Contacts of the helix formed by residues 158 - 165 (chain B) in PDB entry 1PBW
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 LEU 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ASN* 1.3 74.1 - - - +
159B ALA* 1.3 58.4 + - - +
161B LEU* 3.3 9.9 + - + +
162B ARG* 2.9 63.4 + - - +
188B ARG* 3.3 47.8 - - - +
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Residues in contact with ALA 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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157B ASN* 3.1 14.1 + - - +
158B LEU* 1.3 79.3 - - - +
160B GLU* 1.3 58.1 - - + +
162B ARG* 3.6 6.0 + - - +
163B GLN* 2.9 52.6 + - - +
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Residues in contact with GLU 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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173A ASP* 3.9 18.7 - - + +
175A GLU* 6.0 0.3 - - - +
176A MET* 3.5 32.6 - - - +
155B SER 4.7 1.4 - - - +
156B SER* 3.3 21.9 + - - -
157B ASN* 2.7 52.5 + - - +
159B ALA* 1.3 70.3 - - + +
161B LEU* 1.3 66.3 + - - +
163B GLN* 3.3 11.6 + - - +
164B LEU* 3.2 21.5 + - - +
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Residues in contact with LEU 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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156B SER* 4.0 26.9 - - - +
157B ASN 3.2 17.2 + - - +
158B LEU* 3.5 8.1 - - - +
160B GLU* 1.3 79.5 - - - +
162B ARG* 1.3 62.3 + - - +
164B LEU* 3.2 18.5 + - - +
165B LEU* 3.2 18.2 + - - +
181B VAL* 3.9 17.9 - - + +
184B ASP* 3.8 40.8 - - + +
185B ALA* 4.0 9.4 - - + +
188B ARG* 4.5 22.9 - - + -
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Residues in contact with ARG 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 LEU* 2.9 48.6 + - + +
159B ALA* 3.9 6.1 - - - +
161B LEU* 1.3 74.5 - - - +
163B GLN* 1.3 63.1 + - + +
165B LEU* 2.8 10.3 + - + -
166B ASP* 2.6 38.1 + - - +
188B ARG* 3.8 17.3 - - + +
192B ASP* 3.0 41.2 + - - +
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Residues in contact with GLN 163 (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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159B ALA* 2.9 39.5 + - - +
160B GLU* 3.3 11.1 + - - +
162B ARG* 1.3 75.4 - - + +
164B LEU* 1.3 59.4 + - - +
166B ASP* 3.1 32.5 + - - +
169B THR* 3.5 16.3 + - + +
171B SER* 5.9 0.3 - - - -
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Residues in contact with LEU 164 (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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172A VAL* 5.5 3.8 - - + -
176A MET* 4.1 21.5 - - + -
131B LEU* 4.4 9.7 - - - +
135B LEU* 6.1 1.1 - - + -
160B GLU 3.2 10.1 + - - +
161B LEU* 3.2 11.9 + - - +
163B GLN* 1.3 76.2 - - - +
165B LEU* 1.3 63.3 + - + +
166B ASP 4.4 2.4 - - - +
167B CYS* 5.4 1.9 - - - -
171B SER* 4.2 24.3 + - - +
174B LEU* 4.2 26.1 - - + +
177B ILE* 4.1 23.1 - - + -
181B VAL* 4.2 22.2 - - + +
182B LEU* 5.0 2.2 - - + -
185B ALA* 4.0 24.7 - - + -
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Residues in contact with LEU 165 (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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115B LEU* 4.7 17.8 - - + +
131B LEU* 3.7 37.8 - - + +
135B LEU* 4.0 16.8 - - + -
161B LEU 3.4 15.3 - - - +
162B ARG* 2.8 11.0 + - - +
164B LEU* 1.3 80.1 - - + +
166B ASP* 1.3 62.7 + - - +
167B CYS* 3.1 11.6 + - - -
185B ALA* 3.8 25.6 - - + +
188B ARG* 3.9 18.2 - - + +
189B TYR* 3.8 31.0 - - + +
192B ASP* 4.8 4.3 - - - +
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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