Contacts of the strand formed by residues 84 - 92 (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 THR 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLN* 5.1 3.1 - - - +
193A SER* 5.6 1.6 - - - +
14B VAL* 4.1 1.6 - - - -
16B PHE* 3.3 29.2 - - + -
18B ASP* 4.1 7.8 - - - +
32B THR* 5.6 0.7 - - - -
76B ILE* 3.6 8.7 - - - +
77B ASP* 2.9 33.3 + - - +
80B PHE* 3.4 42.2 - - + -
82B ASP* 2.7 20.3 + - + +
83B SER* 1.3 75.8 + - - +
85B LEU* 1.4 64.8 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.1 22.7 - - + +
8B MET* 3.6 21.3 - - + -
9B LEU* 3.9 20.6 - - + -
14B VAL* 3.6 17.6 - - + +
16B PHE 2.8 9.5 + - - +
17B VAL* 3.0 12.1 - - + +
18B ASP 2.6 32.0 + - - -
74B ALA* 4.1 9.6 - - + -
75B VAL* 3.3 37.9 - - - +
76B ILE* 3.5 11.4 - - + +
84B THR* 1.4 73.0 - - - +
86B ILE* 1.3 61.3 + - - +
87B ILE* 4.4 7.4 - - + -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 3.3 11.4 - - + +
20B ARG* 3.5 62.8 - - + +
73B THR 4.0 2.1 - - - +
74B ALA* 3.2 3.1 - - - -
75B VAL* 2.9 46.6 + - + +
77B ASP* 3.5 30.1 - - + +
85B LEU* 1.3 72.0 - - - +
87B ILE* 1.3 77.3 + - - +
88B ARG* 4.3 7.9 - - - +
202B MET* 3.8 19.3 - - + -
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.5 15.0 - - + -
17B VAL* 3.8 23.1 - - + -
18B ASP 2.8 10.3 + - - +
19B LEU* 3.4 11.7 - - + -
20B ARG 2.9 22.2 + - - -
38B VAL* 5.8 1.1 - - + -
42B PHE* 4.9 8.7 - - + -
43B PHE* 4.6 10.8 - - + -
69B PRO* 3.9 11.9 - - + -
70B ASP 3.7 20.6 - - - +
71B ALA* 5.3 0.9 - - - -
73B THR* 3.8 7.9 - - - +
74B ALA* 4.1 12.6 - - + -
85B LEU* 4.4 15.0 - - + -
86B ILE* 1.3 82.8 - - - +
88B ARG* 1.3 74.9 + - - +
89B CYS* 3.6 2.9 + - - -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.2 20.5 + - - +
21B PHE* 5.0 1.5 - - - +
22B THR* 4.4 6.1 + - - -
28B GLU* 2.6 46.2 + - - +
70B ASP* 3.1 27.2 + - - +
73B THR* 2.8 29.2 + - + +
86B ILE* 4.3 8.5 - - - +
87B ILE* 1.3 74.9 - - - +
89B CYS* 1.3 64.4 + - - +
105B ARG* 3.8 18.4 - - - +
233B ASP* 3.4 32.7 + - - +
236B GLN* 3.6 16.0 - - - +
237B ILE* 4.0 26.1 - - - +
368B TYR* 3.7 11.2 + - - -
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Residues in contact with CYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.6 35.4 - - - -
20B ARG 2.6 12.6 + - - +
21B PHE* 3.8 16.1 - - + +
22B THR 5.3 0.2 + - - -
67B LEU* 3.7 29.6 - - + -
68B MET 3.3 10.3 - - - +
69B PRO* 3.8 22.2 - - - -
87B ILE 3.7 9.4 - - - -
88B ARG* 1.3 75.9 - - - +
90B ASP* 1.3 62.4 + - - +
103B ASP* 5.5 0.7 - - - +
105B ARG* 4.0 15.9 - - - +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL 3.2 1.9 - - - +
67B LEU* 3.6 1.9 - - - -
68B MET* 2.7 46.9 + - + +
69B PRO 5.2 0.2 - - - +
70B ASP* 4.3 5.5 - - - +
89B CYS* 1.3 73.9 - - - +
91B ILE* 1.3 63.2 - - - +
92B LEU* 3.6 19.3 + - + -
103B ASP* 3.8 8.8 - - - +
105B ARG* 3.1 30.5 + - - +
106B SER* 4.6 3.2 + - - +
109B LYS* 3.1 37.6 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 4.1 16.4 - - + -
49B PHE* 3.8 17.9 - - + -
57B TRP* 3.8 25.6 - - + -
65B MET* 3.8 30.7 - - + -
66B VAL 3.4 1.6 - - - +
67B LEU* 3.5 32.1 - - + -
90B ASP* 1.3 72.8 - - - +
92B LEU* 1.3 60.8 + - - +
99B GLY* 3.8 2.8 - - - -
100B TYR* 2.9 38.3 + - + +
103B ASP* 2.9 30.4 + - + +
106B SER* 3.9 0.2 + - - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B MET* 3.3 10.7 - - - +
66B VAL* 3.0 37.4 + - + +
68B MET* 3.5 47.8 - - + -
90B ASP* 4.1 16.6 - - + -
91B ILE* 1.3 78.9 - - - +
93B GLU* 1.3 61.5 + - - +
97B LEU* 3.6 32.3 - - + +
98B GLN 4.3 3.1 - - - +
99B GLY* 3.8 22.0 - - - +
100B TYR 4.0 2.9 - - - +
106B 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