Contacts of the strand formed by residues 82 - 90 (chain F) in PDB entry 3F5O
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 VAL 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E ILE* 4.3 16.2 - - + -
81F GLY* 1.3 79.3 - - - +
83F SER* 1.3 63.3 + - - +
84F VAL* 3.9 0.2 - - - +
136F LYS* 3.2 5.1 - - - -
137F HIS* 2.8 57.1 + - + +
149F UOC 3.8 17.7 - - + -
150F COA 3.9 36.1 - - + +
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Residues in contact with SER 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLY* 5.2 0.3 - - - -
90E TYR* 3.3 28.7 - - - +
65F ASP* 3.6 14.0 + - - -
82F VAL* 1.3 72.5 - - - +
84F VAL* 1.3 61.0 + - - +
134F HIS* 2.8 34.5 + - - -
135F THR 3.9 2.0 - - - -
136F LYS* 3.6 3.6 - - - +
150F COA 3.2 46.1 + - - +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR* 3.5 1.6 - - - +
90E TYR* 2.9 32.2 + - - -
83F SER* 1.3 77.2 - - - +
85F ASP* 1.3 80.8 + - + +
113F LEU* 4.6 4.0 - - + -
135F THR* 2.8 19.8 + - + +
136F LYS 4.1 2.0 - - - -
137F HIS* 3.5 39.0 - - + +
150F COA 4.0 5.8 - - + -
84H VAL* 5.9 0.2 - - + -
113H LEU* 3.9 15.0 - - + -
115H PHE* 3.7 24.0 - - + -
135H THR* 4.0 9.6 - - + -
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Residues in contact with ASP 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ILE 3.5 4.4 - - - +
89E THR* 2.6 28.5 + - - +
90E TYR* 4.6 1.6 - - - -
84F VAL* 1.3 93.9 - - - +
86F MET* 1.3 60.4 + - - +
87F ASN* 6.0 1.8 - - - +
133F ARG 4.1 0.2 - - - +
134F HIS* 3.5 3.5 - - - -
135F THR* 2.8 30.7 + - - +
85H ASP* 3.8 33.3 - - - +
87H ASN* 4.9 6.2 + - - -
133H ARG* 4.7 0.5 + - - -
135H THR* 2.7 31.5 + - - +
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Residues in contact with MET 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLY 4.7 2.2 - - - +
61E ALA* 4.3 3.1 - - + -
87E ASN* 3.3 3.2 - - - +
88E ILE* 2.9 45.2 + - + +
90E TYR* 3.6 28.5 - - + +
61F ALA* 3.7 36.8 - - + +
64F VAL* 3.7 25.4 - - + -
65F ASP* 4.0 16.8 - - + +
85F ASP* 1.3 75.9 - - - +
87F ASN* 1.3 72.5 + - - +
88F ILE* 4.0 6.1 - - + -
133F ARG 3.3 12.1 - - - +
134F HIS* 4.0 14.8 - - + -
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Residues in contact with ASN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E MET 3.3 11.0 - - - +
87E ASN* 4.0 11.7 - - + -
85F ASP* 6.0 1.0 - - - +
86F MET* 1.3 77.0 - - - +
88F ILE* 1.3 68.6 + - - +
132F GLY* 3.0 22.5 - - - -
133F ARG* 2.9 36.4 + - - +
87G ASN* 3.5 27.8 - - + +
133G ARG* 2.8 35.2 + - - -
85H ASP* 4.8 8.5 + - - -
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP* 3.5 4.0 - - - +
86E MET* 2.8 44.4 + - + +
88E ILE* 4.3 6.1 - - + -
60F THR* 4.0 13.9 - - + -
61F ALA* 3.7 34.3 - - + -
64F VAL* 4.4 11.9 - - + -
86F MET* 4.0 18.8 - - + -
87F ASN* 1.3 82.6 - - - +
89F THR* 1.3 70.3 + - - +
90F TYR* 3.5 37.8 - - + +
130F ALA* 4.2 3.1 - - + -
131F GLN 3.4 11.0 - - - +
133G ARG* 4.2 0.2 - - - -
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL 3.4 4.5 - - - +
85E ASP* 2.6 25.0 + - - +
88F ILE* 1.3 72.4 - - - +
90F TYR* 1.3 62.3 + - - +
91F MET* 3.5 9.3 - - + +
130F ALA* 3.1 8.5 - - - +
131F GLN 2.7 33.0 + - - -
115G PHE* 3.3 38.8 - - + -
133G ARG* 2.8 43.4 + - - +
135G THR* 3.9 3.5 + - - +
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASP* 4.8 0.3 + - - -
83E SER* 3.3 39.8 - - - +
84E VAL* 2.9 22.5 + - - +
86E MET* 3.6 28.6 - - + +
150E COA 3.1 39.1 + - - +
57F GLY* 2.8 40.9 + - - -
60F THR* 3.7 20.0 - - + -
88F ILE* 3.5 29.7 - - + +
89F THR* 1.3 73.8 - - - +
91F MET* 1.3 60.4 + - - +
92F SER 3.8 0.4 - - - +
129F ILE* 3.8 5.8 - - + +
130F ALA* 4.3 10.8 - - + -
115G PHE* 3.7 10.5 - - - -
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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