Contacts of the helix formed by residues 133 - 143 (chain A) in PDB entry 1DJ9
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 HIS 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PHE* 4.0 9.9 - + - -
131A LEU 4.6 0.4 - - - -
132A SER* 1.3 74.4 - - - +
134A ALA* 1.3 64.2 + - + +
135A SER* 2.6 45.9 + - - -
136A LEU* 2.9 31.9 + - + +
137A LEU* 3.3 8.1 + - - +
175A GLU* 2.5 20.9 + - - +
179A SER* 4.2 6.3 - - - -
400A KAM 3.2 80.3 + + + +
500A MG 3.9 2.0 - - - -
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Residues in contact with ALA 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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109A PHE* 4.8 5.3 - - + -
132A SER 3.6 2.3 + - - -
133A HIS* 1.3 79.8 - - + +
135A SER* 1.3 63.1 + - - +
137A LEU* 4.6 7.4 - - - -
138A GLU* 2.9 29.0 + - + +
352A THR* 6.5 0.9 - - - -
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Residues in contact with SER 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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109A PHE* 3.3 40.4 - - - -
112A ASN* 3.0 23.1 + - - -
113A GLN* 2.7 33.0 + - - +
133A HIS* 2.6 37.4 + - - -
134A ALA* 1.3 72.0 - - - +
136A LEU* 1.3 59.9 + - - +
139A ALA* 3.2 11.4 + - - +
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Residues in contact with LEU 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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112A ASN* 3.5 35.7 - - + +
116A ILE* 3.6 19.4 - - + +
132A SER* 4.0 14.4 - - - -
133A HIS* 2.9 26.8 + - + +
135A SER* 1.3 80.8 + - - +
137A LEU* 1.3 55.0 + - + +
139A ALA* 3.3 1.4 + - - -
140A ALA* 2.6 37.8 + - - +
173A VAL* 4.2 17.9 - - + -
174A THR 5.0 1.1 - - - +
175A GLU* 4.5 5.4 - - + +
202A MET* 4.0 20.0 - - + -
204A ASP* 4.0 25.6 - - + +
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Residues in contact with LEU 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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128A ALA* 4.0 27.8 - - + -
129A ASP 4.4 2.0 - - - +
130A ARG 3.9 19.5 - - - +
132A SER* 3.8 29.4 - - - +
133A HIS 3.3 5.3 + - - +
134A ALA* 4.5 5.4 - - - +
136A LEU* 1.3 78.0 - - - +
138A GLU* 1.3 61.4 + - - +
140A ALA* 4.0 1.6 - - - +
141A SER* 2.8 32.1 + - - -
147A LEU* 4.3 21.7 - - + +
149A ARG* 4.5 17.5 - - + +
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Residues in contact with GLU 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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109A PHE* 3.6 16.4 - - + -
113A GLN* 3.4 22.1 + - - +
134A ALA* 2.9 22.2 + - + +
137A LEU* 1.3 77.9 - - - +
139A ALA* 1.3 54.0 - - - +
141A SER* 2.9 9.1 - - - -
142A LEU* 2.8 51.1 + - + +
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Residues in contact with ALA 139 (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 GLN* 3.8 33.2 - - + +
116A ILE* 3.9 16.9 - - + +
117A ALA* 5.5 0.7 - - + +
135A SER 3.2 16.5 + - - +
136A LEU 3.7 2.9 - - - +
138A GLU* 1.3 79.0 - - - +
140A ALA* 1.3 62.4 + - - +
141A SER 3.1 1.1 - - - -
142A LEU* 3.6 7.0 - - - +
143A SER* 2.7 29.5 + - - -
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Residues in contact with ALA 140 (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* 4.0 5.1 - - + +
126A ILE* 3.5 27.8 - - + -
128A ALA* 5.7 0.4 - - + -
136A LEU 2.6 23.2 + - - +
137A LEU* 4.0 3.6 - - + +
139A ALA* 1.3 73.8 - - - +
141A SER* 1.3 64.8 + - - +
143A SER* 3.2 17.4 + - - +
145A SER* 4.4 4.3 + - - +
147A LEU* 3.3 41.4 - - + +
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Residues in contact with SER 141 (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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137A LEU 2.8 14.5 + - - -
138A GLU* 2.9 17.3 - - - -
140A ALA* 1.3 76.4 - - - +
142A LEU* 1.3 65.1 + - - +
143A SER 3.3 6.9 + - - +
147A LEU* 4.5 11.3 - - - +
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Residues in contact with LEU 142 (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 GLN* 6.0 1.1 - - - +
138A GLU* 2.8 38.5 + - + +
139A ALA* 4.0 6.7 - - - +
141A SER* 1.3 73.4 - - - +
143A SER* 1.3 66.3 + - - +
144A PRO* 3.5 2.9 - - - +
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Residues in contact with SER 143 (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* 4.5 7.0 + - - -
117A ALA* 5.8 2.8 - - - +
120A MET* 3.7 10.6 + - - +
126A ILE* 4.4 3.1 - - - -
139A ALA 2.7 19.0 + - - -
140A ALA* 3.2 15.9 - - - -
141A SER 3.1 9.7 - - - +
142A LEU* 1.3 75.8 - - - +
144A PRO* 1.3 75.4 - - - +
145A SER* 2.5 39.8 + - - +
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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