Contacts of the helix formed by residues 130 - 138 (chain A) in PDB entry 2JFS
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASP* 4.6 13.6 - - - +
128A ASP* 3.1 7.8 + - - +
129A HIS* 1.3 76.7 - - - +
131A VAL* 1.3 66.1 + - - +
132A ALA* 3.7 1.0 + - - +
133A GLY* 2.9 21.1 + - - -
134A GLU* 2.8 22.5 + - - +
152A ARG* 3.2 26.5 + - - +
154A LEU 3.1 14.6 - - - -
155A LEU* 4.6 1.1 - - - -
156A THR* 3.7 6.7 - - - +
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Residues in contact with VAL 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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130A SER* 1.3 72.2 - - - +
132A ALA* 1.3 65.3 + - - +
134A GLU* 3.2 4.7 + - - +
135A LEU* 3.2 27.0 + - + +
149A HIS* 4.2 8.1 - - + -
151A GLN* 3.6 38.9 + - + +
154A LEU* 2.9 45.1 - - + -
156A THR* 4.1 14.8 - - + -
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Residues in contact with ALA 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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130A SER* 3.3 2.5 + - - +
131A VAL* 1.3 79.0 - - - +
133A GLY* 1.3 62.8 + - - +
135A LEU* 3.1 14.1 + - - +
136A VAL* 3.0 26.5 + - - +
141A ILE* 4.3 1.1 - - + +
146A ALA* 4.3 12.3 - - + +
149A HIS* 3.7 25.4 - - + -
151A GLN 3.8 3.4 + - - -
152A ARG* 3.7 28.0 - - + -
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Residues in contact with GLY 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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127A ASP* 5.8 0.2 - - - +
128A ASP* 3.3 33.0 + - - +
130A SER* 2.9 16.1 + - - -
132A ALA* 1.3 78.5 - - - +
134A GLU* 1.3 54.6 + - - +
136A VAL* 3.3 8.7 + - - +
137A ARG* 2.9 28.1 + - - +
143A ARG* 4.4 7.0 + - - -
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Residues in contact with GLU 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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128A ASP 4.3 6.5 - - - +
129A HIS* 3.7 15.4 + - - +
130A SER 2.8 23.1 + - - +
131A VAL* 3.7 4.9 - - - +
133A GLY* 1.3 69.9 - - - +
135A LEU* 1.3 63.1 + - + +
137A ARG* 3.2 14.9 + - - +
138A MET* 2.9 48.5 + - + +
156A THR* 2.7 35.7 + - + +
157A ARG* 4.7 9.5 + - - +
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Residues in contact with LEU 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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131A VAL* 3.2 20.2 + - + +
132A ALA* 3.1 7.9 + - - +
134A GLU* 1.3 77.9 - - + +
136A VAL* 1.3 59.1 - - - +
138A MET* 3.5 11.4 + - - -
139A GLY 3.3 3.1 + - - -
140A GLU* 2.9 49.8 + - + +
141A ILE* 3.5 20.9 + - + -
149A HIS* 3.5 36.6 - - + +
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Residues in contact with VAL 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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132A ALA 3.0 14.5 + - - +
133A GLY 3.6 7.6 - - - +
134A GLU 3.2 0.2 - - - -
135A LEU* 1.3 74.1 - - - +
137A ARG* 1.3 66.3 + - - +
139A GLY* 2.9 15.6 + - - -
141A ILE* 3.4 21.0 - - + +
142A THR* 3.9 5.2 - - - +
143A ARG* 3.7 50.0 - - + +
146A ALA* 3.6 26.5 - - + -
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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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127A ASP* 3.7 36.1 + - + +
128A ASP 5.7 0.2 - - - +
133A GLY 2.9 17.4 + - - +
134A GLU* 3.2 18.8 + - - +
136A VAL* 1.3 77.4 - - - +
138A MET* 1.3 63.9 + - + +
139A GLY* 3.1 1.4 + - - -
143A ARG* 5.9 0.9 - - - +
1238A GOL 3.0 34.7 + - - +
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Residues in contact with MET 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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134A GLU* 2.9 33.3 + - + +
135A LEU* 3.9 14.4 - - + +
136A VAL 3.2 0.2 - - - -
137A ARG* 1.3 79.5 - - + +
139A GLY* 1.3 62.1 + - - +
140A GLU* 3.6 22.3 + - + +
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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