Contacts of the strand formed by residues 163 - 168 (chain I) 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 ARG 163 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I PHE 3.9 0.2 - - - -
80I PRO* 3.4 17.9 - - + +
84I THR* 5.4 0.6 + - - -
86I VAL* 3.4 22.3 - - - +
87I CYS* 3.2 36.6 - - - +
90I GLU* 2.8 31.9 + - - -
162I LEU* 1.3 79.7 - - - +
164I GLY* 1.3 55.4 + - - +
178I THR 3.5 4.2 - - - +
180I ASN* 2.9 38.6 + - + +
181I ASP 4.1 2.2 - - - +
182I LEU* 2.7 33.0 + - - +
184I VAL 3.4 22.2 + - - -
186I ARG* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I PHE* 3.3 0.9 - - - -
78I PHE* 2.8 38.0 + - - +
153I VAL* 4.2 7.0 - - - -
162I LEU* 3.2 12.1 + - - +
163I ARG* 1.3 73.0 - - - +
165I LEU* 1.3 57.2 + - - -
166I PHE* 3.9 5.6 - - - -
178I THR 3.3 5.6 - - - -
179I LEU* 3.6 17.5 - - - -
186I ARG* 3.0 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I VAL* 3.8 14.6 - - + -
76I PHE 3.7 3.8 - - - -
77I PHE* 3.8 15.7 - - + -
94I PHE* 3.7 30.7 - - + -
164I GLY* 1.3 73.3 - - - -
166I PHE* 1.3 68.6 - - - +
167I ILE* 3.8 26.9 - - + -
176I GLN* 4.3 8.7 - - - +
177I ILE* 3.6 3.8 - - - -
178I THR* 2.7 45.7 + - + +
186I ARG* 3.9 22.0 - - + -
191I THR* 3.7 17.7 - - + +
194I LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I ALA* 4.0 10.3 - - + -
74I LEU 3.4 3.3 - - - +
75I VAL* 3.5 2.8 - - - -
76I PHE* 2.8 49.8 + + + +
78I PHE* 3.6 27.4 - + - -
151I TYR* 3.4 53.6 - + + -
153I VAL* 3.6 16.4 - - + -
164I GLY 3.9 8.7 - - - -
165I LEU* 1.3 76.6 - - - +
167I ILE* 1.3 62.6 + - - +
168I ILE* 3.9 2.9 + - + -
174I LEU* 3.8 17.7 - - + -
176I GLN 3.5 2.7 - - - -
177I ILE* 3.8 31.6 - - + -
179I LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 4.0 27.8 - - + -
74I LEU 3.6 4.7 - - - +
75I VAL* 4.6 3.4 - - + -
165I LEU* 3.8 13.7 - - + -
166I PHE* 1.3 75.7 - - - +
168I ILE* 1.3 59.8 + - - +
174I LEU* 3.5 3.3 - - - +
175I ARG* 2.9 33.3 + - + +
176I GLN* 3.0 31.6 + - + +
191I THR* 4.2 20.0 - - + +
194I LEU* 3.6 38.4 - - + -
195I VAL* 4.1 13.9 - - + +
198I PHE* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ALA* 3.6 25.4 - - + -
66I LEU* 4.0 25.4 - - + -
73I TYR* 3.3 6.9 - - - -
74I LEU* 2.7 47.1 + - + +
76I PHE* 4.1 25.6 - - + -
151I TYR* 4.1 7.4 - - - +
166I PHE* 4.5 6.1 - - + +
167I ILE* 1.3 76.5 - - - +
169I ASP* 1.3 64.9 + - - +
172I GLY* 3.6 34.3 - - - +
173I ILE 3.5 4.7 - - - +
174I LEU* 4.0 9.6 - - + -
----------------------------------------------------------
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