Contacts of the helix formed by residues 130 - 137 (chain A) in PDB entry 1JD7
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ASP* 2.9 30.7 + - - +
128A GLY 3.9 0.4 - - - -
129A ASN* 1.3 90.2 - - - +
131A ARG* 1.3 62.2 + - - +
132A TYR* 3.3 13.0 + - - +
133A ARG* 3.1 40.4 + - + +
134A VAL* 3.3 15.8 + - - +
208A ALA* 4.1 1.9 - - - +
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Residues in contact with ARG 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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129A ASN 4.1 0.2 - - - -
130A ASP* 1.3 72.6 + - - +
132A TYR* 1.3 66.0 + - - +
134A VAL* 3.2 6.6 + - - +
135A GLN* 3.1 51.3 + - - +
180A ALA* 5.8 0.6 - - - +
181A ALA 5.8 1.0 - - - +
208A ALA* 3.3 32.6 + - + +
209A VAL* 4.0 14.8 - - + +
213A GLU* 2.7 42.8 + - - -
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Residues in contact with TYR 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 ASP* 3.3 9.1 + - - +
131A ARG* 1.3 81.9 - - - +
133A ARG* 1.3 69.5 + - + +
135A GLN* 5.4 0.4 - - - -
136A ASN* 2.8 73.5 + - + +
137A CYS* 5.6 3.6 - - - -
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Residues in contact with ARG 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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120A CYS* 4.3 7.5 - - - +
121A THR* 2.7 34.9 + - - +
122A ILE* 3.4 5.5 - - - +
123A ASN* 3.6 11.4 + - - -
126A ASP* 2.9 43.7 + - - +
130A ASP* 3.1 26.0 + - - +
132A TYR* 1.3 87.8 - - + +
134A VAL* 1.3 58.8 + - - +
137A CYS* 2.9 53.8 + - - +
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Residues in contact with VAL 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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122A ILE* 3.4 15.7 - - + +
126A ASP* 3.4 37.0 - - + +
127A TYR* 3.7 22.9 - - + +
130A ASP 3.3 5.4 + - - +
131A ARG* 3.2 12.0 + - - +
133A ARG* 1.3 76.8 - - - +
135A GLN* 1.3 60.9 + - + +
136A ASN 3.9 0.2 + - - -
137A CYS 4.2 1.0 - - - +
177A LYS* 4.0 26.7 - - + +
178A HIS* 3.0 43.0 + - + +
208A ALA* 5.6 0.4 - - + -
209A VAL* 4.4 8.3 - - + -
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Residues in contact with GLN 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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117A HIS* 3.5 9.9 - - - -
131A ARG* 3.1 35.6 + - - +
132A TYR* 4.4 1.5 - - - +
134A VAL* 1.3 78.7 - - + +
136A ASN* 1.3 64.9 + - - +
144A ASP* 3.2 1.7 - - - +
147A THR* 5.4 0.5 + - - -
177A LYS 3.2 26.2 + - - +
178A HIS 3.1 12.5 - - - +
179A VAL* 5.1 0.7 - - - -
180A ALA* 3.5 35.0 + - + +
181A ALA 4.5 0.4 - - - +
209A VAL* 3.7 19.6 - - + +
213A GLU* 5.1 0.4 + - - -
214A TYR* 3.3 16.6 + - - -
800A CA 2.7 22.3 - - - -
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Residues in contact with ASN 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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117A HIS* 3.1 49.0 + - + +
118A GLU 4.2 1.9 - - - +
120A CYS* 4.0 6.0 - - - -
132A TYR* 2.8 73.0 + - + +
133A ARG* 4.9 0.2 - - - -
135A GLN* 1.3 86.7 + - - +
137A CYS* 1.3 62.7 + - - +
138A GLU* 5.6 0.2 - - - +
144A ASP* 3.3 12.1 - - - +
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Residues in contact with CYS 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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120A CYS* 2.0 55.9 - - - +
122A ILE* 3.3 27.0 - - + +
132A TYR* 5.6 2.0 - - - -
133A ARG* 2.9 49.4 + - - +
134A VAL 4.2 2.1 - - - +
136A ASN* 1.3 81.2 - - - +
138A GLU* 1.3 63.1 + - - +
139A LEU 3.7 0.3 + - - -
144A ASP* 3.6 14.4 - - - +
178A HIS* 5.8 0.2 - - - +
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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