Contacts of the helix formed by residues 69 - 87 (chain C) in PDB entry 1DXX
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 THR 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY* 4.6 0.7 - - - -
68C SER* 1.3 93.1 + - - +
70C ARG* 1.3 76.3 + - + +
71C VAL* 3.0 34.3 + - + +
72C HIS* 3.1 26.5 + - + +
73C ALA* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER 4.0 1.6 + - - -
69C THR* 1.3 76.5 - - + +
71C VAL* 1.3 57.3 + - + +
73C ALA* 2.7 31.6 + - - +
74C LEU* 2.9 36.5 + - + +
97C THR* 3.8 21.6 - - - +
100C VAL* 4.2 11.8 - - + +
101C ASP* 2.5 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR* 3.0 17.2 + - + +
70C ARG* 1.3 78.6 - - + +
72C HIS* 1.3 64.6 + - + +
74C LEU* 3.3 11.8 + - + +
75C ASN* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 3.1 36.6 + - + +
66C LYS* 4.3 10.9 + - + +
67C GLY* 3.2 38.5 + - - +
69C THR* 3.1 32.2 + - + +
71C VAL* 1.3 76.9 - - + +
73C ALA* 1.3 65.2 + - - +
75C ASN* 3.1 2.0 + - - +
76C ASN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLN 3.7 10.3 - - - +
46C ASP* 3.2 21.5 - - + +
67C GLY 5.8 0.2 - - - -
69C THR 3.0 11.6 + - - +
70C ARG* 2.7 21.0 + - - +
72C HIS* 1.3 73.2 - - - +
74C LEU* 1.3 53.7 + - - +
76C ASN* 3.2 4.3 - - - +
77C VAL* 2.9 30.0 + - - +
100C VAL* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 2.9 44.2 + - + +
71C VAL* 3.5 13.0 - - + +
73C ALA* 1.3 75.5 - - - +
75C ASN* 1.3 66.1 + - - +
77C VAL* 3.6 1.7 - - - +
78C ASN* 2.7 37.0 + - - +
96C SER* 3.6 29.8 - - - +
97C THR* 3.9 14.8 - - + +
100C VAL* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 2.6 46.5 + - - +
71C VAL* 3.0 30.5 + - - +
72C HIS* 3.1 3.9 + - - +
74C LEU* 1.3 79.0 - - - +
76C ASN* 1.3 55.2 + - - +
78C ASN* 3.0 9.2 + - - +
79C LYS* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP 2.9 21.1 + - - +
47C GLY* 3.6 8.3 - - - +
48C ARG* 3.6 25.5 - - - +
51C LEU* 3.5 30.4 - - + +
63C PRO 4.8 0.3 - - - +
64C LYS* 3.7 0.7 - - - +
65C GLU* 3.0 38.7 + - - +
66C LYS 5.3 0.6 + - - -
72C HIS* 2.9 11.8 + - - +
73C ALA 3.2 12.6 - - - +
75C ASN* 1.3 76.1 - - - +
77C VAL* 1.3 60.0 + - - -
79C LYS* 3.6 3.6 + - - +
80C ALA* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.7 21.5 - - - +
50C LEU* 4.5 10.5 - - + -
73C ALA 2.9 20.2 + - - +
74C LEU 3.3 0.4 + - - -
75C ASN 3.1 0.6 - - - -
76C ASN* 1.3 73.8 - - - +
78C ASN* 1.3 55.7 + - - +
80C ALA* 3.0 6.4 + - + +
81C LEU* 2.7 43.6 + - + +
96C SER* 3.5 32.3 - - - -
99C ILE* 4.1 28.9 - - + -
100C VAL* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.3 4.0 - - + +
93B ASN* 2.6 33.2 + - - +
74C LEU* 2.7 33.7 + - - +
75C ASN* 3.4 10.7 + - - +
77C VAL* 1.3 78.9 - - - +
79C LYS* 1.4 57.4 + - - +
81C LEU* 3.2 6.6 + - - +
82C ARG* 2.8 45.6 + - - +
96C SER* 2.9 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.6 22.7 - - + -
