Contacts of the helix formed by residues 155 - 159 (chain D) in PDB entry 3ORH
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 HIS 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.7 28.7 + + - -
118D GLU* 4.9 2.0 + - - -
121D ALA* 3.6 18.6 - - + +
122D PRO* 3.7 36.1 - - + +
151D PHE* 2.8 25.6 + + + +
153D LYS 3.5 1.2 - - - -
154D ASN* 1.3 99.9 + - + +
156D ALA* 1.4 64.9 + - - +
157D PHE 3.3 2.5 - - - -
158D ARG* 3.2 22.9 + - - +
159D LEU* 2.9 43.3 + - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 3.7 13.3 - - + +
151D PHE* 3.2 21.2 + - + -
152D ILE* 3.4 19.9 + - + +
155D HIS* 1.4 74.0 - - - +
157D PHE* 1.3 62.9 + - - +
160D LEU* 3.2 31.1 + - - +
166D LEU* 3.7 34.8 - - + -
202D PHE* 4.4 1.8 - - + -
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Residues in contact with PHE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE 3.6 7.0 + - - +
153D LYS 4.9 4.9 - - - +
155D HIS 3.3 0.6 - - - -
156D ALA* 1.3 81.0 - - - +
158D ARG* 1.3 63.2 + - + +
160D LEU 3.6 1.0 + - - -
200D ALA 3.4 26.2 - - - +
201D GLY* 3.2 31.6 - - - -
202D PHE* 3.8 29.5 - + + -
235D LYS* 2.8 60.7 + - + +
236D GLY 5.3 2.2 - - - -
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Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA 3.5 14.1 + - - -
122D PRO* 4.3 9.3 + - - +
124D LEU 2.6 28.9 + - - -
126D ASP* 2.7 42.9 + - - +
127D GLY* 2.7 30.5 + - - -
154D ASN 3.4 20.8 - - - +
155D HIS* 3.2 38.1 + - - +
157D PHE* 1.3 83.2 - - + +
159D LEU* 1.3 65.4 + - - +
160D LEU 3.9 0.9 - - - +
235D LYS* 4.2 5.3 + - - +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.8 25.8 - - + -
121D ALA* 4.8 3.1 - - + -
124D LEU* 3.7 26.9 - - + -
125D PRO 3.4 20.9 - - - +
127D GLY 3.7 1.8 - - - +
128D HIS 2.9 24.6 + - - -
129D PHE* 3.1 19.2 + - + -
132D ILE* 3.9 13.2 - - + -
151D PHE* 4.6 4.7 - - + -
155D HIS* 2.9 39.0 + - + +
158D ARG* 1.3 99.2 - - - +
160D LEU* 1.3 60.5 + - - +
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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