Contacts of the helix formed by residues 146 - 155 (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 THR 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLU 3.8 6.8 + - - +
143D THR* 3.1 23.5 + - - +
145D HIS* 1.3 86.0 - - + +
147D HIS* 1.4 66.3 + - - +
148D GLN* 3.2 4.5 - - - -
149D PHE* 3.0 39.8 + - + +
150D ASN* 3.6 11.6 + - - -
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Residues in contact with HIS 147 (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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117D TRP* 3.7 7.0 - - + +
118D GLU* 6.1 0.9 - - - +
134D TYR* 2.7 38.3 + + - +
136D THR* 3.2 24.9 + - - -
137D TYR* 4.1 9.5 + - - +
138D PRO* 3.6 31.8 - - + +
139D LEU 5.6 0.4 - - - +
143D THR* 2.9 40.9 + - - +
146D THR* 1.4 71.4 + - - +
148D GLN* 1.4 64.5 + - + +
149D PHE 3.4 0.2 + - - -
150D ASN* 3.4 22.7 + - - +
151D PHE 3.5 7.3 + - - -
169D CYS 5.2 2.0 - - - -
170D ASN* 3.5 31.9 + - + -
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Residues in contact with GLN 148 (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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134D TYR* 3.6 31.4 - - + -
145D HIS 3.7 17.8 + - - +
146D THR 4.4 0.2 - - - -
147D HIS* 1.4 85.6 + - + +
149D PHE* 1.4 65.5 + - + +
151D PHE* 3.2 4.2 + - - +
152D ILE* 2.8 40.9 + - + +
168D TYR* 3.7 27.0 - - + -
169D CYS 5.1 1.8 - - - +
170D ASN* 2.8 39.8 + - - +
173D SER* 5.1 0.6 + - - -
174D TRP* 4.3 1.4 - - - +
193D GLN* 3.0 26.7 + - - +
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Residues in contact with PHE 149 (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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145D HIS 3.6 14.6 - - - -
146D THR* 3.0 32.0 + - + +
148D GLN* 1.4 83.5 - - + +
150D ASN* 1.3 61.8 + - - +
152D ILE* 4.3 11.9 - - + +
153D LYS* 2.8 55.5 + - - +
168D TYR* 4.4 3.8 - - - -
192D THR 3.3 26.5 - - - -
193D GLN* 3.3 34.8 - - - -
196D ALA* 3.4 28.3 - - + -
197D LEU* 5.5 1.6 - - + -
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Residues in contact with ASN 150 (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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117D TRP* 3.8 14.7 - - + -
143D THR* 4.4 14.8 - - - +
146D THR* 3.7 18.7 + - - +
147D HIS* 3.6 15.7 - - - +
149D PHE* 1.3 77.4 - - - +
151D PHE* 1.4 60.9 + - - +
153D LYS* 5.0 4.7 + - - +
154D ASN* 2.9 41.6 + - - +
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Residues in contact with PHE 151 (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* 4.5 8.1 - - + -
67D VAL* 3.9 24.7 - - + -
89D ILE* 5.8 0.7 - - + -
117D TRP* 3.4 40.7 - + + -
121D ALA* 4.4 10.8 - - + -
132D ILE* 3.9 25.1 - - + -
134D TYR* 3.4 42.6 - + + -
147D HIS 3.5 1.6 + - - +
148D GLN 3.2 5.6 + - - +
150D ASN* 1.4 79.7 - - - +
152D ILE* 1.3 62.9 + - + +
155D HIS* 2.8 49.6 + - + -
156D ALA* 3.2 23.1 + - + -
159D LEU* 4.6 4.3 - - + -
166D LEU* 4.7 1.1 - - + -
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Residues in contact with ILE 152 (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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134D TYR* 5.9 0.4 - - + -
148D GLN* 2.8 34.2 + - + +
149D PHE* 3.4 10.5 + - + +
151D PHE* 1.3 79.7 - - + +
153D LYS* 1.3 64.3 + - + +
156D ALA* 3.4 20.8 + - - +
157D PHE* 3.6 6.9 + - - +
166D LEU* 3.7 28.9 - - + -
168D TYR* 3.8 42.8 - - + -
196D ALA 5.3 1.1 - - - +
197D LEU* 3.9 17.9 - - + -
200D ALA* 3.8 22.1 - - + +
202D PHE* 4.0 4.7 - - + -
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Residues in contact with LYS 153 (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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149D PHE* 2.8 43.5 + - + +
150D ASN* 4.3 6.3 + - - +
152D ILE* 1.3 75.3 - - + +
154D ASN* 1.3 66.1 + - - +
157D PHE* 4.9 4.7 - - - +
158D ARG 5.8 0.3 + - - -
196D ALA* 4.1 17.0 - - - +
199D GLU* 4.2 31.7 + - + +
200D ALA* 3.9 33.6 - - + +
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Residues in contact with ASN 154 (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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117D TRP* 5.5 2.0 - - - -
150D ASN* 2.9 35.3 + - - +
153D LYS* 1.3 82.5 - - - +
155D HIS* 1.3 84.6 + - + +
158D ARG* 3.4 16.8 - - - -
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Residues in contact with HIS 155 (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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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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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