Contacts of the strand formed by residues 64 - 69 (chain B) in PDB entry 1FPY
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 ASP 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA 5.5 2.6 - - - +
339A ARG* 2.8 21.9 + - - +
344A ARG* 3.4 23.5 + - - -
4471A ADP 5.7 0.7 + - - -
48B MET* 3.2 29.6 - - + +
49B PHE* 3.5 15.2 + - - +
50B ASP* 4.1 5.5 + - - +
62B GLU 2.8 12.4 + - - +
63B SER* 1.3 69.8 - - - +
65B MET* 1.3 60.5 + - - +
94B PRO* 3.3 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 3.4 4.7 - - - +
49B PHE* 2.9 51.5 + - + +
51B GLY* 4.7 2.9 - - - +
57B TRP* 4.7 7.6 - - + +
62B GLU 4.9 0.2 - - - +
63B SER* 3.4 41.7 + - - +
64B ASP* 1.3 75.1 - - - +
66B VAL* 1.3 63.3 + - - +
91B ILE* 3.8 21.3 - - + -
92B LEU 3.3 20.4 - - - +
93B GLU* 3.8 21.5 - - - +
94B PRO* 4.1 5.8 - - + -
100B TYR* 3.6 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU 3.4 25.4 - - - +
46B GLY* 4.2 1.1 - - - -
47B LYS 3.5 11.0 - - - +
48B MET* 4.1 12.3 - - - -
49B PHE* 4.3 1.6 - - - -
65B MET* 1.3 80.3 - - - +
67B LEU* 1.3 71.5 + - - +
68B MET* 3.5 10.2 + - + +
90B ASP 3.2 4.5 - - - +
91B ILE* 3.4 4.5 - - - +
92B LEU* 3.0 37.4 + - + +
94B PRO* 3.8 27.1 - - + -
97B LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 5.9 0.4 - - + -
19B LEU* 4.3 11.7 - - + -
21B PHE* 3.6 23.1 - - + -
31B VAL* 4.0 27.4 - - + -
42B PHE* 5.2 0.6 - - + -
46B GLY* 3.1 15.6 - - - -
47B LYS* 2.9 22.7 + - + +
48B MET 5.5 0.2 - - - +
49B PHE* 3.6 30.3 - - + -
66B VAL* 1.3 71.0 - - - +
68B MET* 1.3 60.7 + - - +
69B PRO* 3.0 12.8 - - + +
89B CYS* 3.7 23.1 - - + -
90B ASP 3.7 0.2 - - - -
91B ILE* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE 3.4 25.1 - - - +
44B GLU* 3.6 12.1 - - - +
45B GLU* 3.4 11.2 - - - +
46B GLY* 3.4 23.3 - - - +
66B VAL* 3.5 5.6 + - + +
67B LEU* 1.3 71.2 - - - +
69B PRO* 1.3 76.2 - - - +
70B ASP 3.5 0.3 + - - -
89B CYS* 3.3 2.4 - - - -
90B ASP* 2.7 49.8 + - + +
92B LEU* 3.5 37.5 - - + -
97B LEU* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.6 44.6 - - + +
43B PHE* 4.0 28.7 - - + +
46B GLY* 3.8 6.3 - - - -
67B LEU 3.0 12.6 - - - +
68B MET* 1.3 102.0 - - - +
70B ASP* 1.3 60.4 + - - +
71B ALA 3.7 2.5 + - - -
87B ILE* 3.9 13.5 - - + -
88B ARG 3.9 0.2 - - - +
89B CYS* 3.8 15.7 - - - -
90B ASP* 5.2 0.5 - - - +
----------------------------------------------------------
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