Contacts of the strand formed by residues 143 - 150 (chain A) in PDB entry 1PT6
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 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLN* 1.3 90.1 - - - +
144A ASP* 1.3 57.9 + - - +
145A ILE* 4.1 10.8 - - + -
178A GLN 3.9 2.2 + - - -
179A THR* 3.4 11.3 + - + +
180A GLN 2.9 27.7 + - - +
241A ARG* 3.0 7.8 + - - +
244A VAL* 3.8 0.2 - - - -
245A LYS* 3.7 20.9 - - + +
247A VAL* 4.1 18.8 - - + -
331A ILE* 3.5 44.2 - - + +
332A PHE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 1.3 69.7 - - - +
145A ILE* 1.3 60.6 + - - +
180A GLN* 3.2 14.5 - - - +
196A LEU* 3.9 15.0 - - + -
234A PHE* 3.4 21.2 - - + -
240A ALA* 3.3 7.4 - - - +
241A ARG* 2.8 61.8 + - - +
244A VAL* 3.5 6.4 - - - +
245A LYS 2.9 14.7 + - - +
246A LYS* 3.5 3.4 - - + +
247A VAL* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 4.1 13.7 - - + -
144A ASP* 1.3 77.7 - - - +
146A VAL* 1.3 66.6 - - - +
147A ILE* 4.4 9.4 - - + -
168A LEU* 6.4 0.2 - - + -
172A MET* 3.8 25.4 - - + -
179A THR* 3.7 21.3 - - + -
180A GLN 2.8 15.0 + - - +
181A VAL* 3.1 12.0 - - + +
182A GLY 3.1 23.9 + - - +
196A LEU* 3.5 1.2 - - - +
247A VAL* 3.2 19.1 - - + +
249A VAL* 4.2 22.4 - - + -
331A ILE* 3.8 21.5 - - + -
332A PHE* 3.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 1.3 77.1 - - - +
147A ILE* 1.3 71.2 + - - +
148A VAL* 4.1 1.6 - - + -
182A GLY* 3.3 11.0 - - - +
184A VAL* 4.1 8.5 - - + -
196A LEU* 4.2 15.3 - - + -
229A ALA* 3.9 24.7 - - + -
233A ALA* 4.0 23.8 - - + -
234A PHE* 3.5 35.0 - - + -
247A VAL 2.9 9.7 + - - -
248A MET* 3.3 7.8 - - + +
249A VAL 3.0 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.4 11.4 - - + -
146A VAL* 1.3 74.9 - - - +
148A VAL* 1.3 58.9 + - - +
149A LEU* 3.8 27.6 - - + -
164A PHE* 5.3 0.9 - - + -
165A LEU* 3.8 25.4 - - + -
168A LEU* 4.3 20.0 - - + -
169A LEU* 4.3 20.2 - - + -
172A MET* 5.9 0.2 - - + -
181A VAL* 4.4 4.3 - - + -
182A GLY 3.0 6.9 + - - +
183A ILE* 3.4 17.2 - - + +
184A VAL 2.9 31.4 + - - +
249A VAL* 3.3 24.9 - - + +
251A VAL* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.1 3.1 - - + -
147A ILE* 1.3 72.8 - - - +
149A LEU* 1.3 58.9 + - - +
184A VAL* 3.4 8.7 - - + +
186A TYR* 3.6 27.4 - - + -
225A GLY* 3.7 22.2 - - - +
226A THR* 3.9 7.6 - - - +
229A ALA* 3.6 29.6 - - + -
248A MET* 3.9 22.7 - - + -
249A VAL 2.8 10.4 + - - +
250A ILE* 3.4 8.9 - - + -
251A VAL* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 4.0 15.3 - - + -
148A VAL* 1.3 71.5 - - - +
150A ASP* 1.3 65.4 + - - +
151A GLY 3.4 0.5 + - - -
158A TRP* 4.3 18.8 - - + -
161A VAL* 4.0 24.9 - - + -
164A PHE* 5.3 1.3 - - + -
165A LEU* 3.8 32.1 - - + -
183A ILE* 4.2 16.6 - - + -
184A VAL 2.8 15.2 + - - +
185A GLN* 3.3 9.8 - - + +
186A TYR* 2.9 29.0 + - - -
212A ILE* 4.8 7.4 - - + -
251A VAL* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 1.3 73.4 - - - +
151A GLY* 1.3 59.2 + - - +
152A SER* 2.9 37.5 + - - -
155A ILE* 3.1 21.2 - - + +
158A TRP* 3.6 10.9 - - - -
161A VAL* 5.7 0.5 - - - +
186A TYR* 3.5 22.4 - - - +
187A GLY* 5.1 0.7 - - - -
220A THR* 3.3 16.3 - - - +
251A VAL* 2.9 24.2 + - - +
252A THR* 2.7 26.6 + - - -
253A ASP* 3.2 14.9 + - - +
----------------------------------------------------------
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