Contacts of the helix formed by residues 152 - 159 (chain B) in PDB entry 1R74
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 GLN 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASP* 2.8 29.3 + - - +
150B GLY 3.4 0.2 - - - -
151B ASP* 1.3 79.0 - - - +
153B SER* 1.3 68.4 + - - +
154B GLU 3.2 2.5 - - - -
155B HIS* 2.9 44.0 + - + +
156B ARG* 3.2 27.1 + - - +
214B LYS* 3.2 25.0 - - - +
245B TYR* 3.2 25.9 + - - +
247B HIS* 4.3 0.7 + - - -
251B SER* 4.7 11.5 + - - -
255B LEU* 4.0 17.4 - - + +
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Residues in contact with SER 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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149B LYS* 4.8 5.2 - - - +
151B ASP* 3.0 34.1 + - - -
152B GLN* 1.3 81.2 - - - +
154B GLU* 1.3 62.8 + - - +
156B ARG* 3.1 28.5 + - - +
157B LEU* 3.1 14.6 + - - +
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Residues in contact with GLU 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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118B MET* 3.5 33.1 - - + +
145B LEU* 4.0 4.4 - - + +
146B PRO 4.0 11.0 - - - +
147B ASP* 3.4 15.1 - - - +
148B CYS* 3.3 32.7 + - - +
149B LYS* 3.5 28.9 + - + +
152B GLN 3.0 1.4 + - - -
153B SER* 1.3 74.4 + - - +
155B HIS* 1.3 62.4 + - + +
157B LEU* 3.5 1.7 + - - +
158B ALA* 3.0 31.5 + - - +
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Residues in contact with HIS 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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142B PHE* 4.1 15.7 - + + -
145B LEU* 3.1 35.9 + - + -
146B PRO 3.8 11.2 - - - -
147B ASP* 3.8 10.7 + - + +
152B GLN* 2.9 38.0 + - + +
154B GLU* 1.3 79.3 - - + +
156B ARG* 1.3 60.6 + - - +
158B ALA* 4.0 1.2 - - - +
159B LEU* 3.0 37.9 + - + +
245B TYR* 3.6 23.3 - + - -
247B HIS* 3.5 26.0 + + - -
255B LEU* 4.6 8.3 - - + -
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Residues in contact with ARG 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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151B ASP* 3.0 27.9 + - - +
152B GLN* 3.2 16.6 + - - +
153B SER* 3.2 22.8 - - - +
155B HIS* 1.3 77.7 - - - +
157B LEU* 1.3 55.5 + - - +
159B LEU* 3.8 5.6 - - - +
160B LYS* 2.8 33.3 + - - +
255B LEU* 3.8 31.3 - - + +
258B ALA* 5.7 8.3 - - + -
259B ALA* 5.1 2.3 - - - +
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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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118B MET* 3.9 42.0 - - + +
153B SER 3.1 9.4 + - - +
154B GLU 3.8 6.3 - - - +
156B ARG* 1.3 75.9 - - - +
158B ALA* 1.3 54.6 + - - +
160B LYS* 2.8 13.9 + - + +
161B ASN* 2.8 43.3 + - - +
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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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117B TRP* 3.8 33.8 - - + -
118B MET* 4.3 3.5 - - - -
142B PHE* 4.1 6.5 - - + -
145B LEU* 3.8 21.5 - - + -
154B GLU 3.0 18.7 + - - +
155B HIS 4.0 2.9 - - - +
157B LEU* 1.3 75.0 - - - +
159B LEU* 1.3 56.7 + - - +
161B ASN* 3.3 3.6 + - - +
162B ILE* 3.0 33.6 + - - +
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Residues in contact with LEU 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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142B PHE* 3.5 38.4 - - + -
155B HIS* 3.0 26.6 + - + +
156B ARG* 3.8 4.5 - - - +
158B ALA* 1.3 75.8 - - - +
160B LYS* 1.4 61.1 + - - +
162B ILE* 3.8 12.6 - - + +
163B ALA* 2.9 31.5 + - - +
172B LEU* 5.7 1.4 - - + +
174B ILE* 4.1 8.7 - - + -
252B PHE* 4.5 3.6 - - + -
255B LEU* 3.8 32.8 - - + +
256B LEU* 3.9 27.8 - - + -
259B ALA* 3.7 15.8 - - + +
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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