Contacts of the strand formed by residues 146 - 152 (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 PHE 146 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ALA* 4.0 13.5 - - + -
108F GLY* 3.8 22.4 - - - -
109F ASN* 4.2 3.8 - - - -
112F ASN* 4.0 14.6 - - + -
115F ALA* 3.1 29.8 - - + -
136F PHE* 4.0 13.9 - + + -
138F GLY 3.3 20.2 - - - -
139F ARG 3.2 29.6 - - - -
140F SER* 3.7 10.7 - - - -
145F SER* 1.3 75.3 - - - +
147F THR* 1.3 61.6 + - - +
148F LEU* 4.0 1.8 - - + -
164F ARG 3.7 2.1 + - - -
165F ALA* 3.0 28.8 + - - +
166F ILE* 2.8 20.3 + - + +
168F ILE* 3.7 25.8 - - + -
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Residues in contact with THR 147 (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 3.8 0.2 - - - +
107F ALA* 3.4 17.5 - - - -
108F GLY 3.2 20.3 + - - +
109F ASN* 5.3 2.3 - - - +
145F SER 4.1 2.1 + - - -
146F PHE* 1.3 74.2 + - - +
148F LEU* 1.3 63.0 + - - +
149F THR* 4.0 5.7 + - - +
161F THR* 3.3 33.4 - - + -
162F TYR 3.4 6.1 - - - +
163F HIS* 3.5 31.9 - - + +
164F ARG 3.9 2.8 + - - -
17G PHE* 6.0 0.4 - - + -
60G THR 6.0 0.9 - - - -
61G GLY 5.1 2.4 - - - +
62G THR* 5.5 9.6 - - + +
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Residues in contact with LEU 148 (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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75F LEU* 3.5 26.7 - - + -
89F PHE* 3.9 18.6 - - + -
105F VAL* 3.9 17.7 - - + -
106F MET 3.3 4.5 - - - +
107F ALA* 3.7 24.0 - - + -
134F LEU* 5.6 0.4 - - + -
136F PHE* 3.7 21.5 - - + -
146F PHE* 4.0 2.7 - - + -
147F THR* 1.3 74.3 - - - +
149F THR* 1.3 61.5 + - - +
150F ILE* 3.9 5.4 - - + -
161F THR* 3.3 12.0 - - - +
162F TYR* 2.9 53.5 + - + -
165F ALA* 4.0 13.2 - - + -
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Residues in contact with THR 149 (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 3.7 1.4 - - - +
105F VAL* 3.6 2.6 - - - -
106F MET* 2.6 47.1 + - + +
107F ALA* 5.1 0.5 - - - -
147F THR* 4.0 6.9 + - - +
148F LEU* 1.3 78.3 + - - +
150F ILE* 1.3 59.3 + - - +
151F THR* 3.8 7.6 + - - +
159F VAL* 3.6 26.7 - - + -
160F ALA 3.7 2.5 - - - +
161F THR* 4.7 5.5 - - - +
62G THR* 4.8 6.6 - - + +
63G ASN 2.9 38.4 + - - +
64G LEU* 3.8 4.7 - - + -
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Residues in contact with ILE 150 (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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65F THR* 3.8 28.7 - - + -
70F PHE* 5.9 1.3 - - + -
72F CYS* 3.9 23.6 - - + -
89F PHE* 4.1 10.8 - - + -
91F VAL* 3.7 33.4 - - + -
103F VAL* 4.0 13.2 - - + -
104F THR 3.6 5.4 - - - +
105F VAL* 4.7 7.4 - - + +
148F LEU* 4.9 8.5 - - + -
149F THR* 1.3 73.9 - - - +
151F THR* 1.3 67.3 + - - +
152F VAL* 4.7 4.9 - - + -
158F GLN 4.7 0.2 - - - -
159F VAL* 3.4 3.3 - - - +
160F ALA* 2.7 45.9 + - + +
162F TYR* 5.1 6.1 - - + -
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Residues in contact with THR 151 (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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103F VAL* 3.2 6.4 - - - +
104F THR* 3.0 41.5 + - - -
106F MET* 4.3 9.0 - - - +
149F THR* 4.1 9.5 + - - +
150F ILE* 1.3 79.3 + - - +
152F VAL* 1.3 65.9 + - - +
153F PHE* 3.6 31.5 + - + -
157F PRO* 4.7 8.3 - - + -
158F GLN 3.5 7.2 - - - +
159F VAL* 3.9 20.9 - - + +
65G SER* 4.3 12.2 + - - +
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Residues in contact with VAL 152 (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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70F PHE* 3.4 43.3 - - + -
91F VAL* 4.8 0.9 - - + -
97F VAL* 4.0 11.2 - - + -
101F THR* 3.8 20.0 - - + -
102F LEU 3.8 2.9 - - - -
103F VAL* 4.3 16.8 - - + -
124F MET* 4.4 7.2 - - + -
150F ILE* 4.7 7.4 - - + -
151F THR* 1.3 75.9 - - - +
153F PHE* 1.3 53.3 + - - +
154F THR* 2.7 29.4 + - + -
157F PRO* 3.6 0.2 - - - +
158F GLN* 2.7 36.8 + - + +
160F ALA* 6.5 0.4 - - + -
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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