Contacts of the helix formed by residues 149 - 160 (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 LYS 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLU* 3.2 24.7 + - - -
146A ASN 6.1 0.7 - - - +
148A TRP* 1.3 73.7 - - - +
150A ASP* 1.3 57.4 + - - +
151A ALA* 4.3 5.8 - - + +
152A HIS* 2.6 62.2 + - + +
153A ILE* 2.9 11.1 + - - +
301A SO4 4.1 9.1 + - - +
401A NMN 4.7 1.0 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A TRP 3.5 5.1 + - - +
149A LYS* 1.3 70.3 - - - +
151A ALA* 1.3 57.1 + - - +
153A ILE* 3.3 16.4 + - - +
154A GLN* 2.9 30.0 + - - +
181A ILE* 3.5 25.4 - - + +
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Residues in contact with ALA 151 (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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149A LYS* 3.0 5.1 - - + +
150A ASP* 1.3 78.8 - - - +
152A HIS* 1.3 66.6 + - + +
154A GLN* 3.8 9.3 - - - +
155A GLU* 3.0 28.4 + - - +
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Residues in contact with HIS 152 (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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92A GLU* 3.9 27.5 - - + +
94A VAL* 3.5 33.9 - - + +
95A LYS* 5.3 0.7 - - - -
98A ARG* 4.4 3.8 - - - -
148A TRP* 5.0 5.4 - - + -
149A LYS* 2.6 51.4 + - + +
151A ALA* 1.3 77.0 - - + +
153A ILE* 1.3 55.9 - - - +
154A GLN 3.1 1.3 - - - -
155A GLU* 4.3 3.4 - - - +
156A ILE* 2.7 46.3 + - + +
301A SO4 3.1 37.1 + - - -
401A NMN 4.8 5.6 + - - +
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Residues in contact with ILE 153 (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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142A PHE* 3.7 46.4 - - + +
148A TRP* 3.6 25.1 - - + +
149A LYS 2.9 14.2 + - - +
150A ASP* 3.3 25.1 + - - +
152A HIS* 1.3 75.1 - - - +
154A GLN* 1.3 62.7 + - - +
156A ILE* 3.6 8.8 - - - +
157A VAL* 3.1 25.3 + - - +
179A SER* 5.5 0.9 - - - +
181A ILE* 3.9 21.9 - - + +
182A LEU* 4.1 20.6 - - + -
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Residues in contact with GLN 154 (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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150A ASP 2.9 17.2 + - - +
151A ALA* 3.8 8.4 - - - +
152A HIS 3.1 0.2 - - - -
153A ILE* 1.3 75.3 - - - +
155A GLU* 1.3 61.5 + - - +
157A VAL* 3.4 1.9 + - - +
158A GLU* 2.8 54.7 + - - +
181A ILE* 3.7 23.2 - - + +
184A MET* 5.7 4.5 - - - +
185A HIS* 4.2 18.4 + - + +
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Residues in contact with GLU 155 (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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94A VAL* 3.5 16.5 - - + +
98A ARG* 2.7 48.4 + - - +
151A ALA 3.0 18.7 + - - +
152A HIS* 3.2 5.6 + - - +
154A GLN* 1.3 78.2 - - - +
156A ILE* 1.3 59.2 + - - +
158A GLU* 4.7 2.0 - - - -
159A LYS* 2.8 57.3 + - + +
160A PHE* 3.6 8.3 + - + -
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A THR* 4.6 5.8 - - + -
94A VAL* 4.0 22.2 - - + +
97A LEU* 4.0 18.6 - - + -
132A LEU* 4.4 9.6 - - + -
142A PHE* 4.9 7.0 - - + -
148A TRP* 3.5 37.5 - - + -
152A HIS* 2.7 30.7 + - + +
153A ILE* 3.6 5.6 - - - +
155A GLU* 1.3 74.1 - - - +
157A VAL* 1.3 61.0 + - + +
160A PHE* 3.4 12.0 + - - +
161A GLY 2.8 25.7 + - - +
162A LEU* 4.2 27.4 - - + -
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Residues in contact with VAL 157 (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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142A PHE* 4.9 2.0 - - + -
153A ILE 3.1 17.5 + - - +
154A GLN* 4.3 2.0 - - - +
156A ILE* 1.3 78.5 - - + +
158A GLU* 1.3 59.2 + - - +
161A GLY* 3.8 8.0 + - - +
162A LEU* 3.5 29.6 - - + -
181A ILE* 5.5 2.0 - - + +
182A LEU* 3.6 19.7 - - + -
185A HIS* 3.5 26.7 - - + +
188A ASN* 3.1 25.2 - - + +
189A ILE* 3.4 28.9 - - + -
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Residues in contact with GLU 158 (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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154A GLN* 2.8 43.6 + - - +
155A GLU* 4.4 1.5 - - - +
157A VAL* 1.3 74.1 - - - +
159A LYS* 1.3 87.7 + - - +
185A HIS* 3.5 36.9 - - + +
188A ASN* 3.2 16.2 - - - +
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Residues in contact with LYS 159 (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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101A HIS* 5.7 3.8 - - - -
155A GLU* 2.8 40.4 + - + +
158A GLU* 1.3 98.4 + - + +
160A PHE* 1.3 76.6 + - + +
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Residues in contact with PHE 160 (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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94A VAL* 4.3 6.5 - - + -
97A LEU* 3.8 40.8 - - + -
98A ARG* 3.8 26.0 - - + -
101A HIS* 3.7 33.2 - + + -
129A GLU* 4.8 3.8 - - - +
130A LEU* 3.0 39.2 + - + +
131A LYS* 3.4 17.7 + - - +
155A GLU* 3.6 33.2 - - + -
156A ILE* 3.4 9.8 + - - +
157A VAL 4.6 0.4 - - - -
158A GLU 3.4 1.1 - - - -
159A LYS* 1.3 95.1 - - + +
161A GLY* 1.3 62.3 + - - +
188A ASN* 5.0 1.7 - - - +
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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