Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 2PNT
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 GLU 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TYR 3.2 1.2 - - - +
120A GLY* 4.4 0.7 - - - -
121A LEU* 2.9 46.4 + - + +
129A VAL* 1.3 70.8 - - - +
131A MET* 1.3 72.0 + - - +
132A VAL* 3.3 16.1 + - - +
164A GLU* 3.4 32.2 - - - +
165A GLY* 4.5 10.1 - - - +
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Residues in contact with MET 131 (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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118A THR* 3.2 33.7 - - + +
119A TYR 3.3 3.1 - - - -
120A GLY* 3.9 24.5 - - - +
129A VAL* 3.9 11.9 + - - +
130A GLU* 1.3 72.4 - - - +
132A VAL* 1.3 61.7 + - - +
133A THR 4.4 0.2 + - - -
163A VAL 4.6 0.7 - - - +
164A GLU* 3.9 2.6 - - - -
165A GLY* 2.9 44.5 + - - +
166A ILE 3.2 28.6 + - - +
167A ARG* 4.3 10.5 - - + -
168A HIS* 5.2 2.2 - - + +
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Residues in contact with VAL 132 (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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118A THR* 3.4 0.4 - - - -
119A TYR* 2.7 41.5 + - + +
121A LEU* 3.9 24.9 - - + -
130A GLU* 3.8 26.0 - - - +
131A MET* 1.3 79.7 - - - +
133A THR* 1.3 65.8 + - - +
134A PHE* 3.9 8.3 - - + -
154A THR* 3.5 35.2 - - + +
164A GLU* 5.7 7.4 - - + +
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Residues in contact with THR 133 (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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116A ILE* 3.8 35.4 - - + -
117A GLN 3.3 11.2 - - - +
118A THR* 2.7 23.6 + - - +
131A MET 4.2 0.6 + - - -
132A VAL* 1.3 72.9 - - - +
134A PHE* 1.3 63.5 + - - +
154A THR* 3.6 5.0 - - - +
155A ILE* 2.9 38.5 + - + +
163A VAL 5.6 1.4 + - - -
164A GLU* 6.2 0.6 - - - +
166A ILE 4.4 0.5 + - - -
171A ILE* 3.0 34.0 - - + +
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Residues in contact with PHE 134 (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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116A ILE* 3.3 8.1 - - - +
117A GLN* 3.0 72.1 + - + -
118A THR 4.6 0.2 - - - -
119A TYR* 4.1 30.7 - + + -
132A VAL* 3.9 13.0 - - + -
133A THR* 1.3 75.1 - - - +
135A VAL* 1.3 74.0 + - - +
136A CYS* 4.4 8.1 - - + -
152A GLY* 4.7 9.4 - - - +
153A ASP 3.1 15.5 - - - +
154A THR* 4.0 11.4 - - - +
155A ILE* 4.3 1.6 - - - +
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Residues in contact with VAL 135 (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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114A PHE* 4.3 4.5 - - + -
115A GLU 3.4 7.2 - - - +
116A ILE* 4.4 0.7 - - - -
134A PHE* 1.3 77.7 - - - +
136A CYS* 1.3 58.9 + - - +
137A ARG 3.4 14.4 - - - +
138A VAL* 3.4 33.0 - - + -
149A LEU* 3.8 35.0 - - + -
150A THR 3.7 12.8 - - - +
151A PRO* 4.1 1.6 - - + -
152A GLY* 2.8 28.9 + - - -
153A ASP* 2.8 21.3 + - + +
155A ILE* 4.1 17.5 - - + -
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Residues in contact with CYS 136 (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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115A GLU* 2.9 31.9 + - - -
116A ILE 3.9 2.0 - - - -
117A GLN* 3.4 40.2 - - + +
134A PHE* 3.6 10.2 + - + -
135A VAL* 1.3 74.2 - - - +
137A ARG* 1.3 91.9 + - + +
151A PRO* 4.2 11.2 - - - +
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Residues in contact with ARG 137 (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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114A PHE* 3.3 6.7 - - - +
115A GLU* 2.7 76.0 + - + +
117A GLN* 4.1 11.2 - - - +
135A VAL* 3.4 2.2 - - - +
136A CYS* 1.3 103.5 - - - +
138A VAL* 1.3 65.5 + - - +
139A HIS* 4.4 7.0 - - + +
151A PRO* 4.7 4.0 - - - -
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Residues in contact with VAL 138 (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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113A GLY 3.7 3.8 - - - -
114A PHE* 4.2 5.2 - - + -
135A VAL* 3.4 20.4 - - + -
137A ARG* 1.3 81.2 - - - +
139A HIS* 1.3 72.8 + - - +
140A GLU 3.7 1.2 + - - -
142A SER* 4.0 2.5 - - - +
144A ALA* 4.0 5.6 - - + -
145A GLN* 3.7 41.1 + - + +
149A LEU* 3.8 25.6 - - + +
150A THR 4.1 0.7 - - - -
151A PRO* 3.8 23.0 - - + +
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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