Contacts of the strand formed by residues 84 - 92 (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 THR 84 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189G GLN* 5.0 3.4 - - - +
193G SER* 5.5 1.3 - - - +
14L VAL* 4.1 1.1 - - - -
16L PHE* 3.3 29.4 - - + -
18L ASP* 4.1 7.2 - - - +
32L THR* 5.6 1.3 - - - +
76L ILE* 3.6 8.3 - - - +
77L ASP* 2.9 33.3 + - - +
80L PHE* 3.4 42.2 - - + -
82L ASP* 2.7 21.3 + - + +
83L SER* 1.3 75.8 + - - +
85L LEU* 1.4 66.5 + - - +
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Residues in contact with LEU 85 (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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5L VAL* 4.1 22.7 - - + +
8L MET* 3.6 22.0 - - + -
9L LEU* 3.9 20.6 - - + -
14L VAL* 3.6 16.7 - - + +
16L PHE 2.8 10.3 + - - +
17L VAL* 3.0 11.8 - - + +
18L ASP 2.6 31.8 + - - -
74L ALA* 4.0 9.9 - - + -
75L VAL* 3.3 36.6 - - - +
76L ILE* 3.5 11.4 - - + +
84L THR* 1.4 72.8 - - - +
86L ILE* 1.3 61.3 + - - +
87L ILE* 4.4 8.1 - - + -
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Residues in contact with ILE 86 (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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18L ASP* 3.3 12.6 - - + +
20L ARG* 3.5 61.2 - - + +
73L THR 4.0 2.3 - - - +
74L ALA* 3.2 2.1 - - - -
75L VAL* 2.9 46.6 + - + +
77L ASP* 3.5 29.8 - - + +
85L LEU* 1.3 73.1 - - - +
87L ILE* 1.3 78.3 + - - +
88L ARG* 4.8 7.6 - - - +
202L MET* 3.8 19.1 - - + -
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Residues in contact with ILE 87 (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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5L VAL* 4.5 15.0 - - + -
17L VAL* 3.8 22.9 - - + -
18L ASP 2.8 10.9 + - - +
19L LEU* 3.4 12.0 - - + -
20L ARG 2.9 22.6 + - - -
38L VAL* 5.8 0.9 - - + -
42L PHE* 4.9 8.7 - - + -
43L PHE* 4.6 11.4 - - + -
69L PRO* 3.9 12.8 - - + -
70L ASP 3.7 20.2 - - - +
71L ALA* 4.9 0.7 - - - +
73L THR* 3.8 8.5 - - - +
74L ALA* 4.1 12.1 - - + -
85L LEU* 4.4 14.6 - - + -
86L ILE* 1.3 83.0 - - - +
88L ARG* 1.3 74.0 + - - +
89L CYS* 3.6 2.2 + - - -
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Residues in contact with ARG 88 (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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20L ARG* 3.2 21.0 + - - +
21L PHE* 5.0 1.4 - - - +
22L THR* 4.4 6.3 + - - -
28L GLU* 2.6 46.1 + - - +
70L ASP* 3.1 26.7 + - - +
73L THR* 2.8 29.9 + - + +
86L ILE* 4.3 8.7 - - - +
87L ILE* 1.3 73.8 - - - +
89L CYS* 1.3 65.2 + - - +
105L ARG* 3.8 17.7 - - - +
233L ASP* 3.4 32.4 + - - +
236L GLN* 3.6 16.0 - - - +
237L ILE* 4.0 26.1 - - - +
368L TYR* 3.7 10.7 + - - -
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Residues in contact with CYS 89 (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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19L LEU* 3.6 35.4 - - - -
20L ARG 2.6 13.5 + - - +
21L PHE* 3.8 17.0 - - + +
67L LEU* 3.7 29.8 - - + -
68L MET 3.3 9.0 - - - +
69L PRO* 3.8 22.2 - - - -
87L ILE 3.7 9.4 - - - -
88L ARG* 1.3 76.1 - - - +
90L ASP* 1.3 63.8 + - - +
103L ASP* 5.5 0.5 - - - +
105L ARG* 4.0 15.5 - - - +
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Residues in contact with ASP 90 (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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66L VAL 3.2 2.8 - - - +
67L LEU* 3.6 1.6 - - - -
68L MET* 2.7 45.8 + - + +
69L PRO 5.2 0.2 - - - +
70L ASP* 4.3 5.9 - - - +
89L CYS* 1.3 73.4 - - - +
91L ILE* 1.3 63.9 + - - +
92L LEU* 3.6 19.7 + - + -
103L ASP* 3.8 7.7 - - - +
105L ARG* 3.1 30.1 + - - +
106L SER* 4.6 4.3 + - - +
109L LYS* 3.1 36.7 + - - +
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Residues in contact with ILE 91 (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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21L PHE* 4.1 15.9 - - + -
49L PHE* 3.8 17.0 - - + -
57L TRP* 3.8 25.6 - - + -
65L MET* 3.8 30.7 - - + -
66L VAL 3.4 1.6 - - - +
67L LEU* 3.5 32.1 - - + -
90L ASP* 1.3 71.9 - - - +
92L LEU* 1.3 62.7 + - - +
99L GLY* 3.8 2.9 - - - -
100L TYR* 2.9 38.0 + - + +
103L ASP* 2.9 30.8 + - + +
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Residues in contact with LEU 92 (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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65L MET* 3.3 10.1 - - - +
66L VAL* 3.0 37.8 + - + -
68L MET* 3.5 47.3 - - + -
90L ASP* 4.1 15.9 - - + -
91L ILE* 1.3 77.7 - - - +
93L GLU* 1.3 62.1 + - - +
97L LEU* 3.6 32.8 - - + +
98L GLN 4.3 3.6 - - - +
99L GLY* 3.8 21.3 - - - +
100L TYR 4.0 3.1 - - - +
106L SER* 4.8 1.8 - - - +
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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