Contacts of the helix formed by residues 74 - 93 (chain C) in PDB entry 2VT4
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 74 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 6.0 0.2 - - - +
71C ARG 4.1 14.8 - - - +
72C LEU* 3.1 6.6 + - - +
73C GLN* 1.3 79.4 - - - +
75C LEU* 1.3 64.4 + - - +
76C THR* 3.5 8.4 + - - -
77C ASN* 3.1 30.4 + - - +
78C LEU* 3.4 22.5 + - - +
155C ARG* 5.0 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 1.3 73.3 - - - +
76C THR* 1.3 59.3 + - - +
78C LEU* 2.8 31.5 + - + +
79C PHE* 3.3 16.0 + - + -
138C ASP* 5.3 1.1 - - - +
139C ARG* 5.7 1.3 - - - +
149C TYR* 3.6 19.1 - - + +
153C MET* 3.3 44.2 - - + +
154C THR 3.4 20.6 - - - +
155C ARG* 3.5 28.7 - - + +
158C ALA* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.4 8.4 - - - -
75C LEU* 1.3 79.5 - - - +
77C ASN* 1.3 66.1 + - - +
79C PHE* 3.3 15.1 + - - +
80C ILE* 3.1 30.7 + - + +
135C ILE* 5.1 6.6 - - + +
138C ASP* 3.7 4.6 + - - +
139C ARG* 3.4 34.7 + - - +
292C LEU* 4.2 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.5 22.2 - - + +
72C LEU* 2.4 56.3 + - - +
74C THR* 3.1 22.0 + - - +
76C THR* 1.3 84.1 - - - +
78C LEU* 1.3 62.5 + - - +
79C PHE 3.3 0.2 - - - -
80C ILE* 3.5 14.7 - - - +
81C THR* 3.0 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 5.5 3.6 - - + -
73C GLN* 5.3 15.5 - - + +
74C THR 3.4 10.7 + - - +
75C LEU* 2.8 21.2 + - + +
77C ASN* 1.3 78.6 - - - +
79C PHE* 1.3 59.8 + - - +
81C THR* 3.3 18.9 + - - +
82C SER 3.3 8.7 + - - -
155C ARG* 3.8 46.7 - - + +
158C ALA* 4.2 8.1 - - + -
159C LYS* 4.8 17.3 - - + -
162C ILE* 3.4 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.8 17.9 - - + -
76C THR* 3.3 13.7 + - - +
78C LEU* 1.3 73.6 - - - +
80C ILE* 1.3 59.4 + - - +
82C SER* 3.1 6.3 + - - -
83C LEU* 3.1 22.0 + - - +
131C THR* 3.6 15.1 - - + +
134C VAL* 3.9 31.6 - - + -
135C ILE* 3.8 23.6 - - + -
138C ASP* 4.3 24.7 - - + -
153C MET* 5.2 6.7 - - + -
158C ALA* 3.5 46.0 - - + -
161C ILE* 4.3 13.7 - - + -
162C ILE* 3.5 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 4.1 12.8 - - + -
66C ILE* 4.2 7.2 - - + -
76C THR* 3.1 20.7 + - + +
77C ASN* 3.5 21.3 - - - +
79C PHE* 1.3 75.3 - - - +
81C THR* 1.3 60.0 + - - +
83C LEU* 3.3 11.8 - - + +
84C ALA* 2.8 24.9 + - - +
135C ILE* 4.4 13.2 - - + -
292C LEU* 4.3 18.4 - - + -
295C ILE* 5.5 2.5 - - + -
343C TYR* 3.0 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 5.3 0.4 - - - -
63C ILE* 3.8 27.9 + - + +
66C ILE* 3.6 22.3 - - - +
77C ASN 3.0 15.1 + - - -
78C LEU* 3.5 15.4 - - - +
79C PHE 3.2 0.2 - - - -
80C ILE* 1.3 74.4 - - - +
82C SER* 1.3 61.9 + - - +
84C ALA* 3.1 7.0 + - - +
85C CYS* 2.9 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU 3.3 2.9 + - - -
79C PHE* 3.1 11.1 + - - -
81C THR* 1.3 80.7 - - - +
83C LEU* 1.3 63.0 + - - +
85C CYS* 3.3 8.5 + - - +
86C ALA* 3.1 21.5 + - - +
131C THR* 3.8 14.7 + - - -
162C ILE* 3.5 34.6 - - - +
166C TRP* 3.1 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE 3.1 10.8 + - - +
80C ILE* 3.3 11.9 - - + +
82C SER* 1.3 76.5 - - - +
84C ALA* 1.3 60.4 + - - +
86C ALA* 3.3 6.5 + - - +
87C ASP* 3.1 29.1 + - - +
128C SER* 3.9 41.3 - - - +
131C THR* 4.1 10.7 - - + +
132C LEU* 3.6 29.8 - - + -
135C ILE* 4.1 13.2 - - + -
295C ILE* 4.2 8.1 - - + -
