Contacts of the helix formed by residues 150 - 160 (chain B) in PDB entry 2NYM
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 ASP 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B LYS 4.9 5.9 - - - +
147B LYS* 5.2 8.7 - - - +
148B TYR 3.8 1.4 - - - -
149B ILE* 1.3 77.1 - - - +
151B GLN* 1.3 86.7 + - - +
152B LYS* 3.0 14.0 + - + +
153B PHE* 2.4 38.0 + - - +
154B VAL* 3.2 5.7 + - - -
186B LEU* 4.8 5.8 - - - +
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Residues in contact with GLN 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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150B ASP* 1.3 91.1 + - - +
152B LYS* 1.3 56.3 + - - +
154B VAL* 2.9 18.4 + - - +
155B LEU* 2.9 30.5 + - - +
185B GLY 5.7 2.0 + - - -
186B LEU* 4.3 11.1 - - + +
189B TYR* 3.3 57.4 - - + +
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Residues in contact with LYS 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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216A GLU* 5.0 13.7 - - - +
150B ASP* 2.8 13.5 + - + +
151B GLN* 1.3 75.7 - - - +
153B PHE* 1.3 57.6 + - - +
155B LEU* 4.3 11.1 - - + +
156B GLN* 3.1 46.4 + - + +
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Residues in contact with PHE 153 (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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86B VAL* 4.5 13.2 - - + -
89B PHE* 3.4 33.0 - + - -
90B ALA* 4.1 9.4 - - + -
94B PHE* 3.3 38.7 - + - -
131B PHE* 3.6 26.2 - + - -
148B TYR 5.0 2.0 - - - +
149B ILE* 3.6 29.2 - - + -
150B ASP 2.4 31.2 + - - +
152B LYS* 1.3 71.9 - - - +
154B VAL* 1.3 68.2 + - + +
156B GLN* 3.4 1.8 + - - +
157B LEU* 2.9 26.2 + - + +
179B ILE* 4.0 19.1 - - + -
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Residues in contact with VAL 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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149B ILE* 5.2 0.2 - - + -
150B ASP 3.8 2.9 - - - +
151B GLN* 3.1 19.1 - - - +
153B PHE* 1.3 81.7 - - + +
155B LEU* 1.3 57.5 - - - +
157B LEU* 2.6 34.5 + - - +
158B LEU* 2.8 26.5 + - + +
176B LEU* 4.7 5.4 - - + -
179B ILE* 5.2 5.8 - - + -
186B LEU* 3.8 23.3 - - + -
189B TYR* 4.2 9.4 - - + -
190B ILE* 3.1 42.6 - - + -
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Residues in contact with LEU 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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216A GLU* 3.5 42.2 - - + +
217A GLN* 4.1 24.0 - - - +
151B GLN 2.9 13.1 + - - +
152B LYS* 4.3 9.0 - - + +
154B VAL* 1.3 78.8 - - - +
156B GLN* 1.3 67.8 + - + +
158B LEU* 2.9 29.9 + - + +
159B GLU* 3.3 14.6 + - + +
189B TYR* 3.5 21.5 - - + +
193B GLN* 3.8 19.5 - - - +
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Residues in contact with GLN 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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94B PHE* 3.3 51.9 - - + +
152B LYS* 3.1 41.8 + - + +
153B PHE* 3.4 1.0 + - - +
154B VAL 3.3 0.8 - - - -
155B LEU* 1.3 81.7 - - + +
157B LEU* 1.3 62.0 + - - +
158B LEU 3.5 0.2 + - - -
159B GLU* 3.9 14.7 + - - +
160B LEU* 3.3 21.5 + - - +
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Residues in contact with LEU 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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89B PHE* 3.9 26.5 - - + -
94B PHE* 3.8 4.7 - - + -
153B PHE* 2.9 16.1 + - + +
154B VAL* 2.6 22.2 + - - +
156B GLN* 1.3 73.3 - - - +
158B LEU* 1.3 56.4 + - - +
160B LEU* 2.8 34.4 - - + +
161B PHE* 3.9 8.3 - - + -
172B LEU* 3.4 29.8 - - + +
175B THR* 4.2 13.0 - - + -
176B LEU* 4.4 24.5 - - + +
179B ILE* 4.0 27.6 - - + -
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Residues in contact with LEU 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 VAL* 2.8 27.9 + - + +
155B LEU* 2.9 15.6 + - + +
157B LEU* 1.3 73.7 - - + +
159B GLU* 1.3 68.8 + - - +
161B PHE* 2.6 49.7 + - + +
176B LEU* 3.5 20.4 - - + -
190B ILE* 4.5 5.2 - - - +
193B GLN* 3.6 42.0 - - + +
194B ILE* 4.5 5.6 - - + +
197B ILE* 4.4 17.0 - - + +
214B LEU* 4.1 11.9 - - + -
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Residues in contact with GLU 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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216A GLU 5.1 4.9 - - - +
217A GLN* 3.9 23.9 + - - +
218A ASP* 4.7 14.7 + - - +
258A ARG* 6.0 0.2 + - - -
95B ARG 5.5 0.7 - - - +
96B THR* 5.3 11.1 - - - +
97B LEU* 4.0 20.4 - - + +
155B LEU* 3.3 15.0 + - + +
156B GLN* 4.1 13.2 - - - +
158B LEU* 1.3 76.7 - - - +
160B LEU* 1.3 57.2 + - + +
161B PHE* 2.5 16.6 + - - +
162B ASP* 3.4 20.0 + - - +
197B ILE* 4.8 7.1 - - + +
208B HIS* 5.4 1.1 + - - -
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Residues in contact with LEU 160 (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 MSE 3.4 30.3 - - + +
94B PHE* 3.4 30.1 - - + +
95B ARG* 4.0 30.1 - - - +
97B LEU* 3.9 16.3 - - + +
128B TYR* 4.7 0.2 - - - +
156B GLN 3.3 19.5 - - - +
157B LEU* 2.8 25.1 - - + +
159B GLU* 1.3 78.5 - - + +
161B PHE* 1.3 46.8 - - - +
162B ASP* 2.2 22.2 + - - -
163B SER 4.4 1.0 + - - -
168B GLU* 4.4 8.9 - - - +
172B LEU* 3.5 25.9 - - + +
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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