Contacts of the helix formed by residues 155 - 162 (chain B) in PDB entry 1AD5
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 ARG 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B SER* 1.3 68.5 - - - +
156B LYS* 1.4 72.1 + - + +
158B ALA* 3.1 17.8 - - - +
159B GLU* 3.1 15.4 + - - +
175B ARG* 3.6 26.4 - - - +
178B GLU* 3.6 33.3 + - - +
179B THR* 5.3 4.4 - - - +
201B HIS* 3.4 33.7 + - + +
517B ASP* 5.4 0.2 - - - +
518B ASP* 2.7 43.9 + - - -
526B GLN* 3.8 29.0 + - - +
527B PTR 3.4 32.3 + - - +
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Residues in contact with LYS 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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154B SER* 3.2 6.4 + - - +
155B ARG* 1.4 81.5 - - + +
157B ASP* 1.3 60.9 + - - +
159B GLU* 2.8 54.7 + - - +
160B ARG* 2.8 43.2 + - - +
178B GLU* 5.0 1.1 + - - +
365B ASP* 4.6 6.9 + - - -
368B ALA* 6.0 0.2 - - - -
372B GLU* 4.9 2.2 - - - +
517B ASP* 2.8 58.5 + - + +
518B ASP* 4.4 9.6 + - - +
521B THR* 5.7 1.8 + - - -
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Residues in contact with ASP 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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153B ILE* 4.0 20.1 - - + +
154B SER* 2.9 24.8 + - - +
156B LYS* 1.3 76.8 - - - +
158B ALA* 1.3 57.0 + - - +
160B ARG* 3.4 22.5 + - - +
161B GLN* 2.9 35.2 + - + +
320B ASP* 4.0 10.0 - - - +
321B LYS* 2.9 33.1 + - - -
372B GLU* 4.8 0.7 - - - +
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Residues in contact with ALA 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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153B ILE* 3.6 23.2 - - + +
154B SER 2.9 7.3 + - - +
155B ARG 3.1 13.0 - - - +
157B ASP* 1.3 75.0 - - - +
159B GLU* 1.3 58.4 + - - +
161B GLN* 3.3 1.7 + - - +
162B LEU* 2.9 34.8 + - - +
173B MET* 3.9 15.4 - - + +
175B ARG* 4.0 17.0 - - - +
187B SER* 4.2 9.2 - - - +
199B VAL* 5.4 0.4 - - - -
201B HIS* 4.6 1.1 - - - +
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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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155B ARG* 3.1 17.0 + - - +
156B LYS* 2.8 45.5 + - - +
158B ALA* 1.3 77.5 - - - +
160B ARG* 1.3 66.0 + - + +
162B LEU 3.9 0.2 - - - -
163B LEU* 3.0 36.0 + - + +
199B VAL* 3.9 27.9 - - + +
201B HIS* 3.4 28.1 - - + +
518B ASP* 5.1 2.3 - - - +
521B THR* 5.6 1.9 + - - -
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Residues in contact with ARG 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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156B LYS* 2.8 33.6 + - - +
157B ASP* 3.4 31.7 + - - +
159B GLU* 1.3 79.1 - - + +
161B GLN* 1.3 64.2 + - + +
163B LEU* 3.3 6.2 + - - +
164B ALA* 3.2 20.8 + - - +
321B LYS* 3.8 1.5 - - - +
362B LYS* 5.4 4.7 - - - +
365B ASP* 2.9 49.9 + - - +
368B ALA* 3.8 8.7 - - - +
369B GLN* 3.5 22.7 - - - +
372B GLU* 3.0 36.4 + - - -
517B ASP* 4.1 3.8 + - - -
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Residues in contact with GLN 161 (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 PHE* 3.9 26.1 - - - -
153B ILE* 4.0 20.3 - - + +
157B ASP* 2.9 19.0 + - + +
158B ALA 3.6 3.6 - - - +
160B ARG* 1.3 80.1 - - + +
162B LEU* 1.3 60.7 - - - +
164B ALA* 3.3 14.5 - - - +
167B ASN* 3.2 15.8 + - - -
173B MET* 4.0 7.9 - - + +
245B CYS* 3.7 10.4 - - - -
246B MET 3.8 14.6 - - - +
247B SER* 4.9 0.2 - - - -
248B SER* 3.0 30.2 + - - +
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Residues in contact with LEU 162 (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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158B ALA 2.9 16.2 + - - +
161B GLN* 1.3 75.8 - - - +
163B LEU* 1.3 57.7 + - - +
164B ALA 3.3 0.9 - - - -
167B ASN* 3.4 14.6 - - - +
171B SER* 3.5 36.1 - - - +
172B PHE* 4.0 1.1 - - - +
173B MET* 3.9 9.4 - - + -
187B SER* 3.6 42.8 - - - +
188B VAL* 4.2 1.3 - - - +
189B ARG* 3.1 25.3 + - + +
199B VAL* 4.0 21.3 - - + -
245B CYS* 3.5 31.4 - - + -
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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