Contacts of the helix formed by residues 136 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B GLY* 1.3 70.3 - - - -
137B ASP* 1.3 61.9 + - - +
139B LEU* 3.1 14.9 + - - +
140B LYS 3.1 9.4 + - - -
164B CYS* 3.4 13.0 - - - -
165B VAL 2.9 17.9 + - - +
167B ARG* 3.9 13.2 - - + +
170B HIS* 3.6 20.4 - - + -
172B PRO* 3.5 30.1 - - + -
175B TYR* 3.6 6.8 - - - -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 5.2 7.1 + - - -
135B GLY 3.3 1.0 - - - -
136B ALA* 1.3 73.6 - - - +
138B VAL* 1.3 65.8 + - - +
140B LYS* 3.3 10.2 + - - +
141B THR* 3.3 18.7 + - - +
167B ARG* 3.3 32.8 + - - +
170B HIS* 3.4 35.8 + - + +
502B APC 2.8 29.5 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS 6.1 0.2 - - - +
132B LEU* 5.8 2.9 - - + -
134B CYS* 3.8 19.1 - - + -
135B GLY 2.9 9.2 + - - +
137B ASP* 1.3 79.6 - - - +
139B LEU* 1.3 58.9 + - - +
141B THR* 2.5 37.8 + - - +
142B PHE* 3.6 11.1 + - + -
148B TRP* 4.3 22.0 - - + -
402B NMN 5.3 17.0 - - - +
502B APC 3.6 38.8 - - - +
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Residues in contact with LEU 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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134B CYS* 4.6 3.7 - - - -
135B GLY 3.6 2.5 + - - +
136B ALA* 3.1 14.3 + - - +
138B VAL* 1.3 79.2 - - - +
140B LYS* 1.3 61.1 + - - +
142B PHE* 3.2 26.1 + - + +
143B GLN* 4.6 2.9 + - - +
162B LEU* 4.6 19.1 - - + -
164B CYS* 3.7 31.0 - - + -
172B PRO* 4.4 15.3 - - + -
175B TYR* 3.5 25.8 - - + +
176B ILE* 4.4 18.2 - - + -
182B LEU* 3.7 24.7 - - + -
189B ILE* 5.2 0.4 - - + -
191B LEU* 4.6 0.2 - - + -
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Residues in contact with LYS 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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55A LYS* 5.9 1.1 - - - +
56A LYS* 5.3 0.7 - - - +
137A ASP* 5.3 5.7 + - - -
167A ARG* 5.8 0.8 - - - +
201A SER* 5.9 1.8 - - - -
203A THR* 5.2 0.4 - - - -
401A NMN 6.1 1.3 - - - -
501A APC 2.7 44.9 + - - +
136B ALA 3.1 6.8 + - - +
137B ASP 3.6 8.7 - - - +
138B VAL 3.2 0.2 - - - -
139B LEU* 1.3 77.2 - - - +
141B THR* 1.3 62.0 + - - +
143B GLN* 3.2 34.2 + - - +
144B THR* 4.2 1.9 + - - -
169B SER 5.5 2.8 + - - -
170B HIS* 4.1 12.4 - - + +
175B TYR* 3.3 48.4 + - + +
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Residues in contact with THR 141 (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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137B ASP 3.3 16.6 - - - +
138B VAL* 2.5 23.3 + - - +
140B LYS* 1.3 73.7 - - + +
142B PHE* 1.3 62.3 + - - +
143B GLN 2.9 7.4 + - - -
144B THR* 3.0 24.6 + - - +
147B LEU* 3.7 18.3 - - + +
148B TRP* 3.0 29.3 + - - -
402B NMN 5.5 4.7 - - - +
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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