Contacts of the strand formed by residues 177 - 182 (chain B) in PDB entry 3AP3
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 LYS 177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU 2.6 13.1 + - - +
71B ILE* 3.5 2.1 - - - -
72B PHE* 2.7 36.4 + - - +
175B ASN 4.6 5.4 - - - +
176B SER* 1.3 75.8 - - - +
178B PHE* 1.3 59.6 + - - +
231B GLU* 3.2 28.0 + - - +
232B LYS* 3.7 9.6 - - + +
255B PHE* 2.8 46.9 + - + -
256B LEU* 3.4 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.2 44.0 - + + -
163B LEU* 3.9 18.2 - - + -
166B SER* 3.5 29.6 - - - -
169B LEU* 3.4 30.5 - - + -
170B SER* 3.7 20.2 - - - -
176B SER* 3.2 24.7 - - - -
177B LYS* 1.3 78.3 - - - +
179B LEU* 1.3 63.1 + - - +
180B LEU 4.0 0.4 - - - -
228B VAL* 4.8 7.2 - - + -
232B LYS* 3.0 22.3 + - + +
233B CYS* 3.5 12.2 - - + -
234B LEU* 3.0 28.2 + - - +
255B PHE* 4.2 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.3 14.6 - - + -
72B PHE 2.8 11.5 + - - +
73B VAL* 3.8 8.9 - - + +
74B GLY 3.3 27.2 + - - +
84B MET* 4.1 18.8 - - + -
88B LEU* 3.9 28.0 - - + -
163B LEU* 4.3 4.0 - - - +
178B PHE* 1.3 72.8 - - - +
180B LEU* 1.3 59.3 - - - +
181B MET* 3.5 1.4 + - - +
234B LEU* 3.5 21.8 - - + +
236B VAL* 3.5 27.4 - - + -
252B ILE* 3.8 24.2 - - + -
255B PHE* 4.7 7.4 - - + -
256B LEU* 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY 4.0 0.7 - - - -
75B GLY* 4.2 10.8 - - - -
163B LEU* 4.4 13.0 - - + -
178B PHE 4.0 2.0 + - - -
179B LEU* 1.3 68.0 - - - +
181B MET* 1.3 63.3 + - - +
182B VAL* 3.3 14.7 + - + +
218B ILE* 4.7 6.3 - - + -
221B MET* 3.5 38.1 - - + +
222B TYR* 3.7 47.6 - - + +
225B CYS* 3.9 20.4 - - + -
233B CYS* 4.4 3.1 - - - -
234B LEU 3.1 8.8 + - - +
235B PRO* 3.4 9.9 - - + +
236B VAL* 2.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.5 4.3 - - + -
74B GLY 3.2 14.8 + - - +
75B GLY* 4.2 12.5 - - - -
76B VAL 4.8 1.2 + - - -
79B SER* 3.7 30.0 + - - +
80B GLY* 3.8 14.1 - - - +
81B THR* 3.6 28.9 - - + -
84B MET* 3.3 31.4 - - + +
179B LEU* 4.7 2.2 - - - +
180B LEU* 1.3 71.5 - - - +
182B VAL* 1.3 61.9 + - - +
183B ARG 4.0 2.3 + - - -
218B ILE* 5.1 4.7 - - - +
236B VAL* 3.4 22.2 - - + +
238B TYR* 4.5 9.9 - - + -
241B LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.4 32.1 - - + +
181B MET* 1.3 72.8 - - - +
183B ARG* 1.3 61.0 + - - +
214B TRP* 5.9 0.2 - - + -
218B ILE* 4.2 14.6 - - + -
222B TYR* 5.1 0.2 - - + -
235B PRO* 4.5 11.4 - - + -
236B VAL 2.9 12.3 + - - +
237B TYR* 3.6 24.9 - - + -
238B TYR* 3.2 12.1 + - - +
239B GLU* 2.9 17.3 - - - +
323B LEU* 3.6 41.3 - - + -
325B TYR* 3.0 9.3 + - + -
----------------------------------------------------------
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