Contacts of the strand formed by residues 16 - 22 (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 PHE 16 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J VAL* 2.9 9.3 - - - +
15J LYS* 1.3 95.4 - - + +
17J VAL* 1.3 60.9 - - - +
32J THR* 3.6 24.9 - - + -
33J ILE 3.4 2.5 - - - -
34J PRO* 3.9 22.9 - - + -
35J ALA 3.9 0.4 - - - +
82J ASP* 4.0 13.5 - - + -
83J SER 3.3 3.0 + - - -
84J THR* 3.3 14.7 - - + -
85J LEU 2.8 29.4 + - - -
193K SER* 3.5 45.5 - - - -
196K CYS* 3.9 23.3 - - + -
197K LEU* 3.7 25.6 - - + -
209K HIS* 4.5 2.7 - + - -
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Residues in contact with VAL 17 (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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5J VAL* 6.4 0.4 - - + -
9J LEU* 4.3 17.7 - - + -
16J PHE* 1.3 80.7 - - - +
18J ASP* 1.3 63.3 + - - +
19J LEU* 3.6 24.4 + - + -
31J VAL 3.5 1.6 - - - +
32J THR* 3.3 4.8 - - - +
33J ILE* 2.6 50.4 + - + +
35J ALA* 4.3 10.5 - - - -
38J VAL* 3.9 24.7 - - + -
42J PHE* 5.2 0.4 - - + -
85J LEU* 3.0 14.4 - - + +
87J ILE* 3.8 20.6 - - + -
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Residues in contact with ASP 18 (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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16J PHE 4.2 0.4 - - - -
17J VAL* 1.3 73.7 - - - +
19J LEU* 1.3 64.8 + - - +
20J ARG* 2.8 32.7 + - - +
30J HIS* 2.9 29.7 - - - +
31J VAL 3.3 4.2 - - - +
32J THR* 2.7 29.6 + - + -
80J PHE* 4.0 9.7 - - + -
84J THR* 4.1 13.0 + - - +
85J LEU 2.6 13.1 + - - +
86J ILE* 3.3 10.1 - - + +
87J ILE 2.8 26.9 + - - +
189K GLN* 3.9 0.2 + - - -
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Residues in contact with LEU 19 (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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17J VAL* 3.6 27.1 - - + +
18J ASP* 1.3 72.2 - - - +
20J ARG* 1.3 60.9 + - - +
21J PHE* 4.8 2.5 - - - -
30J HIS* 2.9 5.5 - - - -
31J VAL* 2.7 62.3 + - + +
33J ILE* 4.6 20.2 - - + -
42J PHE* 4.1 28.9 - - + -
47J LYS* 5.1 6.1 - - + -
67J LEU* 4.3 15.7 - - + -
87J ILE* 3.4 9.0 - - + +
89J CYS* 3.6 23.6 - - - -
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Residues in contact with ARG 20 (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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18J ASP* 2.8 23.0 + - - +
19J LEU* 1.3 80.4 - - - +
21J PHE* 1.3 59.7 + - - +
28J GLU* 3.4 31.1 + - - +
29J GLN 3.0 7.2 - - - +
30J HIS* 3.6 12.6 - - + +
77J ASP* 2.6 27.3 + - - -
80J PHE* 3.6 8.7 - - - -
86J ILE* 3.5 41.3 - - + +
87J ILE 2.9 9.3 + - - +
88J ARG* 3.2 15.4 - - - +
89J CYS* 2.6 34.2 + - - -
202J MET* 5.2 0.8 - - - +
240J TYR* 3.4 39.8 + - - -
182K VAL* 4.1 5.1 - - - +
183K PRO* 5.7 0.4 - - - +
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Residues in contact with PHE 21 (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 4.8 2.9 - - - -
20J ARG* 1.3 78.7 - - - +
22J THR* 1.3 65.5 + - - +
23J ASP* 4.6 0.4 - - - -
28J GLU* 3.5 4.0 - - - +
29J GLN* 2.6 69.2 + - + +
30J HIS* 4.7 1.3 - - - -
31J VAL* 5.5 0.7 - - + -
49J PHE* 4.3 8.7 - + - -
54J ILE* 3.7 20.2 - - + -
57J TRP* 3.6 35.2 - + - -
67J LEU* 3.6 27.1 - - + -
88J ARG* 5.0 4.9 - - - +
89J CYS 3.8 17.0 - - - +
91J ILE* 4.1 14.6 - - + -
103J ASP* 6.1 0.7 - - - +
180K PHE* 3.9 20.2 - + - -
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Residues in contact with THR 22 (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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21J PHE* 1.3 85.2 + - - +
23J ASP* 1.3 75.9 + - - +
26J GLY* 3.4 15.9 - - - +
27J LYS 3.8 2.5 - - - +
28J GLU* 4.4 0.3 - - - -
57J TRP* 3.6 7.8 - - - -
88J ARG* 4.4 5.7 + - - -
91J ILE* 5.6 0.2 - - - +
103J ASP* 4.5 4.4 + - - +
104J PRO* 3.5 19.2 - - + +
105J ARG* 5.9 4.0 - - - +
236J GLN* 3.1 34.1 + - - +
366J ASN* 4.4 2.0 - - - +
368J TYR* 3.4 35.6 + - + -
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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