Contacts of the strand formed by residues 102 - 108 (chain F) in PDB entry 3WTV
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 LEU 102 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F GLY 3.5 15.3 - - - +
101F THR* 1.3 78.5 - - - +
103F VAL* 1.3 62.1 + - - +
104F THR* 5.4 1.3 - - + -
121F THR* 4.7 15.3 - - + -
122F ALA 3.5 11.7 - - - +
123F ALA* 4.3 10.5 - - + -
153F PHE* 3.0 46.4 + - + +
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Residues in contact with VAL 103 (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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91F VAL* 4.3 6.1 - - + -
101F THR 3.8 2.0 - - - +
102F LEU* 1.3 80.0 - - - +
104F THR* 1.3 66.7 + - - +
121F THR* 3.4 2.6 - - - +
122F ALA 2.7 37.2 + - - +
124F MET* 3.7 31.0 - - + -
129F ALA* 3.7 14.6 - - + -
131F PHE* 3.6 20.5 - - + -
150F ILE* 4.0 21.5 - - + -
151F THR 3.2 13.0 - - - +
152F VAL* 4.3 15.5 - - + -
153F PHE* 4.6 0.2 - - - -
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Residues in contact with THR 104 (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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102F LEU* 5.4 1.8 - - + -
103F VAL* 1.3 80.5 - - - +
105F VAL* 1.3 66.9 + - - +
106F MET* 4.8 8.3 - - - +
120F ALA* 3.1 8.5 - - - -
121F THR* 3.6 24.2 - - + +
131F PHE* 4.2 0.4 - - - -
149F THR 3.7 1.1 - - - +
150F ILE* 3.6 3.3 - - - -
151F THR* 3.0 37.5 + - - -
153F PHE* 3.5 29.9 - - + -
65G SER* 4.3 6.1 + - - +
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Residues in contact with VAL 105 (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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89F PHE* 3.6 22.9 - - + -
104F THR* 1.3 75.2 - - - +
106F MET* 1.3 72.5 + - - +
117F LEU* 3.2 12.6 - - + +
120F ALA* 2.9 32.7 + - + +
131F PHE* 3.4 30.1 - - + -
134F LEU* 4.6 11.4 - - + -
136F PHE* 5.5 0.2 - - + -
148F LEU* 3.9 35.9 - - + -
149F THR 3.6 4.5 - - - +
150F ILE* 4.7 8.1 - - + -
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Residues in contact with MET 106 (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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104F THR* 4.8 8.1 - - - +
105F VAL* 1.3 83.0 - - - +
107F ALA* 1.3 59.9 + - - +
117F LEU* 3.8 6.7 - - - -
148F LEU* 3.3 5.0 - - - +
149F THR* 2.6 45.0 + - + +
151F THR* 4.3 11.4 - - - +
30G THR* 5.4 2.5 - - - -
54G GLU* 4.7 16.6 - - - +
63G ASN* 3.9 24.7 - - + +
64G LEU* 3.4 44.0 - - - +
65G SER* 3.4 20.0 - - - +
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Residues in contact with ALA 107 (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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106F MET* 1.3 77.7 - - - +
108F GLY* 1.3 60.6 + - - +
114F SER* 3.5 1.0 + - - -
115F ALA* 2.9 32.8 + - + -
117F LEU* 4.2 7.5 - - + +
136F PHE* 4.3 8.5 - - + -
146F PHE* 4.0 18.8 - - + -
147F THR 3.4 7.9 - - - +
148F LEU* 3.7 20.6 - - + -
149F THR* 5.1 0.4 - - - -
63G ASN* 3.5 15.8 + - - +
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Residues in contact with GLY 108 (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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107F ALA* 1.3 78.4 - - - +
109F ASN* 1.3 66.1 + - - +
112F ASN 3.1 14.1 - - - -
113F TYR 3.9 2.2 - - - -
146F PHE* 3.8 10.2 - - - -
147F THR* 3.2 27.0 + - - -
60G THR 4.4 0.3 - - - +
61G GLY 3.0 21.3 + - - +
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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