Contacts of the strand formed by residues 84 - 92 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C GLN* 5.1 3.4 - - - +
193C SER* 5.7 1.3 - - - +
14D VAL* 4.1 1.8 - - - -
16D PHE* 3.3 30.3 - - + -
18D ASP* 4.1 7.2 - - - +
32D THR* 5.6 0.7 - - - -
76D ILE* 3.6 8.8 - - - +
77D ASP* 2.9 33.2 + - - +
80D PHE* 3.4 41.8 - - + -
82D ASP* 2.7 20.6 + - + +
83D SER* 1.3 75.5 + - - +
85D LEU* 1.4 65.7 + - - +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.1 22.9 - - + +
8D MET* 3.6 22.0 - - + -
9D LEU* 3.9 19.7 - - + -
14D VAL* 3.6 17.1 - - + +
16D PHE 2.8 10.1 + - - +
17D VAL* 3.0 11.8 - - + +
18D ASP 2.6 31.3 + - - -
74D ALA* 4.0 10.3 - - + -
75D VAL* 3.3 37.7 - - - +
76D ILE* 3.5 11.4 - - + +
84D THR* 1.4 72.1 - - - +
86D ILE* 1.3 61.0 + - - +
87D ILE* 4.4 7.9 - - + -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASP* 3.3 11.2 - - + +
20D ARG* 3.5 60.3 - - + +
28D GLU* 5.6 0.2 - - - +
73D THR 4.0 1.5 - - - +
74D ALA* 3.2 2.3 - - - -
75D VAL* 2.9 47.6 + - + +
77D ASP* 3.5 29.6 - - + +
84D THR* 4.8 0.2 - - - +
85D LEU* 1.3 72.2 - - - +
87D ILE* 1.3 76.7 + - - +
88D ARG* 4.8 8.1 - - - +
202D MET* 3.8 19.3 - - + -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 4.5 15.3 - - + -
17D VAL* 3.8 24.5 - - + -
18D ASP 2.8 10.5 + - - +
19D LEU* 3.4 11.5 - - + -
20D ARG 2.9 22.3 + - - -
38D VAL* 5.8 1.1 - - + -
42D PHE* 4.9 9.2 - - + -
43D PHE* 4.6 11.0 - - + -
69D PRO* 3.9 12.3 - - + -
70D ASP 3.7 19.5 - - - +
71D ALA* 4.9 0.9 - - - +
73D THR* 3.8 8.3 - - - +
74D ALA* 4.1 12.1 - - + -
85D LEU* 4.4 14.1 - - + -
86D ILE* 1.3 83.5 - - - +
88D ARG* 1.3 73.9 + - - +
89D CYS* 3.6 2.8 + - - -
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG* 3.2 21.3 + - - +
21D PHE* 5.0 1.9 - - - +
22D THR* 4.4 5.5 + - - -
28D GLU* 2.6 46.8 + - - +
70D ASP* 3.1 27.4 + - - +
73D THR* 2.8 28.5 + - + +
86D ILE* 4.3 8.3 - - - +
87D ILE* 1.3 73.2 - - - +
89D CYS* 1.3 64.2 + - - +
105D ARG* 3.8 18.4 - - - +
233D ASP* 3.4 32.9 + - - +
236D GLN* 3.6 15.7 - - - +
237D ILE* 4.0 26.1 - - - +
368D TYR* 3.7 11.0 + - - -
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Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.6 35.4 - - - -
20D ARG 2.6 13.7 + - - +
21D PHE* 3.8 16.4 - - + +
67D LEU* 3.7 28.5 - - + -
68D MET 3.3 9.6 - - - +
69D PRO* 3.8 22.7 - - - -
87D ILE 3.7 8.7 - - - -
88D ARG* 1.3 76.7 - - - +
90D ASP* 1.3 62.9 + - - +
103D ASP* 5.5 0.3 - - - +
105D ARG* 4.0 15.3 - - - +
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Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL 3.2 2.6 - - - +
67D LEU* 3.6 1.9 - - - -
68D MET* 2.7 45.3 + - + +
69D PRO 5.2 0.2 - - - +
70D ASP* 4.3 5.9 - - - +
89D CYS* 1.3 75.8 - - - +
91D ILE* 1.3 62.9 + - - +
92D LEU* 3.6 19.1 + - + -
103D ASP* 3.8 9.0 - - - +
105D ARG* 3.1 30.4 + - - +
106D SER* 4.6 3.6 + - - +
109D LYS* 3.1 37.0 + - - +
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PHE* 4.1 16.4 - - + -
22D THR 5.6 0.2 - - - +
49D PHE* 3.8 17.7 - - + -
57D TRP* 3.8 26.5 - - + -
65D MET* 3.8 30.3 - - + -
66D VAL 3.4 1.8 - - - +
67D LEU* 3.5 31.9 - - + -
90D ASP* 1.3 72.5 - - - +
92D LEU* 1.3 61.7 + - - +
99D GLY* 3.8 2.8 - - - -
100D TYR* 2.9 37.9 + - + +
103D ASP* 2.9 30.8 + - + +
106D SER* 3.9 0.2 + - - -
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D MET* 3.3 10.0 - - - +
66D VAL* 3.0 38.6 + - + +
68D MET* 3.5 47.8 - - + -
90D ASP* 4.1 15.9 - - + -
91D ILE* 1.3 79.0 - - - +
93D GLU* 1.3 61.6 + - - +
97D LEU* 3.6 32.8 - - + +
98D GLN 4.3 3.4 - - - -
99D GLY* 3.8 21.3 - - - +
100D TYR 4.0 2.9 - - - +
106D 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