Contacts of the strand formed by residues 84 - 92 (chain J) in PDB entry 1F1H
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J VAL* 4.1 0.7 - - - -
16J PHE* 3.0 13.7 + - - +
18J ASP* 4.0 16.8 + - - +
32J THR* 5.5 0.2 - - - +
76J ILE* 3.6 10.8 - - - +
77J ASP* 3.0 32.3 + - + +
80J PHE* 3.4 25.8 - - + -
82J ASP 2.6 30.7 - - - +
83J SER* 1.3 73.6 + - - +
85J LEU* 1.3 59.6 + - - +
1492J MPD 2.9 38.4 + - + +
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Residues in contact with LEU 85 (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* 4.0 22.0 - - + -
8J MET* 4.1 26.9 - - + -
9J LEU* 3.8 22.4 - - + -
14J VAL* 3.8 17.1 - - + +
16J PHE 2.8 7.7 + - - +
17J VAL* 3.1 11.0 - - + +
18J ASP 2.7 28.7 + - - -
74J ALA* 4.2 8.3 - - + -
75J VAL* 3.6 30.3 - - - +
76J ILE* 3.8 13.9 - - + +
84J THR* 1.3 73.6 - - - +
86J ILE* 1.3 63.2 + - - +
87J ILE* 4.3 8.5 - - + -
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Residues in contact with ILE 86 (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* 3.4 11.7 - - + +
20J ARG* 3.5 58.6 - - + +
73J THR 3.9 2.1 - - - +
74J ALA* 3.3 1.4 - - - -
75J VAL* 2.6 46.8 + - + +
77J ASP* 3.5 30.7 - - + +
84J THR* 5.1 0.2 - - - +
85J LEU* 1.3 72.6 - - - +
87J ILE* 1.3 70.7 + - - +
88J ARG* 4.7 9.2 - - - +
202J MET* 3.6 26.9 - - + -
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Residues in contact with ILE 87 (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* 4.2 26.9 - - + -
17J VAL* 3.9 23.8 - - + -
18J ASP 2.9 9.2 + - - +
19J LEU* 3.5 12.2 - - + -
20J ARG 3.0 20.8 + - - -
38J VAL* 5.7 0.9 - - + -
42J PHE* 4.8 8.1 - - + -
43J PHE* 4.6 9.9 - - + -
69J PRO* 3.9 19.7 - - + -
70J ASP 3.7 17.7 - - - +
71J ALA* 4.7 2.2 - - - +
73J THR* 3.9 3.1 - - - +
74J ALA* 4.2 12.1 - - + +
85J LEU* 3.9 7.6 + - + -
86J ILE* 1.3 81.7 - - - +
88J ARG* 1.3 73.2 + - - +
89J CYS* 3.7 2.8 - - - -
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Residues in contact with ARG 88 (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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20J ARG* 3.3 21.4 + - - +
21J PHE* 5.1 3.1 - - - +
22J THR* 4.9 3.2 + - - -
28J GLU* 2.5 46.0 + - - +
70J ASP* 3.0 25.8 + - - +
73J THR* 2.9 30.7 + - + +
75J VAL* 6.2 1.0 - - - +
86J ILE* 4.2 11.1 - - - +
87J ILE* 1.3 74.9 - - - +
89J CYS* 1.3 63.9 + - - +
105J ARG* 3.8 17.5 - - - +
233J ASP* 3.4 35.4 + - - +
236J GLN* 3.7 15.3 - - - +
237J ILE* 3.8 29.1 - - - +
368J TYR* 3.8 10.3 + - - +
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Residues in contact with CYS 89 (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* 3.8 26.7 - - - -
20J ARG 2.7 16.1 + - - +
21J PHE* 4.0 11.2 - - + +
67J LEU* 3.6 31.6 - - + -
68J MET 3.3 9.6 - - - +
69J PRO* 3.8 19.3 - - - -
70J ASP 4.4 0.2 - - - +
87J ILE 3.7 11.4 - - - -
88J ARG* 1.3 80.8 - - - +
90J ASP* 1.3 64.5 + - - +
91J ILE* 5.5 0.2 - - - +
103J ASP* 5.6 0.3 - - - +
105J ARG* 3.8 17.9 - - - +
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Residues in contact with ASP 90 (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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66J VAL 3.4 1.7 - - - +
67J LEU* 3.7 2.6 - - - -
68J MET* 2.8 44.3 + - + +
70J ASP* 4.3 5.2 - - - +
89J CYS* 1.3 73.3 - - - +
91J ILE* 1.3 65.1 + - - +
92J LEU* 3.9 18.2 - - + -
103J ASP* 3.7 7.9 - - - +
105J ARG* 3.0 40.2 + - - +
106J SER* 4.4 4.5 + - - +
109J LYS* 3.1 30.0 + - - +
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Residues in contact with ILE 91 (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* 3.9 23.8 - - + -
49J PHE* 4.0 15.9 - - + -
57J TRP* 3.7 24.5 - - + -
65J MET* 3.7 31.6 - - + -
66J VAL 3.4 2.2 - - - +
67J LEU* 3.6 30.5 - - + -
90J ASP* 1.3 72.2 - - - +
92J LEU* 1.3 61.4 + - - +
99J GLY* 3.7 3.6 - - - -
100J TYR* 3.0 32.3 + - + +
103J ASP* 2.8 32.8 + - + +
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Residues in contact with LEU 92 (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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65J MET* 3.4 7.2 - - - +
66J VAL* 2.9 39.6 + - + +
68J MET* 3.3 50.7 - - + -
90J ASP* 4.1 14.4 - - + -
91J ILE* 1.3 79.1 - - - +
93J GLU* 1.3 62.3 + - - +
97J LEU* 3.8 30.5 - - + +
98J GLN 4.1 4.5 - - - +
99J GLY* 3.5 25.1 - - - +
100J TYR 4.4 0.7 - - - -
106J SER* 4.6 2.0 - - - +
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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