Contacts of the strand formed by residues 174 - 180 (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 LEU 174 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 3.8 30.3 - - + -
43C LYS 3.8 17.0 - - - +
44C ILE* 3.6 3.5 - - - +
45C SER* 2.8 29.3 + - - -
46C LYS 2.9 17.6 + - - +
48C ALA* 3.9 15.0 - - + +
49C PRO* 4.5 8.1 - - + -
151C TYR* 4.8 1.3 - - + -
166C PHE* 3.9 27.4 - - + -
167C ILE 3.3 18.4 - - - +
168C ILE* 3.9 6.3 - - + +
172C GLY 3.8 2.0 + - - -
173C ILE* 1.3 70.3 - - - +
175C ARG* 1.3 67.1 + - - +
176C GLN 3.6 18.6 - - - +
177C ILE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 4.0 4.8 - - - +
73C TYR* 3.5 13.2 + - + +
167C ILE* 2.8 14.9 + - + +
169C ASP* 3.2 37.0 + - + +
173C ILE* 3.5 21.2 - - - +
174C LEU* 1.3 80.1 - - - +
176C GLN* 1.3 61.0 + - + +
198C PHE* 3.3 42.3 - - + -
201C THR* 4.8 1.4 + - - -
202C ASP* 2.9 28.3 + - - -
181G ASP* 2.9 59.9 + - - +
183G PRO* 3.8 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 4.2 1.9 - - - +
165C LEU* 4.2 5.2 - - - +
166C PHE* 3.5 4.0 - - - -
167C ILE* 3.1 47.3 + - + +
174C LEU* 3.6 3.9 - - - +
175C ARG* 1.3 78.6 - - - +
177C ILE* 1.3 91.5 + - - +
178C THR* 2.7 29.9 + - - -
194C LEU* 3.7 24.9 - - + +
198C PHE* 4.0 12.3 - - + -
178G THR* 3.6 12.1 - - - +
179G LEU 3.4 6.5 + - - +
180G ASN* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 4.2 19.5 - - + +
44C ILE* 3.9 24.2 - - + +
165C LEU 3.5 3.6 - - - -
166C PHE* 3.7 28.9 - - + -
174C LEU* 4.4 7.4 - - + -
176C GLN* 1.3 84.5 + - - +
178C THR* 1.3 64.2 + - - +
179C LEU* 3.7 33.0 - - + -
177G ILE 3.9 0.7 - - - +
178G THR* 3.6 1.0 - - - -
179G LEU* 2.8 59.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ARG 3.4 2.4 - - - +
164C GLY* 3.3 1.7 - - - -
165C LEU* 2.7 51.2 + - + +
176C GLN* 2.7 32.0 + - - +
177C ILE* 1.3 72.4 - - - +
179C LEU* 1.3 60.4 + - - +
180C ASN* 3.9 8.3 - - - +
186C ARG* 4.7 13.6 - - + -
194C LEU* 4.7 4.2 - - - +
176G GLN* 3.6 21.1 - - - +
177G ILE 3.6 3.1 - - - -
178G THR* 4.6 5.4 - - + +
190G GLU* 6.1 0.7 - - - +
194G LEU* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C HIS* 5.9 3.1 - - - +
152C GLY 5.1 8.5 - - - +
153C VAL* 4.0 16.4 - - + -
162C LEU* 4.2 11.4 - - + -
163C ARG 3.5 1.8 - - - -
164C GLY* 3.7 16.6 - - - -
166C PHE* 4.3 3.4 - - + -
177C ILE* 3.7 26.5 - - + -
178C THR* 1.3 79.0 - - - +
180C ASN* 1.3 62.0 + - - +
44G ILE* 3.4 18.4 - - + +
176G GLN* 3.3 6.4 + - - +
177G ILE* 2.8 63.8 + - + +
179G LEU* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.6 5.7 - - - +
163C ARG* 2.9 38.4 + - + -
178C THR* 3.9 7.6 - - - +
179C LEU* 1.3 72.6 - - - +
181C ASP* 1.3 63.4 + - - +
184C VAL* 3.0 31.4 + - - +
185C GLY 3.4 18.4 + - - -
186C ARG* 3.8 13.1 - - - +
44G ILE* 4.3 4.5 - - - -
175G ARG 4.1 2.5 - - - -
176G GLN* 3.0 30.2 + - + +
194G LEU* 3.7 16.0 - - - +
198G PHE* 4.8 2.0 - - + -
----------------------------------------------------------
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