Contacts of the strand formed by residues 82 - 90 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E GLY* 1.3 79.5 - - - +
83E SER* 1.3 62.2 + - - +
84E VAL* 3.8 0.2 - - - +
136E LYS* 3.2 5.0 - - - -
137E HIS* 2.8 55.2 + - + +
149E UOC 3.8 6.7 - - + -
150E COA 3.9 39.7 - - + +
52F ILE* 4.1 26.0 - - + -
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Residues in contact with SER 83 (chain E).
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* 3.5 12.8 + - - -
82E VAL* 1.3 72.0 - - - +
84E VAL* 1.3 60.2 + - - +
134E HIS* 2.7 36.5 + - - -
135E THR 3.9 1.8 - - - -
136E LYS* 3.5 4.3 - - - +
149E UOC 4.3 0.2 + - - -
150E COA 3.1 51.2 + - - +
90F TYR* 3.3 28.6 - - - +
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Residues in contact with VAL 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E VAL 3.8 0.2 - - - +
83E SER* 1.3 75.1 - - - +
85E ASP* 1.3 76.6 + - - +
113E LEU* 4.6 3.8 - - + -
135E THR* 2.8 22.4 + - + +
136E LYS 4.0 1.8 - - - -
137E HIS* 3.5 41.5 - - + +
150E COA 4.1 5.4 - - + -
89F THR* 3.4 1.4 - - - +
90F TYR* 2.9 31.8 + - - -
84G VAL* 6.0 0.9 - - + -
113G LEU* 3.9 19.7 - - + -
115G PHE* 3.6 22.7 - - + -
135G THR* 4.0 6.3 - - + -
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Residues in contact with ASP 85 (chain E).
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* 1.3 92.4 - - - +
86E MET* 1.3 62.9 + - - +
87E ASN* 6.0 1.1 - - - +
133E ARG 4.6 0.3 - - - -
134E HIS* 3.4 4.2 - - - -
135E THR* 2.9 30.0 + - - +
88F ILE 3.5 5.2 - - - +
89F THR* 2.6 27.0 + - - +
90F TYR* 4.8 0.9 - - - -
85G ASP* 3.7 35.3 - - + +
87G ASN* 4.8 6.9 + - - -
133G ARG* 4.7 0.9 + - - +
135G THR* 2.7 32.0 + - - +
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Residues in contact with MET 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ALA* 3.7 37.2 - - + +
64E VAL* 3.7 25.4 - - + -
65E ASP* 3.9 20.4 - - + +
85E ASP* 1.3 77.3 - - - +
87E ASN* 1.3 71.2 + - - +
88E ILE* 4.2 9.2 - - + -
133E ARG 3.3 12.1 - - - +
134E HIS* 4.0 14.1 - - + -
57F GLY 4.6 1.1 - - - +
61F ALA* 4.3 3.1 - - + -
87F ASN* 3.3 3.1 - - - +
88F ILE* 2.8 41.5 + - + +
90F TYR* 3.6 30.2 - - + +
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Residues in contact with ASN 87 (chain E).
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* 6.0 1.6 - - - +
86E MET* 1.3 76.9 - - - +
88E ILE* 1.3 67.5 + - - +
132E GLY* 3.0 22.5 - - - -
133E ARG* 2.9 43.0 + - - +
86F MET 3.3 11.2 - - - +
87F ASN* 4.0 11.4 - - + -
85G ASP* 4.8 5.9 + - - -
87G ASN* 6.3 0.2 - - + -
87H ASN* 3.4 27.3 - - + +
89H THR* 4.8 2.4 + - - -
133H ARG* 2.8 36.4 + - - -
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E THR* 4.0 15.0 - - + -
61E ALA* 3.7 33.4 - - + -
64E VAL* 4.4 11.9 - - + -
86E MET* 4.2 17.5 - - + -
87E ASN* 1.3 81.9 - - - +
89E THR* 1.3 70.7 + - - +
90E TYR* 3.7 30.3 - - + +
130E ALA* 4.2 3.6 - - + -
131E GLN 3.5 11.7 - - - +
85F ASP* 3.5 3.1 - - - +
86F MET* 2.9 54.9 + - + +
88F ILE* 4.3 4.7 - - + -
133H ARG* 4.3 0.7 - - - -
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Residues in contact with THR 89 (chain E).
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* 1.3 71.7 - - - +
90E TYR* 1.3 62.4 + - - +
91E MET* 3.3 9.8 - - + +
130E ALA* 3.1 7.0 - - - +
131E GLN 2.7 33.9 + - - -
84F VAL 3.5 4.0 - - - +
85F ASP* 2.6 24.7 + - - +
115H PHE* 3.3 37.9 - - + -
133H ARG* 2.8 43.4 + - - +
135H THR* 3.9 3.8 + - - +
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Residues in contact with TYR 90 (chain E).
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* 2.8 42.0 + - - -
60E THR* 3.7 24.9 - - + -
88E ILE* 3.7 29.3 - - + +
89E THR* 1.3 71.6 - - - +
91E MET* 1.3 60.3 + - - +
92E SER 3.8 0.4 - - - -
129E ILE* 3.9 6.3 - - + +
130E ALA* 4.4 5.2 - - + -
83F SER* 3.3 37.9 - - - +
84F VAL* 2.9 23.9 + - - +
86F MET* 3.6 28.9 - - + +
150F COA 3.1 42.2 + - - +
115H PHE* 3.8 10.2 - - - -
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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