Contacts of the helix formed by residues 136 - 142 (chain A) in PDB entry 1NUS
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 ALA 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLY* 1.3 71.0 - - - -
137A ASP* 1.3 61.7 + - - +
139A LEU* 3.2 7.8 + - - +
140A LYS 3.2 15.8 + - - -
164A CYS* 3.3 16.1 - - - -
165A VAL 3.0 15.7 + - - +
167A ARG* 3.9 10.5 - - + +
170A HIS* 3.9 16.8 - - + -
172A PRO* 3.4 34.5 - - + -
175A TYR* 3.5 7.7 - - + -
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Residues in contact with ASP 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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135A GLY 3.3 2.9 - - - -
136A ALA* 1.3 71.4 - - - +
138A VAL* 1.3 68.0 + - - +
140A LYS* 3.0 13.0 + - - +
141A THR* 3.2 16.8 + - + +
167A ARG* 3.2 31.8 + - - +
170A HIS* 3.3 36.6 + - + +
501A APC 2.8 31.0 + - - +
140B LYS* 5.3 5.5 + - - -
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Residues in contact with VAL 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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12A CYS 6.1 0.2 - - - +
132A LEU* 5.5 4.0 - - + -
134A CYS* 3.9 19.1 - - + -
135A GLY 3.0 8.7 + - - +
137A ASP* 1.3 79.8 - - - +
139A LEU* 1.3 66.5 + - - +
141A THR* 2.5 34.5 + - + +
142A PHE* 3.5 11.7 + - + -
148A TRP* 4.3 19.7 - - + -
401A NMN 5.5 18.4 - - - +
501A APC 3.6 34.8 - - - +
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Residues in contact with LEU 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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134A CYS* 4.8 3.8 - - - -
135A GLY 3.7 2.4 + - - +
136A ALA* 3.2 14.1 + - - +
138A VAL* 1.3 80.4 - - - +
140A LYS* 1.3 60.7 + - - +
142A PHE* 3.2 36.2 + - + +
143A GLN* 4.5 4.0 + - - +
162A LEU* 3.5 35.4 - - + -
164A CYS* 3.9 27.6 - - + -
172A PRO* 4.2 17.5 - - + +
175A TYR* 4.1 9.4 - - + +
176A ILE* 4.2 25.8 - - + -
182A LEU* 4.4 14.1 - - + +
189A ILE* 5.0 2.9 - - + -
191A LEU* 4.8 0.4 - - + -
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Residues in contact with LYS 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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136A ALA 3.2 2.4 + - - -
137A ASP 3.0 11.0 + - - +
139A LEU* 1.3 79.7 - - - +
141A THR* 1.3 62.6 + - - +
142A PHE 3.2 0.7 + - - -
143A GLN* 3.2 32.8 + - - +
144A THR* 4.4 1.9 + - - -
169A SER 5.3 3.8 + - - -
170A HIS* 3.8 15.7 + - + +
175A TYR* 3.2 44.7 + - + +
55B LYS* 5.8 1.3 - - - +
137B ASP* 5.2 6.5 + - - -
167B ARG* 5.9 0.8 - - - +
402B NMN 5.9 3.8 - - - -
502B APC 3.4 48.9 + - - +
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Residues in contact with THR 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 ASP 3.4 14.8 - - - +
138A VAL* 2.5 27.3 + - + +
140A LYS* 1.3 73.9 - - + +
142A PHE* 1.3 63.8 + - - +
143A GLN 3.0 2.9 - - - -
144A THR* 2.9 27.0 + - - +
147A LEU* 3.6 22.9 - - + +
148A TRP* 3.2 19.5 + - - -
401A NMN 5.6 4.3 - - - +
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Residues in contact with PHE 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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132A LEU* 5.4 1.8 - - + -
138A VAL* 4.2 11.9 - - + -
139A LEU* 3.2 44.9 + - + +
140A LYS 3.1 2.0 - - - -
141A THR* 1.3 79.1 + - - +
143A GLN* 1.3 61.2 + - + +
144A THR 3.3 6.0 + - - +
148A TRP* 3.4 60.5 - + - +
153A ILE* 3.7 37.1 - - + +
156A ILE* 4.9 10.3 - - + -
157A VAL* 4.9 0.7 - - + -
162A LEU* 3.8 23.6 - - + -
182A LEU* 4.0 24.0 - - + -
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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