Contacts of the helix formed by residues 78 - 91 (chain C) in PDB entry 7BRU
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 78 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 5.4 2.1 - - - +
76C ASP 4.3 6.5 - - - +
77C LEU* 1.3 78.0 - - - +
79C VAL* 1.3 60.2 + - - +
80C GLY* 3.6 2.3 + - - -
81C GLN* 3.1 38.8 + - - +
82C PHE* 2.9 27.5 + - - +
109C THR 3.5 13.7 + - - +
110C SER* 4.1 16.2 - - - +
111C ALA 3.4 9.6 - - - +
112C THR* 4.1 4.7 - - + +
113C MET* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 1.3 72.1 - - - +
80C GLY* 1.3 52.1 + - - +
82C PHE* 3.2 2.0 + - + +
83C TYR* 2.6 38.1 + - + +
100C PHE* 4.1 23.1 - - + -
107C PRO* 4.1 23.3 - - + +
108C PRO 4.0 15.9 - - - +
109C THR* 3.8 0.9 + - - -
111C ALA* 2.9 27.0 + - + +
112C THR 4.4 3.4 - - - +
113C MET* 3.8 27.8 - - - -
116C LEU* 4.9 9.4 - - + -
129C ILE* 5.3 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN 5.4 0.2 - - - +
105B VAL* 4.0 17.4 - - - +
78C THR* 4.0 0.7 - - - -
79C VAL* 1.3 76.5 - - - +
81C GLN* 1.3 56.9 + - - +
83C TYR* 3.3 12.1 + - - +
84C PHE* 3.0 26.5 + - - +
109C THR* 3.1 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 4.8 10.0 - - - +
15B PHE* 3.6 45.3 - - + -
105B VAL* 4.3 11.7 - - + -
203B PO4 4.1 23.8 + - - -
76C ASP 5.1 0.2 - - - +
77C LEU* 3.3 20.5 - - + +
78C THR* 3.1 39.7 + - - +
80C GLY* 1.3 73.4 - - - +
82C PHE* 1.3 66.2 + - - +
84C PHE* 3.2 8.2 + - - +
85C LEU* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.9 9.6 - - + -
53C VAL* 4.7 1.3 - - + -
55C VAL* 4.1 23.8 - - + -
71C TYR* 4.2 14.6 - + + -
73C VAL* 4.0 32.8 - - + -
77C LEU* 3.9 15.1 - - + +
78C THR 2.9 14.4 + - - +
79C VAL* 3.5 9.0 - - + +
81C GLN* 1.3 74.5 - - - +
83C TYR* 1.3 58.0 + - - +
85C LEU* 3.1 9.7 + - + +
86C ILE* 2.9 59.3 + - + +
100C PHE* 4.1 14.8 - + - -
113C MET* 3.8 29.4 - - + -
129C ILE* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 6.0 3.6 - - + -
135B SER* 4.4 15.9 + - - -
136B VAL* 5.6 2.5 - - + -
79C VAL* 2.6 22.3 + - + +
80C GLY* 3.4 11.4 - - - +
82C PHE* 1.3 72.8 - - - +
84C PHE* 1.3 67.4 + - + +
86C ILE* 3.2 1.6 + - - +
87C ARG* 2.9 62.7 + - + +
98C LEU* 2.8 47.3 + - + -
99C PHE* 4.5 2.7 - - - -
100C PHE* 3.7 37.9 - + + -
109C THR* 6.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.6 8.3 - + + -
19B PHE* 3.6 43.7 - + - -
104B ASN* 3.8 47.3 - - + +
105B VAL* 5.3 1.3 - - + -
136B VAL* 5.0 17.0 - - + -
80C GLY 3.0 14.2 + - - +
81C GLN* 3.3 11.7 - - - +
83C TYR* 1.3 82.1 - - + +
85C LEU* 1.3 76.8 + - + +
87C ARG* 3.3 8.1 + - + +
88C LYS* 3.0 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.4 40.8 - - + -
10B ILE* 4.8 14.4 - - + +
15B PHE* 4.5 12.8 - - + -
19B PHE* 4.5 17.5 - - + -
77C LEU* 4.1 17.3 - - + -
81C GLN 3.1 16.0 + - - +
82C PHE* 3.6 8.3 - - + +
84C PHE* 1.3 88.3 - - + +
86C ILE* 1.3 65.2 + - + +
88C LYS* 3.0 13.8 + - + +
89C ARG* 3.0 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 4.7 4.7 - - + -
66C LEU* 4.2 22.2 - - + -
71C TYR* 3.8 36.6 - - + +
82C PHE* 2.9 52.3 + - + +
83C TYR 3.8 2.9 - - - +
85C LEU* 1.3 75.7 - - + +
87C ARG* 1.3 63.8 + - - +
89C ARG* 3.0 15.7 + - + +
90C ILE* 3.0 24.3 + - + +
98C LEU* 4.8 1.8 - - + -
100C PHE* 4.0 23.8 - - + -
131C TYR* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 4.1 6.7 + - - -
136B VAL* 3.8 34.5 - - - +
83C TYR* 2.9 50.7 + - + +
84C PHE* 3.4 12.1 - - + +
86C ILE* 1.3 76.0 - - - +
88C LYS* 1.3 64.1 + - + +
90C ILE* 3.1 13.8 + - - +
91C HIS 3.3 8.3 + - - -
92C LEU* 3.5 29.5 + - + +
93C ARG 2.9 25.7 + - - -
94C ALA* 3.9 0.6 - - - +
96C ASP 2.8 28.3 + - - -
98C LEU* 3.6 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 5.5 4.3 - - + -
84C PHE* 3.0 55.4 + - + +
85C LEU* 3.0 17.8 + - + +
87C ARG* 1.3 75.4 - - + +
89C ARG* 1.3 55.7 + - - +
91C HIS* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.3 19.1 - - + +
71C TYR* 5.2 3.6 - - + +
85C LEU 3.0 9.8 + - - +
86C ILE* 3.0 13.6 + - + +
88C LYS* 1.3 76.5 - - - +
90C ILE* 1.3 60.5 + - - +
91C HIS* 3.2 16.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 4.4 13.0 - - + -
64C GLY* 4.0 24.2 - - - +
65C ASP 5.2 3.8 - - - +
66C LEU* 4.3 15.0 - - + +
86C ILE* 3.0 26.5 + - + +
87C ARG* 3.1 6.7 + - - +
89C ARG* 1.3 76.3 - - - +
91C HIS* 1.3 71.7 + - - +
92C LEU* 4.1 16.3 - - + +
98C LEU* 4.4 11.4 - - + -
131C TYR* 3.8 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG 3.3 1.3 + - - -
88C LYS* 3.1 17.6 + - - +
89C ARG* 3.4 18.3 + - - -
90C ILE* 1.3 78.5 + - - +
92C LEU* 1.3 65.3 + - - +
93C ARG* 3.8 3.6 + - - +
----------------------------------------------------------
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