Contacts of the helix formed by residues 129 - 134 (chain B) in PDB entry 5J3V
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 LEU 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 4.5 7.6 - - + -
114B ILE* 4.2 14.8 - - + -
118B ALA* 3.7 30.3 - - + -
123B LEU* 4.2 12.3 - - + -
126B TRP* 3.9 35.7 - - + +
127B PRO 3.0 7.5 + - - -
128B ASP* 1.3 79.0 - - - +
130B LEU* 1.3 63.7 - - + +
131B PRO* 3.4 0.9 - - - +
132B LYS* 3.5 3.9 - - - +
133B LEU* 2.5 67.3 + - + +
155B ILE* 3.8 13.5 - - + -
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Residues in contact with LEU 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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123B LEU* 5.8 4.9 - - + +
127B PRO 4.5 0.2 + - - -
129B LEU* 1.3 83.4 - - + +
131B PRO* 1.3 69.1 - - + +
132B LYS 3.0 4.4 + - - -
133B LEU* 4.9 1.6 - - - -
134B CYS* 3.2 23.9 + - - +
152B LEU* 3.8 25.7 - - + +
155B ILE* 4.7 18.4 - - + -
156B CYS* 5.8 4.5 - - - -
168B LEU* 3.7 37.0 - - + +
171B PRO* 3.9 19.7 - - + -
175B MET* 3.3 27.9 - - + +
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Residues in contact with PRO 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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127B PRO 3.3 25.4 - - - +
128B ASP* 4.9 1.6 - - - -
129B LEU 4.5 0.4 - - - +
130B LEU* 1.3 92.4 - - + +
132B LYS* 1.3 57.7 + - + +
134B CYS* 4.3 7.0 - - + +
135B SER* 4.5 10.2 + - - -
168B LEU* 5.6 1.3 - - + -
169B ASP* 3.8 21.8 - - + +
171B PRO* 6.5 0.2 - - + -
175B MET* 5.3 0.2 - - + -
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Residues in contact with LYS 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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96B LEU* 3.6 33.9 - - + -
128B ASP* 3.4 43.9 + - + +
129B LEU* 3.0 7.5 + - - +
131B PRO* 1.3 79.6 - - - +
133B LEU* 1.3 62.3 + - + +
134B CYS 3.1 1.6 - - - -
135B SER* 3.1 21.1 + - - -
136B LEU* 3.4 15.1 + - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.4 15.3 - - + -
99B ILE* 5.4 1.1 - - + -
114B ILE* 4.5 5.8 - - + -
129B LEU* 2.5 51.1 + - + +
132B LYS* 1.3 70.9 - - + +
134B CYS* 1.3 63.3 + - - +
135B SER 3.1 0.7 - - - -
136B LEU* 3.2 37.5 + - + +
137B LEU* 3.3 19.5 + - - +
148B ALA* 4.3 14.7 - - + +
151B ALA* 4.2 20.2 - - + -
152B LEU* 3.7 37.8 - - + +
155B ILE* 4.5 4.5 - - + -
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Residues in contact with CYS 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 LEU 3.2 20.6 + - - +
131B PRO* 4.4 8.1 - - + +
132B LYS 3.1 0.2 - - - -
133B LEU* 1.3 77.4 - - - +
135B SER* 1.3 58.4 + - - +
136B LEU 3.3 0.2 - - - -
137B LEU* 3.7 16.6 + - + +
138B ASP* 3.2 5.7 - - - +
152B LEU* 4.9 1.9 - - - +
174B ILE* 5.2 14.8 - - - -
175B MET* 4.3 17.7 - - + +
178B LYS* 2.7 75.0 + - - -
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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