Contacts of the helix formed by residues 150 - 157 (chain B) in PDB entry 1DWQ
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 GLY 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ASP* 3.4 33.2 - - - -
131B THR* 3.3 12.9 + - - +
148B LYS 3.6 1.2 + - - -
149B LEU* 1.3 75.3 - - - +
151B PHE* 1.3 54.3 + - - -
152B VAL 3.4 2.7 - - - -
153B LEU* 3.0 5.2 + - - +
154B LEU* 2.7 32.7 + - - +
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Residues in contact with PHE 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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130B ASP* 3.1 4.7 + - - +
148B LYS* 6.3 1.3 - - + -
149B LEU 4.0 9.0 - - - -
150B GLY* 1.3 70.3 - - - -
152B VAL* 1.3 62.1 + - + +
154B LEU* 3.4 28.3 - - + -
155B ARG* 2.8 22.5 + - - +
167B TYR* 3.0 22.4 + - - +
171B LYS* 3.8 46.0 - - + -
174B MET* 5.5 5.2 - - + -
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Residues in contact with VAL 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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129B ARG* 3.3 33.0 - - + +
130B ASP* 2.8 26.8 + - + +
151B PHE* 1.3 71.2 - - + +
153B LEU* 1.4 57.7 + - - +
155B ARG* 4.4 4.3 - - + -
156B GLU* 2.7 50.5 + - - +
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Residues in contact with LEU 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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125B PHE* 3.9 21.8 - - + -
128B TRP* 3.7 34.5 - - + +
129B ARG* 3.9 9.6 - - + +
130B ASP* 3.0 15.8 + - - +
131B THR* 3.2 22.2 - - - +
149B LEU* 4.3 11.9 - - + -
150B GLY 3.0 9.8 + - - +
152B VAL* 1.4 74.7 - - - +
154B LEU* 1.3 56.4 + - - +
157B ASN* 2.7 62.6 + - + +
158B LEU* 3.3 19.0 + - + -
210B ILE* 4.3 1.6 - - + -
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Residues in contact with LEU 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 LEU* 3.6 41.1 - - + +
150B GLY 2.7 13.6 + - - +
151B PHE* 3.4 39.7 - - + +
153B LEU* 1.3 73.4 - - + +
155B ARG* 1.3 62.2 + - - +
158B LEU* 4.3 11.7 - - + -
159B PHE* 3.0 40.6 + - + +
167B TYR* 3.9 8.7 - - + -
170B ALA* 4.9 0.4 - - + -
171B LYS* 4.4 15.0 - - + +
174B MET* 4.1 27.6 - - + -
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Residues in contact with ARG 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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151B PHE 2.8 22.7 + - - +
152B VAL* 3.2 5.1 + - - +
154B LEU* 1.3 75.5 - - - +
156B GLU* 1.3 70.0 + - + +
159B PHE* 2.8 26.7 + - - -
160B THR* 3.4 28.5 + - - +
162B CYS 3.1 22.8 + - - -
164B ASP* 2.8 29.1 + - - +
167B TYR* 3.6 47.2 - - + +
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Residues in contact with GLU 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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129B ARG* 3.0 32.8 + - - +
152B VAL* 2.7 35.2 + - + +
155B ARG* 1.3 85.8 - - + +
157B ASN* 1.3 56.0 + - - +
160B THR* 2.6 29.8 + - - +
209B LYS* 3.8 6.4 - - - +
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Residues in contact with ASN 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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125B PHE* 3.7 14.3 - - - -
129B ARG* 3.1 37.0 + - - +
153B LEU* 2.7 40.5 + - + +
156B GLU* 1.3 73.8 + - - +
158B LEU* 1.3 66.2 + - + +
160B THR* 3.3 9.0 + - - -
209B LYS* 2.9 48.3 + - - +
210B ILE* 3.7 10.3 + - + +
236B HIS* 3.9 2.1 - - - +
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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