Contacts of the strand formed by residues 64 - 69 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J MET* 3.2 29.4 - - + +
49J PHE* 3.5 15.4 + - - +
50J ASP* 4.1 5.0 + - - +
62J GLU 2.8 11.5 + - - +
63J SER* 1.3 71.1 - - - +
65J MET* 1.3 60.1 + - - +
94J PRO* 3.3 23.4 - - - +
336K ALA 5.5 2.9 - - - +
339K ARG* 2.7 22.2 + - - +
344K ARG* 3.3 24.2 + - - -
4481K ADP 5.7 1.0 + - - -
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Residues in contact with MET 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J MET* 3.4 5.1 - - - +
49J PHE* 2.9 50.9 + - + +
51J GLY* 4.7 3.1 - - - +
57J TRP* 4.7 7.6 - - + +
62J GLU 4.9 0.4 - - - +
63J SER* 3.4 41.1 + - - +
64J ASP* 1.3 75.3 - - - +
66J VAL* 1.3 62.6 + - - +
91J ILE* 3.8 22.0 - - + -
92J LEU 3.3 19.3 - - - +
93J GLU* 3.8 22.4 - - - +
94J PRO* 4.1 6.1 - - + -
100J TYR* 3.6 37.9 - - + +
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Residues in contact with VAL 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J GLU 3.4 25.4 - - - +
46J GLY* 4.2 1.1 - - - -
47J LYS 3.5 10.8 - - - +
48J MET* 4.1 11.7 - - - -
49J PHE* 4.3 2.0 - - - -
65J MET* 1.3 80.5 - - - +
67J LEU* 1.3 73.0 + - - +
68J MET* 3.5 10.2 + - + +
90J ASP 3.2 4.5 - - - +
91J ILE* 3.4 4.5 - - - +
92J LEU* 3.0 37.4 + - + +
94J PRO* 3.8 27.1 - - + -
97J LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J LEU* 4.3 12.8 - - + -
21J PHE* 3.6 24.5 - - + -
31J VAL* 4.0 26.7 - - + -
42J PHE* 5.2 0.4 - - + -
46J GLY* 3.1 15.6 - - - -
47J LYS* 2.9 21.6 + - + +
48J MET 5.5 0.4 - - - +
49J PHE* 3.6 30.9 - - + -
66J VAL* 1.3 71.2 - - - +
68J MET* 1.3 61.4 + - - +
69J PRO* 3.0 13.1 - - + +
89J CYS* 3.7 22.2 - - + -
90J ASP 3.7 0.4 - - - -
91J ILE* 3.5 24.2 - - + -
180K PHE* 5.8 0.4 - - + -
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Residues in contact with MET 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J PHE 3.4 24.5 - - - +
44J GLU 3.6 11.9 - - - +
45J GLU* 3.4 10.8 - - - +
46J GLY* 3.4 23.3 - - - +
66J VAL* 3.5 5.3 + - + -
67J LEU* 1.3 71.6 - - - +
69J PRO* 1.3 77.1 - - - +
70J ASP 3.5 0.3 + - - -
89J CYS* 3.3 2.7 - - - -
90J ASP* 2.7 51.3 + - + +
92J LEU* 3.5 37.9 - - + -
97J LEU* 4.9 5.4 - - + -
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Residues in contact with PRO 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J PHE* 3.6 45.3 - - + +
43J PHE* 4.0 27.2 - - + +
46J GLY* 3.8 5.4 - - - -
67J LEU 3.0 13.7 - - - +
68J MET* 1.3 101.9 - - - +
70J ASP* 1.3 60.2 + - - +
71J ALA 3.7 2.4 + - - -
87J ILE* 3.9 12.6 - - + -
88J ARG 3.9 0.7 - - - +
89J CYS* 3.8 14.6 - - - -
90J ASP* 5.2 0.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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