Contacts of the strand formed by residues 64 - 69 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339G ARG* 2.8 23.1 + - - +
344G ARG* 3.4 24.0 + - - -
4477G ADP 5.7 0.9 + - - -
48L MET* 3.2 30.4 - - + +
49L PHE 3.5 14.6 + - - +
50L ASP* 4.1 4.6 + - - +
62L GLU 2.8 12.2 + - - +
63L SER* 1.3 70.9 - - - +
65L MET* 1.3 59.4 + - - +
94L PRO* 3.3 23.4 - - - +
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Residues in contact with MET 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L MET* 3.4 5.5 - - - +
49L PHE* 2.9 51.2 + - + +
51L GLY* 5.4 2.0 - - - +
57L TRP* 4.7 8.3 - - + +
62L GLU 4.9 0.4 - - - +
63L SER* 3.4 41.5 + - - +
64L ASP* 1.3 75.1 - - - +
66L VAL* 1.3 62.3 + - - +
91L ILE* 3.8 22.2 - - + -
92L LEU 3.3 19.7 - - - +
93L GLU* 3.8 22.4 - - - +
94L PRO* 4.2 6.1 - - + -
100L TYR* 3.6 37.9 - - + +
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Residues in contact with VAL 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L GLU 3.4 25.8 - - - +
46L GLY* 4.2 0.9 - - - -
47L LYS 3.5 10.8 - - - +
48L MET* 4.1 12.3 - - - -
49L PHE* 4.3 2.0 - - - -
65L MET* 1.3 80.0 - - - +
67L LEU* 1.3 73.0 + - - +
68L MET* 3.5 10.7 + - + +
90L ASP 3.2 4.3 - - - +
91L ILE* 3.4 4.5 - - - +
92L LEU* 3.0 38.9 + - + +
94L PRO* 3.8 26.7 - - + -
97L LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G PHE* 5.8 0.4 - - + -
19L LEU* 4.3 12.1 - - + -
21L PHE* 3.6 22.2 - - + -
31L VAL* 4.0 26.9 - - + -
42L PHE* 5.2 0.6 - - + -
46L GLY* 3.1 15.6 - - - -
47L LYS* 2.9 21.9 + - + +
48L MET 5.5 0.2 - - - +
49L PHE* 3.6 32.1 - - + -
66L VAL* 1.3 71.0 - - - +
68L MET* 1.3 60.7 + - - +
69L PRO* 3.0 12.2 - - - +
89L CYS* 3.7 23.6 - - + -
90L ASP 3.7 0.4 - - - -
91L ILE* 3.5 24.7 - - + -
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Residues in contact with MET 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L PHE 3.4 24.5 - - - +
44L GLU 3.6 12.6 - - - +
45L GLU* 3.4 11.0 - - - +
46L GLY* 3.4 22.7 - - - +
66L VAL* 3.5 5.3 + - + -
67L LEU* 1.3 72.4 - - - +
69L PRO* 1.3 75.9 - - - +
70L ASP 3.5 0.3 + - - -
89L CYS* 3.3 2.8 - - - +
90L ASP* 2.7 49.3 + - + +
92L LEU* 3.5 37.2 - - + -
97L LEU* 4.9 5.4 - - + -
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Residues in contact with PRO 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L PHE* 3.6 45.8 - - + +
43L PHE* 4.0 27.0 - - + +
46L GLY* 3.8 6.3 - - - -
67L LEU 3.0 13.2 - - - +
68L MET* 1.3 103.0 - - - +
70L ASP* 1.3 60.3 + - - +
71L ALA 3.7 2.0 + - - -
87L ILE* 3.9 13.5 - - + -
88L ARG 3.9 0.7 - - - +
89L CYS* 3.8 14.8 - - - -
90L 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