339C ASN* 3.9 23.8 - - - +
343C TYR* 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 3.5 27.3 - - - +
62C VAL* 4.1 12.1 - - + -
63C ILE* 3.7 25.1 - - + -
80C ILE 2.8 16.3 + - - +
81C THR* 3.1 9.6 + - - +
83C LEU* 1.3 72.0 - - - +
85C CYS* 1.3 57.3 + - - +
87C ASP* 2.9 6.2 + - - +
88C LEU* 2.8 26.9 + - - +
339C ASN* 5.6 0.6 - - - +
343C TYR* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 4.0 17.2 - - - +
81C THR* 2.9 25.0 + - - +
82C SER* 3.6 11.4 - - - +
84C ALA* 1.3 74.0 - - - +
86C ALA* 1.3 61.9 + - - +
88C LEU* 3.1 10.9 + - - +
89C VAL* 3.1 29.9 + - + +
166C TRP* 4.8 7.4 - - + +
----------------------------------------------------------
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 SER 3.1 10.1 + - - +
83C LEU* 3.8 8.7 - - - +
84C ALA 3.2 0.4 - - - -
85C CYS* 1.3 75.7 - - - +
87C ASP* 1.3 61.6 + - - +
89C VAL* 4.7 0.7 - - - -
90C VAL* 3.4 25.5 + - - +
124C CYS* 3.7 18.0 - - + +
127C ALA* 4.9 2.7 - - + -
128C SER* 4.2 19.1 - - - +
166C TRP* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 3.3 10.6 - - - +
59C ASN* 3.5 25.5 - - - +
83C LEU* 3.1 17.0 + - - +
84C ALA 2.9 8.1 + - - +
86C ALA* 1.3 78.3 - - - +
88C LEU* 1.3 57.4 + - - +
90C VAL* 3.3 3.8 + - - +
91C GLY 3.0 23.4 + - - -
128C SER* 4.7 8.8 + - - -
335C ASN* 4.8 6.3 + - - -
336C SER* 2.7 39.1 + - - +
339C ASN* 3.6 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 5.0 1.1 - - - -
56C VAL* 3.8 26.2 - - + +
59C ASN* 3.9 15.4 - - + +
60C VAL* 3.7 33.0 - - + +
63C ILE* 4.2 17.7 - - + -
84C ALA 2.8 11.0 + - - +
85C CYS* 3.4 12.3 - - - +
87C ASP* 1.3 73.8 - - - +
89C VAL* 1.3 68.7 + - + +
91C GLY* 3.0 3.0 + - - +
92C LEU* 2.8 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C CYS* 3.1 17.0 + - + +
86C ALA* 4.7 1.8 - - - -
88C LEU* 1.3 74.0 - - + +
90C VAL* 1.3 54.8 + - - +
92C LEU* 4.6 5.4 - - - +
93C LEU* 2.6 43.8 + - + -
94C VAL* 3.4 3.0 + - + -
120C LEU* 4.5 27.6 - - + -
124C CYS* 3.6 27.6 - - - -
166C TRP* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ILE* 4.8 0.7 - - + -
86C ALA 3.4 15.7 + - - +
87C ASP* 3.3 8.9 + - - +
88C LEU 3.1 0.6 - - - -
89C VAL* 1.3 77.4 - - - +
91C GLY* 1.3 60.8 + - - +
92C LEU 3.2 0.7 + - - -
94C VAL* 3.2 24.5 + - + -
95C VAL* 2.8 48.2 + - + +
121C ASP* 5.8 0.9 - - - +
124C CYS* 3.8 21.3 - - + -
125C VAL* 6.4 1.3 - - + -
333C TYR* 4.4 16.2 - - + +
336C SER* 3.9 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 3.4 23.9 - - - +
55C ILE* 3.5 32.7 - - - +
56C VAL* 3.8 9.8 - - - +
87C ASP 3.0 12.1 + - - -
88C LEU 3.0 2.2 + - - -
90C VAL* 1.3 76.7 - - - +
92C LEU* 1.3 56.8 + - - +
95C VAL* 4.7 2.0 - - - -
96C PRO* 3.4 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 5.7 1.3 - - + -
56C VAL* 3.6 30.3 - - + -
88C LEU* 2.8 38.7 + - + +
89C VAL* 3.9 4.3 - - - +
91C GLY* 1.3 80.2 - - - +
93C LEU* 1.3 71.4 + - + +
96C PRO* 3.2 17.2 - - - +
97C PHE* 5.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 2.6 26.6 + - + +
92C LEU* 1.3 89.2 - - + +
94C VAL* 1.3 68.5 + - - +
95C VAL 3.5 0.9 - - - -
96C PRO* 3.7 1.2 - - - +
97C PHE* 3.1 46.1 + - + +
117C TRP* 4.3 2.6 - - + -
120C LEU* 3.6 32.3 - - + -
----------------------------------------------------------
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