Contacts of the strand formed by residues 114 - 121 (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 PHE 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.9 10.5 - - + -
112A PHE* 3.6 31.6 - + + -
113A GLY* 1.3 79.1 - - - +
115A GLU* 1.3 70.8 + - - +
116A ILE* 3.5 29.8 - - + -
135A VAL* 4.3 3.6 - - + -
137A ARG 3.3 13.7 - - - +
138A VAL* 4.2 3.4 - - + -
139A HIS* 4.6 2.3 + - - -
144A ALA* 3.9 12.8 - - + -
149A LEU* 3.6 23.6 - - + -
155A ILE* 4.0 11.9 - - + -
175A ILE* 4.3 17.0 - - + -
182A LEU* 4.2 16.8 - - + -
184A LEU* 4.2 7.0 - - + -
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Residues in contact with GLU 115 (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* 1.3 79.7 - - - +
116A ILE* 1.3 65.8 + - - +
135A VAL* 3.4 8.5 - - - +
136A CYS* 2.9 33.3 + - - -
137A ARG* 2.7 59.4 + - + -
139A HIS* 3.7 22.9 + - - +
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Residues in contact with ILE 116 (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* 3.5 26.9 - - + -
115A GLU* 1.3 81.6 - - - +
117A GLN* 1.3 68.4 + - - +
133A THR* 3.8 21.1 - - + -
134A PHE 3.3 13.7 - - - +
135A VAL* 4.4 0.4 - - - -
136A CYS* 3.9 3.4 - - - -
155A ILE* 3.9 14.8 - - + -
168A HIS* 3.4 20.7 - - + +
171A ILE* 4.4 9.0 - - + -
172A VAL* 3.9 24.7 - - + -
175A ILE* 4.1 21.3 - - + -
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Residues in contact with GLN 117 (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* 1.3 79.5 - - - +
118A THR* 1.3 63.3 + - - +
133A THR* 3.3 3.9 - - - +
134A PHE* 3.0 60.1 + - + +
136A CYS* 3.4 28.4 - - - +
137A ARG* 4.1 13.7 - - - +
168A HIS* 4.0 5.6 - - + -
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Residues in contact with THR 118 (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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117A GLN* 1.3 73.9 - - - +
119A TYR* 1.3 61.1 - - - +
120A GLY 4.0 1.2 + - - -
131A MET* 3.2 47.7 - - + +
132A VAL 3.4 5.8 - - - +
133A THR* 2.7 24.9 + - - +
134A PHE* 4.6 1.1 - - - -
166A ILE 4.0 6.1 - - - +
168A HIS* 2.9 40.2 + - - +
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Residues in contact with TYR 119 (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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117A GLN 4.2 0.8 - - - -
118A THR* 1.3 73.4 - - - +
120A GLY* 1.3 74.0 + - - +
121A LEU* 3.1 35.9 + - + -
122A HIS* 6.1 1.1 - + - -
130A GLU 3.2 0.5 - - - +
131A MET* 3.3 3.1 - - - -
132A VAL* 2.7 43.5 + - + +
134A PHE* 4.1 21.5 - + + -
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Residues in contact with GLY 120 (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 4.0 0.8 + - - -
119A TYR* 1.3 80.4 - - - +
121A LEU* 1.3 66.2 + - - +
122A HIS* 3.8 16.3 + - - -
129A VAL* 4.6 8.0 - - - +
130A GLU 3.9 4.5 - - - -
131A MET* 3.9 22.3 - - - +
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Residues in contact with LEU 121 (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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119A TYR* 3.1 32.3 + - + +
120A GLY* 1.3 73.7 - - - -
122A HIS* 1.3 63.6 + - - +
129A VAL* 3.2 10.6 - - - -
130A GLU* 2.9 47.2 + - + +
132A VAL* 3.9 24.9 - - + -
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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