Contacts of the helix formed by residues 129 - 140 (chain B) in PDB entry 1JWL
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 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 1.3 75.4 - - - +
130B ASP* 1.3 56.0 + - - +
131B GLN 3.5 1.6 - - - +
132B ASP* 3.0 26.0 + - - +
133B ALA* 2.7 31.1 + - - +
192B VAL* 4.3 1.0 - - - +
195B ARG* 2.8 34.3 + - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU 3.9 0.7 + - - +
129B ASP* 1.3 72.0 - - - +
131B GLN* 1.3 63.1 + - + +
133B ALA* 3.2 3.9 + - - +
134B ILE* 2.9 33.8 + - + +
151B SER* 4.5 9.0 + - - -
153B GLN* 4.5 10.9 + - - +
154B THR* 2.6 47.0 + - + +
155B PRO* 4.9 4.9 - - + +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ASP* 3.5 1.2 - - - +
130B ASP* 1.3 76.0 - - + +
132B ASP* 1.3 57.5 + - - +
134B ILE* 2.9 15.5 + - + +
135B ALA* 2.7 36.0 + - - +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 3.1 41.8 - - + +
128B LEU* 4.3 7.0 - - + -
129B ASP* 3.0 31.9 + - - +
131B GLN* 1.3 78.1 - - - +
133B ALA* 1.3 63.9 + - - +
135B ALA* 3.0 10.1 + - - +
136B VAL* 3.0 26.5 + - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.9 25.3 - - + +
129B ASP 2.7 17.0 + - - +
130B ASP 3.4 9.2 - - - +
132B ASP* 1.3 75.4 - - - +
134B ILE* 1.3 56.3 + - - +
136B VAL* 3.4 0.3 + - - +
137B GLU* 2.9 29.3 + - - +
147B PHE* 3.6 6.8 - - + -
150B VAL* 4.2 6.7 - - + -
154B THR* 4.1 6.5 - - + -
156B ILE* 3.6 25.4 - - + -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP* 2.9 19.9 + - + +
131B GLN* 2.9 19.1 + - + +
133B ALA* 1.3 77.7 - - - +
135B ALA* 1.3 56.5 + - - +
137B GLU* 3.4 11.7 - - + +
138B ALA* 3.0 27.0 + - + +
154B THR* 4.7 1.3 - - + -
155B PRO* 3.7 32.3 - - + +
156B ILE* 4.6 9.2 - - + -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 5.6 0.4 - - + -
108B LYS* 4.2 24.4 - - - +
131B GLN 2.7 15.4 + - - +
132B ASP* 3.4 12.3 - - - +
134B ILE* 1.3 71.8 - - - +
136B VAL* 1.3 65.8 + - - +
138B ALA* 3.0 10.5 + - - +
139B ALA* 2.9 21.0 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.6 7.0 - - + -
107B CYS* 4.5 10.3 - - - +
108B LYS* 4.4 22.0 - - + -
111B VAL* 3.9 25.4 - - + -
124B ILE* 4.2 9.2 - - + -
128B LEU* 3.9 20.0 - - + -
132B ASP 3.0 16.1 + - - +
133B ALA 3.7 7.0 - - - +
135B ALA* 1.3 70.8 - - - +
137B GLU* 1.3 69.8 + - - +
139B ALA* 2.9 20.0 + - - +
140B CYS* 3.2 14.5 + - - -
147B PHE* 4.0 17.9 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA 2.9 18.3 + - - +
134B ILE* 3.4 13.2 - - + +
136B VAL* 1.3 77.2 - - - +
138B ALA* 1.3 65.4 + - + +
140B CYS* 3.3 22.7 + - - +
143B VAL 5.2 3.1 - - - +
144B PRO* 6.1 0.3 - - - +
145B ALA* 4.4 15.3 + - - +
147B PHE* 4.1 17.8 - - + -
156B ILE* 4.0 25.2 - - + +
157B ASN* 4.5 8.7 + - - -
314B LYS* 5.7 1.0 + - - -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ILE* 3.0 14.8 + - + +
135B ALA* 3.0 13.3 + - - +
137B GLU* 1.3 75.8 - - + +
139B ALA* 1.3 66.2 + - - +
140B CYS 3.0 9.9 + - - +
141B THR* 4.0 2.9 + - - -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 5.7 11.2 - - + -
111B VAL* 5.1 10.3 - - + -
115B LEU* 3.4 13.0 - - + +
135B ALA 2.9 11.2 + - - +
136B VAL* 2.9 15.9 + - - +
138B ALA* 1.3 72.4 - - - +
140B CYS* 1.3 50.5 + - - +
141B THR* 2.6 27.5 + - - -
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.9 7.6 - - - -
115B LEU* 4.2 4.7 - - - -
122B LEU* 3.8 29.4 - - - -
124B ILE* 5.3 0.4 - - - -
136B VAL* 3.5 18.4 - - - -
137B GLU* 3.4 13.0 - - - +
138B ALA 3.0 6.0 + - - +
139B ALA* 1.3 72.2 - - - +
141B THR* 1.3 52.8 + - - +
142B ASN* 2.8 18.4 + - - -
143B VAL* 3.4 33.7 - - + +
145B ALA* 3.8 20.6 - - + -
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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