Contacts of the strand formed by residues 82 - 90 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 4.2 15.7 - - + -
81B GLY* 1.3 80.0 - - - +
83B SER* 1.3 62.1 + - - +
84B VAL* 3.8 0.7 - - - +
136B LYS* 3.2 5.0 - - - +
137B HIS* 2.8 60.2 + - + +
149B UOC 3.7 17.3 - - + -
150B COA 3.8 39.3 - - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.4 27.7 - - - +
65B ASP* 3.6 12.8 + - - -
82B VAL* 1.3 72.2 - - - +
84B VAL* 1.3 60.6 + - - +
134B HIS* 2.7 36.4 + - - -
135B THR 3.9 1.8 - - - -
136B LYS* 3.6 3.8 - - - +
150B COA 3.2 49.0 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.4 4.5 - - - +
90A TYR* 2.8 32.7 + - - -
82B VAL 3.8 0.2 - - - +
83B SER* 1.3 76.6 - - - +
85B ASP* 1.3 79.2 + - + +
113B LEU* 4.5 3.6 - - + -
135B THR* 2.8 17.6 + - + +
136B LYS 4.0 2.5 - - - -
137B HIS* 3.5 40.6 - - + +
150B COA 4.1 4.9 - - + -
84D VAL* 6.1 0.7 - - + -
85D ASP* 5.7 0.2 - - - +
113D LEU* 3.9 20.6 - - + -
115D PHE* 3.7 20.4 - - + -
135D THR* 4.1 7.0 - - + -
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE 3.4 4.7 - - - +
89A THR* 2.7 26.6 + - - +
90A TYR* 4.7 1.8 - - - -
84B VAL* 1.3 92.6 - - - +
86B MET* 1.3 60.5 + - - +
87B ASN* 6.1 1.1 - - - +
133B ARG 4.1 0.3 - - - +
134B HIS* 3.5 2.9 - - - -
135B THR* 2.9 30.6 + - - +
85D ASP* 3.7 35.9 - - - +
87D ASN* 4.8 7.4 + - - -
133D ARG* 5.9 0.2 - - - +
135D THR* 2.7 32.7 + - - +
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY 4.6 2.0 - - - +
61A ALA* 4.3 2.7 - - + -
87A ASN* 3.3 3.3 - - - +
88A ILE* 2.9 49.8 + - + +
90A TYR* 3.6 29.1 - - + +
61B ALA* 3.8 33.7 - - + +
64B VAL* 3.8 24.9 - - + -
65B ASP* 4.1 16.8 - - + +
85B ASP* 1.3 76.0 - - - +
87B ASN* 1.3 71.3 + - - +
88B ILE* 4.1 7.6 - - + -
133B ARG 3.3 12.3 - - - +
134B HIS* 4.0 14.8 - - + -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MET 3.4 9.6 - - - +
87A ASN* 4.0 11.9 - - + -
85B ASP* 6.1 1.4 - - - +
86B MET* 1.3 77.2 - - - +
88B ILE* 1.3 66.8 + - - +
132B GLY* 3.0 3.8 - - - -
133B ARG* 2.9 61.9 + - - +
87C ASN* 3.5 27.7 + - + +
89C THR* 4.8 2.2 + - - -
133C ARG* 2.8 36.7 + - - -
85D ASP* 4.8 6.5 + - - -
87D ASN* 6.1 0.2 - - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.5 4.2 - - - +
86A MET* 2.8 43.4 + - + +
88A ILE* 5.7 0.4 - - + -
60B THR* 4.3 6.7 - - + -
61B ALA* 3.5 37.9 - - + -
64B VAL* 4.3 13.9 - - + -
86B MET* 4.1 19.1 - - + -
87B ASN* 1.3 82.8 - - - +
89B THR* 1.3 71.4 + - - +
90B TYR* 3.6 36.7 - - + +
130B ALA* 4.2 9.4 - - + -
131B GLN 3.4 11.0 - - - +
132B GLY* 4.4 0.2 - - - -
133C ARG* 4.1 0.7 - - - -
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL 3.5 4.0 - - - +
85A ASP* 2.6 23.4 + - - +
88B ILE* 1.3 71.1 - - - +
90B TYR* 1.3 62.5 + - - +
91B MET* 3.6 10.4 - - + +
130B ALA* 3.1 7.1 - - - +
131B GLN 2.8 32.7 + - - -
115C PHE* 3.3 38.4 - - + -
133C ARG* 2.8 43.2 + - + +
135C THR* 4.0 2.6 + - - +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASP* 4.1 0.7 + - - -
83A SER* 3.3 41.5 - - - +
84A VAL* 2.8 23.7 + - - +
86A MET* 3.8 27.9 - - + +
150A COA 3.0 40.1 + - + -
57B GLY* 2.8 42.3 + - - -
60B THR* 3.9 18.4 - - + -
61B ALA 4.4 0.2 + - - -
88B ILE* 3.6 30.3 - - + +
89B THR* 1.3 73.4 - - - +
91B MET* 1.3 60.7 + - - +
92B SER 3.9 0.7 - - - +
129B ILE* 3.8 6.5 - - + +
130B ALA* 4.4 9.4 - - + -
115C PHE* 3.7 9.2 - - - -
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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