Contacts of the helix formed by residues 85 - 97 (chain C) in PDB entry 3TKR
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 PHE 85 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE 4.8 2.0 - - - -
84C THR* 1.3 94.2 + - - +
86C VAL* 1.3 68.5 + - - +
87C CYS 3.3 0.7 - - - -
88C PRO* 3.2 14.2 - - - +
89C THR* 3.5 2.8 - - - +
163C ARG* 5.8 0.2 - - - +
117F PHE* 3.8 34.3 - + - -
207G VAL* 4.0 11.4 - - + -
219G ILE* 3.3 30.9 - - + +
221G PRO* 3.4 41.3 - - + -
222G ASP* 3.4 25.4 - - - -
223G PRO* 4.1 2.5 - - + -
226G LYS* 3.8 29.2 - - + -
230G PHE* 3.7 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 1.3 76.3 - - - +
87C CYS* 1.3 64.1 + - - +
89C THR* 2.6 28.9 + - - +
90C GLU* 3.2 10.0 + - + -
163C ARG* 3.4 32.0 - - - +
182C LEU 4.3 3.4 - - - +
183C PRO 4.1 5.6 - - - +
185C GLY* 3.6 29.2 - - - -
207G VAL* 3.5 30.7 - - + -
208G CYS 3.4 21.1 - - - +
209G PRO 4.6 0.2 - - - -
219G ILE* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 3.7 19.5 - - + +
80C PRO* 3.6 21.3 - - - -
81C LEU 3.6 18.6 - - - +
84C THR* 3.4 18.6 - - - +
86C VAL* 1.3 76.0 - - - +
88C PRO* 1.3 71.6 - - + +
90C GLU* 3.1 8.3 + - - +
91C ILE* 3.0 25.0 + - - +
122C TRP* 4.0 4.3 - - + -
163C ARG* 3.2 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR 3.3 22.0 - - - +
85C PHE 3.2 18.2 - - - +
87C CYS* 1.3 94.8 - - + +
89C THR* 1.3 55.1 + - - +
91C ILE* 3.8 0.2 - - - +
92C ILE* 2.8 39.2 + - + +
122C TRP* 3.5 21.1 - - + -
130C GLY 4.0 10.3 - - - +
131C GLY 4.4 5.2 - - - +
132C LEU* 3.8 18.8 - - + -
230G PHE* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE 3.5 18.4 - - - +
86C VAL 2.6 15.0 + - - -
88C PRO* 1.3 75.0 - - - +
90C GLU* 1.3 56.0 + - - +
92C ILE* 3.9 6.6 - - - +
93C ALA* 2.9 29.5 + - - +
209G PRO* 3.4 11.9 - - + +
210G ALA* 2.9 25.4 + - - +
219G ILE* 3.8 14.4 - - + -
229G TYR* 3.7 27.6 - - + +
230G PHE* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 4.6 11.0 - - + -
79C TYR* 4.4 2.0 - - + +
86C VAL* 3.7 17.3 - - + +
87C CYS* 3.1 7.8 + - - +
89C THR* 1.3 79.8 + - - +
91C ILE* 1.3 65.6 + - - +
93C ALA* 3.7 0.7 - - - +
94C PHE* 3.1 37.5 + - + -
163C ARG* 2.9 26.7 + - - -
185C GLY* 3.4 3.3 - - - -
186C ARG* 2.7 66.2 + - + +
210G ALA* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 4.2 16.4 - - + -
79C TYR* 3.5 49.1 - - + +
87C CYS 3.0 14.8 + - - +
88C PRO 3.8 2.7 - - - +
90C GLU* 1.3 76.0 - - + +
92C ILE* 1.3 58.6 + - - +
94C PHE* 3.9 1.7 - - - +
95C GLY* 2.9 26.7 + - - -
110C ALA* 4.5 2.2 - - + -
122C TRP* 3.5 21.5 - - + -
132C LEU* 3.9 20.9 - - + -
135C ILE* 3.8 19.9 - - + +
137C ILE* 4.2 6.1 - - + +
139C LEU* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PRO* 2.8 30.4 + - + +
89C THR* 4.1 5.4 - - - +
91C ILE* 1.3 70.6 - - + +
93C ALA* 1.3 61.9 + - - +
95C GLY 4.5 0.2 - - - +
96C ASP* 2.8 36.4 + - + +
127C ARG* 3.4 51.4 - - + +
131C GLY 3.8 22.7 - - - +
132C LEU* 4.0 15.5 - - + +
135C ILE* 4.7 6.3 - - + -
230G PHE* 5.8 4.3 - - + -
233G LEU* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR 2.9 21.1 + - - +
90C GLU 3.2 4.6 + - - +
92C ILE* 1.3 80.8 - - - +
94C PHE* 1.3 61.4 + - - +
96C ASP* 4.2 1.7 - - - +
97C ARG* 3.3 31.6 + - - +
188C VAL* 3.6 21.2 - - + +
210G ALA* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 4.2 7.0 - - + -
77C PHE* 3.7 26.9 - + + -
90C GLU* 3.1 32.7 + - + +
91C ILE 4.0 2.7 - - - +
93C ALA* 1.3 74.7 - - - +
95C GLY* 1.3 65.7 + - - +
97C ARG* 3.1 5.1 + - - -
98C LEU* 3.0 24.0 + - - +
101C PHE* 3.7 36.3 - + - -
108C VAL* 4.1 22.4 - - + -
137C ILE* 4.5 4.5 - - + -
165C LEU* 3.8 17.0 - - + -
186C ARG* 5.3 10.3 - - + -
187C SER 4.7 0.7 - - - -
188C VAL* 4.0 23.8 - - + -
191C THR* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ILE 2.9 18.0 + - - -
92C ILE 3.8 0.4 - - - -
94C PHE* 1.3 76.9 - - - +
96C ASP* 1.3 61.4 + - - +
97C ARG 3.3 1.0 + - - -
98C LEU* 3.3 16.5 + - - +
135C ILE* 4.0 18.2 - - - -
136C ARG* 4.3 16.6 + - - +
137C ILE* 4.2 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 2.8 28.3 + - + +
93C ALA* 4.3 3.6 - - - +
95C GLY* 1.3 73.7 - - - +
97C ARG* 1.3 64.3 + - + +
98C LEU 3.5 0.6 + - - -
127C ARG* 2.9 43.6 + - - -
135C ILE* 5.7 0.9 - - - +
136C ARG* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA* 3.3 19.4 + - - +
94C PHE* 3.1 7.5 + - - +
96C ASP* 1.3 82.8 - - + +
98C LEU* 1.3 65.3 + - - +
99C GLU* 3.2 3.6 - - - -
100C GLU* 2.7 63.5 + - - +
101C PHE* 3.7 6.2 - - + -
188C VAL* 3.6 30.8 - - + +
189C ASP* 2.8 43.6 + - - -
192C LEU* 3.6 8.7 - - - +
----------------------------------------------------------
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