Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 2VUT
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 SER 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A HIS* 4.3 1.6 - - - -
108A TYR* 3.0 19.3 - - - +
138A VAL* 3.8 21.0 - - - +
139A ARG* 4.9 4.7 + - - +
143A LEU 2.8 12.9 + - - -
144A PRO* 1.3 74.3 - - - +
146A THR* 1.3 66.5 + - - +
147A PHE* 3.5 21.2 - - - -
212A ASN* 3.0 10.6 + - - -
213A GLY* 2.7 31.7 + - - -
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A HIS* 2.7 30.3 + - - -
108A TYR 3.3 3.4 + - - -
109A ILE* 3.3 13.3 - - - +
110A TYR 3.0 24.8 + - - +
145A SER* 1.3 77.7 + - - +
147A PHE* 1.3 71.0 + - - +
148A VAL* 4.2 1.8 - - + -
203A ILE* 4.1 9.9 - - + -
211A TRP* 3.2 28.5 + - + +
214A HIS 3.6 11.7 - - - +
216A ILE* 3.7 24.0 - - + -
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 3.3 33.0 - + + +
112A SER* 4.6 1.1 - - - -
135A GLU* 3.2 56.8 - - + +
138A VAL* 4.0 9.4 - - + -
139A ARG* 3.4 45.5 - - + -
145A SER* 3.5 27.8 - - - -
146A THR* 1.3 76.5 - - - +
148A VAL* 1.3 56.8 + - - +
149A TYR* 4.1 9.1 - - + -
213A GLY* 4.3 3.6 - - - -
214A HIS 2.8 16.9 + - - +
215A ARG* 3.2 3.5 - - - -
216A ILE* 2.6 35.9 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 5.1 0.7 - - - +
78A PHE* 4.2 16.6 - - + -
109A ILE* 4.1 12.8 - - + -
110A TYR 3.3 4.7 + - - +
111A SER* 3.4 26.1 + - - +
112A SER 2.9 24.1 + - - +
146A THR* 4.2 2.0 + - + -
147A PHE* 1.3 76.0 - - - +
149A TYR* 1.3 63.9 + - - +
150A ALA* 3.9 0.7 - - + +
200A LEU* 4.3 4.5 - - + -
203A ILE* 3.8 29.6 - - + -
216A ILE* 3.2 13.5 - - + +
218A LEU* 4.1 24.9 - - + -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 3.6 19.3 - - - +
113A MET* 3.8 2.9 - - - -
114A PRO* 3.8 39.3 - - + -
132A PHE* 3.6 12.6 - - - -
135A GLU* 2.5 32.3 + - - -
147A PHE* 4.1 6.5 - - + -
148A VAL* 1.3 77.9 - - - +
150A ALA* 1.3 62.3 + - - +
215A ARG* 3.5 25.7 + - + -
216A ILE 2.7 15.8 + - - +
217A ALA* 4.4 1.1 - - - -
218A LEU* 2.6 28.6 + - - +
277A PHE* 3.5 22.0 - + + -
279A LEU* 3.6 20.8 - - + +
282A PHE* 3.8 20.4 - + + -
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Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 4.0 24.7 - - - +
111A SER* 4.9 3.0 + - - +
112A SER 4.4 0.8 + - - -
113A MET* 3.9 6.7 - - - +
148A VAL 3.9 3.4 + - - -
149A TYR* 1.3 72.3 - - - +
151A GLY* 1.3 62.1 + - - +
153A TYR* 4.3 1.6 - - + -
190A LEU* 3.7 18.2 - - + -
218A LEU* 3.6 12.3 - - + +
276A TYR* 3.6 5.2 - - - -
277A PHE* 3.5 9.7 - - - -
1353A NAD 3.1 33.0 - - + -
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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