Contacts of the strand formed by residues 170 - 173 (chain A) in PDB entry 3FPL
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 VAL 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.1 24.5 - - + -
168A ALA* 4.1 6.5 - - + +
169A THR* 1.3 79.2 - - - +
171A ALA* 1.3 66.8 + - - +
172A VAL* 4.4 3.6 - - + -
186A ALA* 4.2 13.9 - - + -
191A ALA* 3.9 22.4 - - + -
193A ARG 3.0 7.7 + - - +
194A ILE* 3.3 6.5 - - + +
195A ILE* 2.8 32.9 + - - +
236A VAL* 4.6 3.4 - - - -
238A ALA* 3.3 17.0 - - + +
240A ILE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 1.3 79.0 - - - +
172A VAL* 1.3 62.1 + - - +
173A LEU* 4.1 3.8 - - + -
195A ILE* 3.2 11.0 - - + +
227A ILE* 4.5 9.9 - - + -
236A VAL* 4.1 17.8 - - + +
238A ALA 2.9 7.2 + - - +
239A ALA* 3.3 2.9 - - + -
240A ILE 2.8 26.5 + - - +
255A ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 4.4 3.4 - - + -
171A ALA* 1.3 78.2 - - - +
173A LEU* 1.3 60.7 - - - +
174A GLY 3.5 22.2 + - - +
175A ILE* 4.7 1.1 - - + +
179A GLY* 3.6 21.8 - - - +
182A ALA* 4.0 7.9 - - + +
183A VAL* 3.8 33.0 - - + +
186A ALA* 5.2 0.2 - - + -
194A ILE* 4.2 13.2 - - + -
195A ILE 2.8 12.0 + - - +
196A ALA* 4.6 1.6 - - - -
197A VAL* 2.9 28.6 + - - +
240A ILE* 3.6 24.0 - - + +
242A ALA* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 4.7 1.6 - - + +
172A VAL* 1.3 71.2 - - - +
174A GLY* 1.3 59.2 + - - +
197A VAL* 3.6 31.4 - - + -
223A ILE* 4.7 6.1 - - + -
227A ILE* 4.6 2.2 - - + -
239A ALA* 4.5 6.1 - - + -
240A ILE 2.8 15.6 + - - +
241A ILE* 4.2 9.2 - - + -
242A ALA* 2.9 26.2 + - - -
243A GLY 3.2 8.8 + - - +
248A ILE* 3.9 35.9 - - + -
251A THR* 4.6 2.0 - - + -
252A ALA* 3.8 35.9 - - + +
255A ILE* 4.1 22.4 - - + -
----------------------------------------------------------
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