Contacts of the strand formed by residues 147 - 151 (chain B) in PDB entry 2PWY
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 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B THR* 3.9 17.7 - - + -
112B ALA* 3.8 19.7 - - + -
121B VAL* 3.5 16.6 - - + +
123B SER* 4.5 2.9 - - - -
138B VAL* 4.6 6.3 - - + -
139B ARG* 5.5 1.9 + - - -
142B TRP* 4.6 8.1 - - + +
144B VAL 4.6 1.3 + - - +
145B GLU* 3.5 4.3 - - - +
146B ASN* 1.3 94.8 - - - +
148B ARG* 1.3 67.4 - - - +
149B PHE* 3.6 48.5 + - + -
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Residues in contact with ARG 148 (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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96B ARG* 4.1 8.7 - - - +
120B LEU* 3.5 37.3 - - + +
121B VAL 2.8 8.7 + - - +
122B GLU* 3.2 25.8 + - - +
123B SER 2.9 27.1 + - - -
145B GLU 6.1 0.2 - - - +
146B ASN 5.6 0.2 - - - -
147B VAL* 1.3 75.0 - - - +
149B PHE* 1.3 60.6 + - - +
150B HIS* 3.3 15.0 - - + +
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Residues in contact with PHE 149 (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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102B THR* 3.8 23.6 - - + -
108B THR* 4.4 2.2 - - + -
123B SER* 3.5 7.0 - - - -
131B LEU* 3.7 19.7 - - + -
135B GLU* 3.3 48.0 - - + +
138B VAL* 3.9 34.3 - - + -
139B ARG* 4.1 22.0 - - + -
147B VAL* 3.6 34.5 - - + -
148B ARG* 1.3 69.5 - - - +
150B HIS* 1.3 74.3 + - - +
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Residues in contact with HIS 150 (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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122B GLU* 2.7 33.1 + - + +
123B SER 2.8 11.7 + - - +
124B TYR* 3.3 51.4 + + + +
125B GLU 3.0 25.6 + - - -
131B LEU* 3.9 6.3 - - - +
148B ARG* 3.3 28.5 + - + -
149B PHE* 1.3 82.4 + - - +
151B LEU* 1.3 63.1 + - - +
152B GLY 3.6 0.2 + - - -
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Residues in contact with LEU 151 (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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124B TYR* 5.2 1.3 - - - -
125B GLU 3.4 16.8 - - - +
126B ALA 3.8 8.1 - - - +
127B ARG 4.1 0.7 - - - -
128B PRO* 3.7 44.6 - - + -
131B LEU* 3.7 18.9 - - + +
150B HIS* 1.3 71.7 - - - +
152B GLY* 1.3 58.8 + - - +
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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