Contacts of the helix formed by residues 126 - 138 (chain C) in PDB entry 5T46
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 LEU 126 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 4.0 15.7 - - - +
83C SER* 3.9 28.3 - - - +
117C LEU* 3.7 15.7 - - + -
121C GLN 3.2 5.1 + - - -
122C ARG* 3.4 20.2 + - + +
125C ASP* 1.3 75.8 - - - +
127C ASP* 1.3 60.3 + - - +
129C PHE* 4.8 0.9 - - - -
130C TRP* 2.9 27.5 + - - +
154C VAL* 3.8 12.1 - - + -
156C VAL* 4.4 7.2 - - + -
161C ASP* 3.6 40.4 - - + +
163C ILE* 3.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 4.6 2.2 + - - +
81C LEU* 3.7 32.1 - - + +
82C SER* 3.3 12.0 + - - -
83C SER* 2.5 50.8 + - - -
122C ARG 4.6 1.4 + - - +
123C ARG 5.7 1.0 - - - +
125C ASP 3.4 0.2 - - - -
126C LEU* 1.3 75.4 - - - +
128C ARG* 1.3 59.0 + - - +
130C TRP* 3.4 6.5 + - - +
131C LEU* 2.9 31.2 + - - +
302C GOL 4.0 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C SER 2.9 19.4 + - - +
125C ASP* 2.5 35.0 + - - +
126C LEU 3.2 0.8 - - - -
127C ASP* 1.3 79.3 - - - +
129C PHE* 1.3 79.6 + - - +
131C LEU* 3.5 1.4 + - - +
132C GLU* 3.0 28.7 + - - +
188C GLY 5.0 5.1 + - - -
190C PRO* 5.6 1.8 - - - +
302C GOL 3.6 22.6 - - - +
303C GOL 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 3.7 15.3 - - + -
117C LEU* 4.2 9.6 - - + -
125C ASP* 2.9 36.5 + - + +
128C ARG* 1.3 98.9 - - - +
130C TRP* 1.3 64.4 + - - +
132C GLU* 3.4 3.0 + - - +
133C THR* 2.8 29.4 + - - -
163C ILE* 3.5 15.0 - - + -
187C LEU* 3.2 47.5 - - + +
188C GLY 4.5 0.7 - - - -
189C LEU* 3.7 20.2 - - + -
190C PRO* 4.2 13.9 - - + -
193C ILE* 3.9 17.5 - - + -
303C GOL 3.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.9 3.8 - - + +
76C TYR* 5.0 8.0 - + - -
82C SER* 3.4 25.8 + - - +
91C TYR* 3.9 23.6 - + + +
92C SER 4.6 0.7 - - - -
93C LEU* 4.2 7.4 - - + -
126C LEU 2.9 17.4 + - - +
127C ASP* 3.8 5.8 - - - +
129C PHE* 1.3 77.7 - - - +
131C LEU* 1.3 64.1 + - - +
133C THR* 3.1 10.2 + - + -
134C LEU* 2.9 57.0 + - + +
152C ALA* 3.6 33.9 - - + -
153C VAL 3.6 24.7 - - - -
154C VAL* 3.6 29.8 - - + +
163C ILE* 3.6 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 4.1 13.0 - - + -
73C TRP* 3.8 33.0 - - + -
76C TYR* 3.8 37.2 - - + +
127C ASP 2.9 18.0 + - - +
128C ARG 3.9 2.9 - - - +
130C TRP* 1.3 77.6 - - - +
132C GLU* 1.3 64.3 + - - +
134C LEU* 3.1 7.8 + - + -
135C LEU* 2.9 35.7 + - + +
302C GOL 4.0 21.1 - - - +
618D LEU* 4.6 11.7 - - + -
621D GLN* 5.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ARG* 3.0 18.7 + - - +
129C PHE* 3.7 6.3 - - - +
130C TRP 3.3 0.4 - - - -
