Contacts of the helix formed by residues 67 - 81 (chain C) in PDB entry 3C6Q
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 ASP 67 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.7 27.4 - - + +
65C PRO* 4.1 1.6 - - - -
66C SER* 1.3 81.0 - - - +
68C PRO* 1.3 69.2 - - - +
69C THR* 2.6 22.9 + - - -
70C ALA* 2.6 35.3 + - - +
71C VAL* 2.9 26.8 + - - +
134C THR* 4.0 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PRO* 4.2 5.6 - - + +
66C SER 4.2 0.9 - - - +
67C ASP* 1.3 88.7 - - - +
69C THR* 1.3 65.8 + - - +
71C VAL* 3.2 8.3 - - - +
72C ILE* 3.3 6.8 - - - +
91C ASP 3.9 11.7 - - - +
92C SER* 2.8 34.8 + - - -
93C PRO* 5.0 1.6 - - + -
134C THR* 3.0 28.7 - - - +
135C ALA* 4.5 0.9 - - - +
136C MET* 3.4 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 2.6 15.0 + - - -
68C PRO* 1.3 76.5 - - - +
70C ALA* 1.3 64.4 + - - +
72C ILE* 3.1 33.2 + - + +
73C PRO* 3.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 3.4 31.6 - - + -
47C LEU* 4.1 16.1 - - + +
67C ASP* 2.6 21.4 + - - +
69C THR* 1.3 73.0 - - - +
71C VAL* 1.3 60.7 + - - +
73C PRO* 3.4 12.7 - - - +
74C THR* 4.4 2.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
43C ILE* 3.5 19.3 - - + -
47C LEU* 4.2 13.2 - - + -
50C LEU* 5.6 1.1 - - + -
63C ILE* 4.8 9.2 - - + -
65C PRO* 3.6 20.0 - - + -
67C ASP 2.9 17.0 - - - +
68C PRO 3.2 16.2 - - - +
70C ALA* 1.3 75.7 - - - +
72C ILE* 1.3 73.3 + - - +
73C PRO* 3.4 0.7 - - - -
74C THR* 3.2 7.6 + - - -
75C ILE* 3.1 35.4 + - + +
92C SER* 3.6 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO 3.3 15.7 - - - +
69C THR* 3.1 26.4 + - + +
71C VAL* 1.3 79.9 - - - +
73C PRO* 1.3 74.7 - - + +
75C ILE* 2.9 4.0 + - - +
76C LYS* 2.9 23.8 + - + +
92C SER* 3.9 7.4 - - - +
94C ASP* 4.0 37.5 - - + +
95C SER* 4.0 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C THR 3.9 3.8 - - - +
70C ALA 3.4 16.6 - - - +
71C VAL 3.5 0.7 - - - -
72C ILE* 1.3 97.6 - - + +
74C THR* 1.3 62.5 + - - +
76C LYS* 3.2 9.4 + - + +
77C LYS* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.8 24.8 - - + +
50C LEU* 3.7 34.7 - - + +
51C GLU* 3.5 34.0 + - + +
54C ILE* 3.7 12.5 - - + +
70C ALA 4.4 3.1 + - - -
71C VAL* 3.2 8.7 + - - -
73C PRO* 1.3 79.9 - - - +
75C ILE* 1.3 61.0 + - - +
77C LYS* 3.8 5.9 + - + +
78C ALA* 3.3 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.5 12.8 - - + -
63C ILE* 4.1 15.7 - - + -
65C PRO* 5.0 2.5 - - + -
71C VAL* 3.1 28.0 + - + +
72C ILE 2.9 8.6 + - - +
74C THR* 1.3 75.6 - - - +
76C LYS* 1.3 65.9 + - - +
77C LYS 3.1 2.0 + - - -
78C ALA* 3.2 6.6 + - - +
79C LEU* 3.0 32.4 + - + +
85C VAL* 3.8 33.4 - - + -
87C THR* 5.3 0.9 - - + -
92C SER* 5.1 0.2 - - - -
95C SER* 3.8 39.7 - - - +
97C ARG* 4.5 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 2.9 16.1 + - + +
73C PRO* 3.7 10.8 - - + +
75C ILE* 1.3 77.6 - - - +
77C LYS* 1.3 55.9 + - - +
79C LEU* 3.6 14.3 - - + +
80C GLU* 3.0 59.6 + - - +
95C SER 4.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLU* 3.3 29.2 + - - +
54C ILE* 4.4 17.3 - - + -
73C PRO 3.1 14.8 + - - +
74C THR* 3.8 6.7 - - - +
75C ILE 3.1 0.8 - - - -
76C LYS* 1.3 75.3 - - - +
78C ALA* 1.3 66.5 + - - +
80C GLU* 2.8 30.9 + - - +
81C MET* 2.9 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.9 1.3 - - + -
54C ILE* 3.7 27.8 - - + +
61C ILE* 4.3 10.5 - - + -
74C THR 3.3 7.0 + - - +
75C ILE* 3.2 8.8 + - - +
77C LYS* 1.3 76.8 - - - +
79C LEU* 1.3 61.9 + - - +
81C MET* 3.1 13.8 + - - +
83C ILE* 2.9 31.1 + - + +
85C VAL* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 3.0 26.0 + - + +
76C LYS* 3.6 17.3 - - + +
78C ALA* 1.3 76.1 - - - +
80C GLU* 1.3 52.6 + - - +
82C GLY* 2.7 26.3 + - - -
83C ILE 3.4 19.0 + - - +
85C VAL* 3.7 22.2 - - + +
95C SER 4.3 0.2 - - - +
96C GLY* 3.4 35.4 - - - +
98C TYR* 4.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.4 18.6 - - - +
76C LYS* 3.0 47.4 + - - +
77C LYS* 2.8 33.7 + - + +
79C LEU* 1.3 66.1 - - - +
81C MET* 1.3 59.5 + - + +
82C GLY* 2.8 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 4.3 11.2 - - - +
54C ILE* 4.1 23.6 - - + +
77C LYS* 2.9 30.5 + - + +
78C ALA* 3.1 11.8 + - - +
80C GLU* 1.3 75.0 - - - +
82C GLY* 1.3 61.0 + - - +
83C ILE* 4.0 15.5 - - + +
----------------------------------------------------------
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