62C LEU* 4.4 17.9 - - + +
63C PRO* 3.0 52.5 + - - +
65C GLU* 6.5 1.3 - - - -
75C ASN 2.9 16.2 + - - +
76C ASN* 4.0 2.7 - - - +
77C VAL 3.2 0.2 - - - -
78C ASN* 1.4 76.9 - - - +
80C ALA* 1.3 57.9 + - - +
82C ARG* 3.2 10.2 + - - +
83C VAL* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.2 19.3 - - + -
51C LEU* 4.0 12.1 - - + -
54C LEU* 3.6 24.5 - - + -
76C ASN 3.3 12.2 + - - +
77C VAL* 3.0 10.6 + - + +
79C LYS* 1.3 77.9 - - - +
81C LEU* 1.3 60.1 + - + +
83C VAL* 3.7 3.1 - - - +
84C LEU* 2.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.7 27.1 - - + -
93B ASN* 3.8 8.5 - - - +
77C VAL* 2.7 31.0 + - + +
78C ASN* 3.2 2.9 + - - +
80C ALA* 1.3 74.5 - - + +
82C ARG* 1.3 51.5 + - - +
84C LEU* 3.1 5.6 + - + -
85C GLN* 2.7 36.0 + - - +
91C LEU* 3.6 30.6 - - + +
94C ILE* 3.7 22.4 - - + +
95C GLY 3.9 1.3 - - - -
96C SER* 3.6 33.7 - - - +
99C ILE* 5.8 0.2 - - + -
110C LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP* 3.3 33.7 + - - -
92B VAL* 4.3 24.9 + - + +
93B ASN* 5.6 1.4 - - - +
78C ASN* 2.8 29.9 + - - +
79C LYS* 3.2 8.5 + - - +
81C LEU* 1.3 73.2 - - - +
83C VAL* 1.4 66.2 + - + +
85C GLN* 3.1 11.3 + - - +
86C ASN* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 5.7 0.2 - - + -
54C LEU* 3.9 12.8 - - + -
58C THR* 3.7 22.4 - - + -
60C GLN* 4.1 13.5 - - - +
62C LEU* 3.4 36.8 - - + -
79C LYS* 2.9 23.6 + - + +
80C ALA* 3.8 7.0 - - - +
82C ARG* 1.4 75.2 - - - +
84C LEU* 1.4 66.4 + - - +
86C ASN* 3.1 9.8 + - - +
87C ASN* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.4 0.7 - - + -
54C LEU* 3.8 28.0 - - + -
80C ALA* 2.7 30.0 + - + +
81C LEU* 3.7 9.4 - - + +
83C VAL* 1.4 78.9 - - - +
85C GLN* 1.3 56.7 + - - +
87C ASN* 2.8 21.5 + - - +
88C ASN 3.1 8.5 + - - -
89C VAL* 3.2 36.4 + - + -
91C LEU* 4.3 6.7 - - + -
110C LEU* 3.7 30.1 - - + -
114C ILE* 3.6 33.2 - - + -
118C TRP* 3.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN* 6.4 2.2 - - + -
89B VAL 3.8 3.8 - - - +
90B ASP* 3.0 32.3 + - - +
91B LEU* 2.7 31.8 + - - +
92B VAL* 3.4 17.7 + - + +
81C LEU 2.7 20.4 + - - +
82C ARG* 3.6 11.0 - - - +
84C LEU* 1.3 70.7 - - - +
86C ASN* 1.4 67.3 + - - +
88C ASN* 3.0 17.1 + - - +
89C VAL 4.8 3.8 - - - +
91C LEU* 3.9 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C GLN* 5.8 4.7 - - - +
82C ARG* 2.8 34.6 + - - +
83C VAL* 3.8 9.5 - - - +
85C GLN* 1.4 77.2 + - - +
87C ASN* 1.3 62.9 + - - +
88C ASN* 3.1 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR* 4.3 10.7 - - - +
60C GLN* 4.7 6.3 - - - +
83C VAL* 2.9 37.7 + - - +
84C LEU 2.8 8.6 + - - +
86C ASN* 1.3 80.2 - - - +
88C ASN* 1.4 72.7 + - - +
89C VAL* 3.3 1.8 - - + -
117C HIS* 3.0 26.0 + - - +
118C TRP* 4.0 33.3 + - + -
----------------------------------------------------------
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