131C LEU* 1.3 75.4 - - - +
133C THR* 1.3 57.5 + - - +
135C LEU* 3.3 10.6 + - - +
136C CYS* 3.0 29.2 + - - -
183C TYR* 5.5 0.4 - - + -
186C ARG* 3.0 60.7 + - + +
187C LEU* 4.6 6.5 - - + -
303C GOL 3.7 14.2 - - - -
614D ARG* 2.8 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PHE 2.8 18.5 + - - -
130C TRP* 3.1 15.7 + - + -
132C GLU* 1.3 75.1 - - - +
134C LEU* 1.3 66.6 + - - +
136C CYS* 3.1 6.2 + - - +
137C LEU* 3.1 21.9 + - + +
152C ALA* 3.5 30.7 - - + -
163C ILE* 3.6 10.1 - - + +
165C ILE* 3.7 11.7 - - + -
183C TYR* 2.8 39.3 + - - +
187C LEU* 4.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 5.2 4.7 - - + -
72C PHE* 4.0 22.4 - - + -
76C TYR* 3.9 29.2 - - + -
93C LEU* 3.7 39.0 - - + -
130C TRP* 2.9 54.6 + - + +
131C LEU* 3.1 8.0 + - - +
133C THR* 1.3 76.5 - - - +
135C LEU* 1.3 57.9 + - - +
137C LEU* 3.2 9.5 + - + +
138C ILE* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 4.2 10.1 - - + -
73C TRP* 4.0 27.6 - - + -
131C LEU* 2.9 30.8 + - + +
132C GLU* 3.6 19.5 - - - +
133C THR 3.2 0.2 - - - -
134C LEU* 1.3 74.7 - - - +
136C CYS* 1.3 59.4 + - - +
138C ILE* 4.1 4.9 - - + -
139C GLY* 2.9 27.5 + - - -
141C SER* 3.9 2.4 + - - -
186C ARG* 3.9 12.2 + - - +
612D TYR 4.8 0.3 - - - +
614D ARG* 4.2 17.5 - - + +
617D LEU* 3.7 22.7 - - + +
618D LEU* 4.2 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLU 3.0 19.4 + - - -
133C THR* 3.1 9.2 + - - +
135C LEU* 1.3 76.3 - - - +
137C LEU* 1.3 64.9 + - + +
140C GLU* 3.4 1.2 + - - -
141C SER* 3.1 34.4 + - - -
142C PHE* 3.8 32.1 - - + -
146C SER* 4.7 0.2 + - - -
165C ILE* 4.7 1.6 - - + -
183C TYR* 4.5 10.1 - - - -
186C ARG* 3.8 44.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.2 39.3 - - + -
93C LEU* 3.6 37.2 - - + +
133C THR 3.1 16.6 + - - +
134C LEU* 3.6 9.6 - - - +
136C CYS* 1.3 78.8 - - - +
138C ILE* 1.3 64.5 + - - +
140C GLU* 3.1 16.6 + - - +
142C PHE* 4.6 2.7 - - + -
146C SER* 5.3 0.2 + - - -
149C VAL* 4.0 20.2 - - + -
151C GLY 3.8 1.8 - - - -
152C ALA* 3.7 21.3 - - + +
165C ILE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.7 34.6 - - + +
40C GLN 4.9 0.3 + - - -
43C TRP* 3.9 22.3 + - + +
66C PHE* 4.1 9.6 - - + -
69C VAL* 5.6 0.7 - - - -
72C PHE* 3.5 44.0 - - + -
93C LEU* 3.8 24.2 - - + -
134C LEU 3.0 19.0 + - - +
135C LEU* 4.1 3.4 - - + -
137C LEU* 1.3 76.5 - - - +
139C GLY* 1.3 62.1 + - - +
140C GLU* 3.3 9.6 + - - +
610D LYS 4.8 1.0 - - - +
612D TYR* 4.5 2.4 - - - -
617D LEU* 4.0 28.9 - - + -
----------------------------------------------------------
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