Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 5TIN
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 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.8 1.6 - - - +
37A VAL* 3.7 21.1 - - + +
39A VAL* 3.5 30.1 - - + -
94A TRP* 4.0 12.6 - - + -
96A PRO* 4.3 8.7 - - + -
97A ASP* 3.8 10.3 - - - +
158A SER* 3.7 22.4 - - - +
161A TYR* 3.4 27.9 - - + +
162A THR 3.0 12.8 + - - +
163A MET* 3.7 6.2 - - - -
165A ASP* 1.3 78.0 - - - +
167A ILE* 1.3 68.2 + - - +
168A PHE* 3.7 22.2 - - + -
208A THR* 3.6 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.8 13.2 - - + -
37A VAL 2.9 8.6 + - - +
38A GLN* 3.5 28.5 - - - +
39A VAL* 2.8 29.6 + - - +
163A MET* 3.6 54.5 - - + +
166A LEU* 1.3 78.7 - - - +
168A PHE* 1.3 74.7 + - - +
169A GLU* 3.9 10.5 - - - +
208A THR* 3.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.5 25.8 - - + -
41A CYS* 4.5 4.9 - - - -
96A PRO* 4.2 5.8 - - + -
98A LEU* 3.7 41.7 - - + -
156A LEU* 3.6 20.9 - - + -
157A GLU* 3.5 25.1 - - - -
158A SER* 3.6 6.7 - - - -
166A LEU* 3.7 30.7 - - + -
167A ILE* 1.3 82.7 - - - +
169A GLU* 1.3 72.5 + - - +
197A TYR* 4.5 2.8 - - - -
208A THR* 2.9 23.5 + - + +
210A ILE* 3.6 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLN* 4.2 9.9 - - - +
39A VAL 3.0 11.2 + - - +
40A THR* 3.3 9.0 - - - +
41A CYS* 2.9 25.1 + - - +
167A ILE* 3.9 14.7 - - - +
168A PHE* 1.3 81.5 - - - +
170A TRP* 1.3 71.7 + - - +
197A TYR* 2.2 41.2 + - - -
210A ILE* 3.9 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 4.2 1.8 - - - +
41A CYS 3.4 24.5 - - - -
43A ILE* 4.3 19.1 - - + -
156A LEU* 4.0 25.6 - - + -
169A GLU* 1.3 84.5 + - - +
171A GLN* 1.3 70.6 + - - +
172A ASP* 3.7 5.5 + - - +
175A PRO* 3.9 25.4 - - + -
176A VAL* 4.4 4.7 - - + -
195A LEU* 3.7 34.0 - - + +
196A ARG 4.7 3.6 - - - -
197A TYR* 6.1 0.6 - + - -
210A ILE* 3.6 31.7 - - + +
211A GLU 3.1 25.5 + - - +
212A VAL* 3.7 32.5 - - + -
----------------------------------------------------------
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