Contacts of the strand formed by residues 182 - 186 (chain B) in PDB entry 1PG3
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 182 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.5 33.2 - - + -
127B LEU* 4.4 5.2 - - + -
129B ILE* 4.1 20.6 - - + -
134B VAL 4.2 1.4 + - - -
135B VAL* 4.0 17.3 - - + -
136B ALA* 2.8 31.6 + - - +
180B SER* 3.4 2.3 - - - -
181B ARG* 1.3 81.8 - - - +
183B VAL* 1.3 74.1 + - - +
184B ILE* 4.3 2.5 - - + -
214B VAL* 4.5 1.7 - - - +
216B HIS* 2.9 48.2 - - + +
217B VAL 4.0 0.9 - - - +
218B ILE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 3.2 13.5 - - + +
138B TYR* 4.7 8.1 - - + -
171B VAL* 6.1 1.6 - - + -
175B ILE* 3.8 29.6 - - + -
180B SER* 5.2 0.4 - - - -
182B LEU* 1.3 80.6 - - - +
184B ILE* 1.3 72.2 + - - +
185B THR* 4.5 2.5 - - - -
202B VAL* 3.8 32.8 - - + -
206B LEU* 4.9 0.7 - - + -
214B VAL* 4.1 17.5 - - + -
216B HIS 3.1 5.9 + - - +
217B VAL* 3.2 15.8 - - + +
218B ILE 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 3.7 30.3 - - + -
124B LEU* 4.7 0.9 - - + -
135B VAL* 3.7 25.6 - - + -
136B ALA 2.8 15.0 + - - +
137B ILE* 4.1 9.0 - - + -
138B TYR 2.8 27.9 + - - -
139B MET* 3.5 17.9 - - + +
148B ALA* 3.7 17.5 - - + -
152B CYS* 4.9 1.8 - - - -
182B LEU* 4.3 10.8 - - + -
183B VAL* 1.3 76.7 - - - +
185B THR* 1.3 61.7 + - - +
218B ILE* 3.6 11.0 - - + +
237B TRP* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 2.8 27.0 + - - -
139B MET* 3.5 10.5 - - - +
183B VAL* 4.5 1.1 - - - -
184B ILE* 1.3 74.2 - - - +
186B ALA* 1.3 78.0 + - - +
198B LEU* 3.4 12.5 - - - +
199B LYS* 4.2 12.3 - - + -
202B VAL* 3.9 24.2 - - + -
217B VAL* 4.1 20.6 - - + -
218B ILE 3.0 10.6 + - - +
219B VAL* 3.3 2.9 - - + -
220B LEU* 2.9 20.6 + - - +
237B TRP* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR 4.1 1.4 + - - -
139B MET* 4.0 1.2 - - - -
140B PRO* 4.0 24.0 - - + -
185B THR* 1.3 78.9 + - - +
187B ASP* 1.3 68.5 + - - +
188B GLU 3.9 16.2 - - - +
198B LEU* 3.2 7.4 - - + +
199B LYS* 3.1 16.5 + - - +
219B VAL* 3.9 5.6 - - - -
220B LEU* 3.2 25.1 - - + +
222B ARG* 4.3 5.6 - - + -
----------------------------------------------------------
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