91.4 - - - +
83C ASP* 1.3 61.0 + - - +
85C VAL* 3.5 9.7 + - + +
86C ALA* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.7 9.0 - - + -
47C ASN* 4.6 8.5 + - - +
81C SER* 2.7 24.7 + - - -
82C PRO* 1.3 73.5 - - - +
84C ILE* 1.3 67.4 + - - +
86C ALA* 3.6 5.2 + - - +
87C GLU* 3.5 24.8 + - - +
118C ARG* 2.4 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 5.7 1.1 - - + -
54C ASP* 3.7 39.5 - - + +
67C TYR* 4.4 1.6 - - - +
80C LEU* 4.2 14.1 - - + -
81C SER* 3.0 14.8 + - - +
83C ASP* 1.3 78.4 + - - +
85C VAL* 1.3 65.5 + - - +
87C GLU* 3.1 7.6 + - - +
88C GLN* 3.0 45.8 + - + +
118C ARG* 3.3 60.1 - - + +
119C VAL* 4.1 6.5 - - + +
121C ILE* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLY 6.1 0.7 - - - +
80C LEU* 3.5 31.6 - - + +
81C SER 3.0 15.0 + - - +
82C PRO* 3.6 11.2 - - + +
84C ILE* 1.3 76.5 - - - +
86C ALA* 1.3 58.3 + - - +
88C GLN* 3.3 13.2 + - - +
89C LYS* 3.0 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO 3.1 16.9 + - - +
83C ASP* 4.0 7.4 - - - +
84C ILE 3.3 0.6 - - - -
85C VAL* 1.3 78.0 - - - +
87C GLU* 1.3 65.5 + - - +
89C LYS* 3.5 11.3 + - - +
90C LYS* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 5.0 0.9 - - - +
39C SER* 2.6 25.1 + - - -
44C MET* 3.5 18.3 - - - +
46C PHE* 4.3 9.2 - - + -
83C ASP 3.5 14.6 - - - +
84C ILE 3.1 3.7 + - - +
86C ALA* 1.3 76.5 - - - +
88C GLN* 1.3 61.0 + - - +
89C LYS 3.1 1.8 - - - -
90C LYS* 2.9 32.2 + - - +
91C LEU* 3.0 30.7 + - - +
115C TRP* 3.0 31.4 + - + +
119C VAL* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 3.7 12.3 - - - -
80C LEU* 3.1 34.9 - - - +
84C ILE* 3.0 22.6 + - + +
85C VAL* 3.4 11.9 - - + +
87C GLU* 1.3 79.3 - - - +
89C LYS* 1.3 56.2 + - + +
91C LEU* 3.5 0.8 + - - -
92C GLU* 3.2 30.2 + - - +
119C VAL* 3.0 26.3 + - + +
121C ILE* 3.5 12.3 - - - +
124C PHE* 3.3 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.0 40.0 + - + +
86C ALA* 3.6 12.6 - - - +
87C GLU 3.1 0.2 - - - -
88C GLN* 1.3 76.5 - - + +
90C LYS* 1.3 62.6 + - + +
92C GLU* 3.8 15.9 + - - +
93C ALA* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.9 24.2 - - + +
37C VAL* 4.1 15.9 - - + -
38C GLU 2.9 17.3 + - - +
39C SER* 2.7 29.9 + - - +
44C MET* 3.6 15.1 - - - +
86C ALA* 3.2 16.4 - - - +
87C GLU* 2.9 29.9 + - - +
89C LYS* 1.3 75.4 - - - +
91C LEU* 1.3 67.3 + - - +
93C ALA* 3.4 5.2 + - - +
94C ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.1 16.2 - - + -
87C GLU 3.0 12.3 + - - +
88C GLN 3.6 8.5 - - - +
89C LYS 3.3 0.4 - - - -
90C LYS* 1.3 77.3 - - - +
92C GLU* 1.3 63.2 + - - +
93C ALA 3.1 1.2 + - - -
94C ALA* 3.2 9.8 + - - +
97C VAL* 4.2 20.0 - - + -
99C PHE* 5.9 0.2 - - + -
115C TRP* 4.3 13.5 - - + -
119C VAL* 3.7 17.5 - - + -
120C PHE* 3.4 31.4 - - + -
124C PHE* 3.8 17.7 - - + -
137C PHE* 4.0 12.1 - - + -
140C LYS* 3.0 22.7 + - + +
181C PHE* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 4.0 14.1 + - - -
88C GLN* 3.2 20.5 + - - +
89C LYS* 3.9 17.8 - - - +
90C LYS 3.4 0.2 - - - -
91C LEU* 1.3 78.5 - - - +
93C ALA* 1.3 57.8 + - - +
124C PHE* 3.7 22.7 - - + -
137C PHE* 5.6 3.1 - - + -
140C LYS* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.6 47.5 + - - +
89C LYS 3.5 14.4 + - - +
90C LYS* 3.4 5.7 + - - +
91C LEU 3.1 0.8 - - - -
92C GLU* 1.3 79.8 - - - +
94C ALA* 1.3 63.8 + - - +
95C ASP* 3.6 6.1 + - - +
140C LYS* 4.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.9 8.1 - - - -
5C ALA 4.4 0.9 - - - -
6C LEU* 3.7 28.7 - - + +
90C LYS 3.0 18.7 + - - +
91C LEU* 3.2 5.1 + - - +
93C ALA* 1.3 75.2 - - - +
95C ASP* 1.3 61.4 + - - +
96C LEU 3.9 9.4 - - - +
97C VAL* 4.0 9.4 - - + +
140C LYS* 2.9 33.0 + - - +
----------------------------------------------------------
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