Contacts of the helix formed by residues 115 - 124 (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 SER 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASP* 1.3 76.6 - - - +
116C GLN* 1.3 67.0 + - - +
117C PHE* 3.2 17.2 + - - +
118C GLU* 2.9 39.8 + - - +
119C HIS* 3.0 21.5 + - - -
141C SER* 3.5 6.5 - - - -
143C LEU* 3.6 24.5 - - - +
81F LEU* 4.2 10.9 - - - +
82F ASP 4.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C THR* 4.0 33.7 + - + +
56C VAL* 3.5 17.0 - - + +
61C PHE* 3.5 42.1 - - + -
115C SER* 1.3 77.9 - - - +
117C PHE* 1.3 86.4 + - + +
119C HIS* 3.3 3.3 + - + -
120C LEU* 3.0 19.4 + - - +
141C SER* 3.7 19.2 + - - -
143C LEU* 4.3 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.5 29.2 - + - -
115C SER* 3.1 11.4 - - - +
116C GLN* 1.3 104.2 - - + +
118C GLU* 1.3 57.9 + - - +
120C LEU* 3.5 3.3 + - - +
121C ALA* 3.0 28.8 + - - +
221D PRO 5.7 0.2 - - - -
223D PRO* 4.4 8.1 - - + -
81F LEU* 3.9 16.2 - - + -
82F ASP 4.3 0.9 - - - +
83F PHE* 3.8 24.5 - - + +
84F THR* 3.6 27.1 - - + -
85F PHE* 3.8 31.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASP* 3.4 8.6 - - + +
83C PHE* 3.9 4.1 - - + -
114C ASP* 3.6 2.6 - - - +
115C SER* 2.9 38.2 + - - +
117C PHE* 1.3 74.1 - - - +
119C HIS* 1.3 65.0 + - - +
121C ALA* 3.3 6.3 + - - +
122C TRP* 2.9 25.8 + - - +
143C LEU* 5.1 0.9 - - - +
82F ASP* 3.7 7.0 - - - +
83F PHE* 3.8 18.8 - - + -
114F ASP* 2.4 35.4 - - - +
118F GLU* 2.8 48.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.6 11.7 - - + -
79C TYR* 3.0 24.5 + - - -
82C ASP* 2.6 27.9 + - - -
112C SER* 3.2 19.0 + - - -
114C ASP* 3.8 8.7 + - + -
115C SER 3.0 13.9 + - - -
116C GLN* 3.5 10.3 - - - +
118C GLU* 1.3 75.7 - - - +
120C LEU* 1.3 57.6 + - - +
122C TRP* 3.2 4.7 + - - +
123C ILE* 2.9 34.4 + - - +
139C LEU* 3.4 40.2 - - + +
140C LEU 3.0 25.2 + - - -
141C SER* 4.0 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.1 7.8 - - + +
59C GLY* 3.7 36.6 - - - +
61C PHE* 4.1 13.9 - - + -
116C GLN 3.0 16.3 + - - +
117C PHE 3.9 4.5 - - - +
119C HIS* 1.3 73.1 - - - +
121C ALA* 1.3 61.8 + - - +
123C ILE* 3.3 11.3 + - + +
124C ASN* 2.9 53.0 + - - +
223D PRO* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.9 7.0 - - + -
117C PHE 3.0 18.9 + - - +
118C GLU 3.3 4.5 + - - +
120C LEU* 1.3 76.7 - - - +
122C TRP* 1.3 54.5 + - - +
124C ASN* 3.4 10.5 + - - +
125C THR* 2.7 31.3 + - - -
83F PHE* 3.7 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 3.6 4.7 - + - -
82C ASP* 3.3 35.4 - - - -
83C PHE* 3.2 51.8 - + + +
84C THR 4.3 0.2 - - - -
87C CYS* 4.0 6.7 - - + -
88C PRO* 3.5 49.8 - - + -
91C ILE* 3.5 24.7 - - + -
118C GLU 2.9 17.3 + - - +
119C HIS 3.5 4.5 - - - +
121C ALA* 1.3 74.7 - - - +
123C ILE* 1.3 66.2 + - - +
124C ASN 3.2 0.2 - - - -
125C THR* 2.9 14.1 + - - -
130C GLY 3.0 19.8 + - - -
131C GLY* 3.6 9.3 - - - -
132C LEU* 3.2 39.5 + - + -
139C LEU* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.7 30.5 - - + +
59C GLY* 5.5 5.6 - - - +
119C HIS 2.9 19.4 + - - +
120C LEU* 3.6 12.8 - - + +
122C TRP* 1.3 75.5 - - - +
124C ASN* 1.3 67.1 + - - +
125C THR 3.1 4.0 + - - -
132C LEU* 4.1 5.2 - - + -
133C GLY* 3.2 43.1 - - - +
134C PRO* 3.9 12.2 - - + +
135C ILE* 3.7 28.7 - - + +
139C LEU* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 2.9 42.7 + - - +
121C ALA* 3.4 10.3 + - - +
122C TRP 3.2 0.4 - - - -
123C ILE* 1.3 84.1 - - - +
125C THR* 1.3 58.7 + - - +
126C PRO* 4.0 5.0 - - - +
----------------------------------------------------------
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