Contacts of the helix formed by residues 149 - 159 (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 LYS 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B GLU* 5.1 3.8 - - + +
148B TRP* 1.3 73.5 - - - +
150B ASP* 1.3 66.3 + - - +
151B ALA* 4.1 13.3 - - + +
152B HIS* 2.8 63.0 + - + +
153B ILE* 3.0 11.5 + - - +
302B SO4 3.8 18.6 + - - -
402B NMN 4.7 1.2 + - - +
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Residues in contact with ASP 150 (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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142B PHE 5.5 0.5 - - - +
148B TRP 3.5 4.3 + - - +
149B LYS* 1.3 69.8 - - - +
151B ALA* 1.3 62.1 + - - +
153B ILE* 3.2 14.5 + - - +
154B GLN* 3.0 22.3 + - - +
181B ILE* 3.6 32.1 - - + +
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Residues in contact with ALA 151 (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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149B LYS* 3.0 14.5 - - - +
150B ASP* 1.3 79.3 - - - +
152B HIS* 1.3 67.6 + - + +
154B GLN* 3.5 9.1 + - - +
155B GLU* 3.1 27.4 + - - +
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Residues in contact with HIS 152 (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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92B GLU* 3.7 25.9 - - + +
94B VAL* 3.4 39.0 - - + +
95B LYS* 5.0 0.2 - - - -
98B ARG* 4.8 2.9 - - - -
148B TRP* 5.1 7.0 - - + -
149B LYS* 2.8 50.9 + - + +
151B ALA* 1.3 79.9 - - + +
153B ILE* 1.3 65.3 + - - +
154B GLN 3.1 1.3 - - - -
155B GLU* 3.2 2.9 + - - -
156B ILE* 2.9 33.0 + - + +
302B SO4 3.1 36.3 + - - -
402B NMN 4.7 5.2 + - - +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 3.7 48.0 - - + +
148B TRP* 3.8 25.4 - - + +
149B LYS 3.0 11.7 + - - +
150B ASP* 3.2 22.4 + - - +
152B HIS* 1.3 75.7 - - - +
154B GLN* 1.3 62.7 + - - +
156B ILE* 3.4 10.0 + - - +
157B VAL* 3.2 22.9 + - - +
179B SER* 5.2 1.1 - - - +
181B ILE* 3.9 17.3 - - + -
182B LEU* 3.8 28.0 - - + -
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Residues in contact with GLN 154 (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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150B ASP 3.0 16.6 + - - +
151B ALA* 3.7 8.9 - - - +
153B ILE* 1.3 74.7 - - - +
155B GLU* 1.3 61.4 + - - +
156B ILE 3.3 0.2 + - - -
157B VAL* 3.3 2.8 + - - +
158B GLU* 2.9 60.3 + - - +
181B ILE* 3.8 20.6 - - + +
184B MET* 5.4 6.1 - - - +
185B HIS* 3.8 19.4 + - - +
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Residues in contact with GLU 155 (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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94B VAL* 4.6 7.3 - - + +
98B ARG* 2.7 54.0 + - - +
151B ALA 3.1 18.1 + - - +
152B HIS* 3.2 8.2 + - - +
154B GLN* 1.3 76.5 - - - +
156B ILE* 1.3 59.1 + - - +
158B GLU* 4.6 4.3 - - - -
159B LYS* 2.9 58.6 + - + +
160B PHE* 3.3 13.3 + - + -
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Residues in contact with ILE 156 (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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93B THR* 4.9 0.7 - - + -
94B VAL* 3.4 23.8 - - + +
97B LEU* 4.1 14.4 - - + -
132B LEU* 4.1 27.1 - - + -
142B PHE* 4.7 7.4 - - + -
148B TRP* 3.9 28.3 - - + -
152B HIS 2.9 28.9 + - - +
153B ILE* 3.6 8.5 - - - +
154B GLN 3.2 0.2 - - - -
155B GLU* 1.3 79.9 - - - +
157B VAL* 1.3 61.1 + - + +
160B PHE* 3.4 8.7 + - - +
161B GLY* 2.7 40.1 + - - +
162B LEU* 4.5 7.6 - - + -
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Residues in contact with VAL 157 (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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142B PHE* 5.4 0.7 - - + -
153B ILE 3.2 16.3 + - - +
154B GLN* 3.7 2.2 - - - +
156B ILE* 1.3 79.0 - - + +
158B GLU* 1.3 59.3 + - - +
161B GLY* 4.3 6.5 - - - +
162B LEU* 3.8 26.2 - - + -
181B ILE* 4.6 2.0 - - + +
182B LEU* 3.7 30.3 - - + -
185B HIS* 3.5 41.5 - - + +
188B ASN* 3.2 26.3 - - - +
189B ILE* 3.9 14.6 - - + -
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Residues in contact with GLU 158 (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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154B GLN* 2.9 45.5 + - - +
155B GLU* 4.6 3.7 - - - -
157B VAL* 1.3 79.8 - - - +
159B LYS* 1.3 67.0 + - - +
160B PHE 3.6 0.2 - - - -
185B HIS* 3.5 27.6 - - + +
188B ASN* 3.5 13.5 - - - +
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Residues in contact with LYS 159 (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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98B ARG* 5.1 4.9 - - - -
101B HIS* 3.5 29.4 + - - -
155B GLU* 2.9 40.0 + - + +
158B GLU* 1.3 85.0 - - + +
160B PHE* 1.3 90.3 + - + +
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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