Contacts of the helix formed by residues 146 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A GLU 3.7 6.9 + - - +
143A THR* 3.2 21.9 + - - +
145A HIS* 1.3 92.0 - - + +
147A HIS* 1.4 67.4 + - - +
148A GLN* 3.2 3.8 - - - -
149A PHE* 3.1 37.9 + - + +
150A ASN* 3.6 10.8 + - - -
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Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.8 7.0 + - + +
134A TYR* 2.7 39.8 + + - +
136A THR* 3.3 23.5 + - - -
137A TYR* 3.9 12.2 + - - -
138A PRO* 3.6 29.1 - - + +
139A LEU 5.2 1.1 - - - +
143A THR* 2.9 36.6 + - - +
146A THR* 1.4 71.2 + - - +
148A GLN* 1.3 61.9 + - + +
149A PHE 3.4 0.5 + - - -
150A ASN* 3.4 23.4 + - - +
151A PHE 3.5 7.3 + - - -
169A CYS 5.2 1.8 - - - -
170A ASN* 3.4 38.2 + - + +
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.6 31.6 - - + -
145A HIS 3.6 17.3 + - - +
146A THR 3.7 0.9 - - - -
147A HIS* 1.3 81.7 + - + +
149A PHE* 1.3 72.1 + - + +
151A PHE* 3.3 4.2 + - - +
152A ILE* 2.8 35.6 + - + +
168A TYR* 3.7 26.5 - - + -
169A CYS 5.1 1.6 - - - +
170A ASN* 2.8 39.0 + - - +
173A SER* 5.2 0.6 + - - -
174A TRP* 4.3 2.0 - - - +
193A GLN* 3.1 26.1 + - - +
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS 3.5 16.2 - - - -
146A THR* 3.1 33.1 + - + +
148A GLN* 1.3 85.0 - - + +
150A ASN* 1.3 61.1 + - - +
152A ILE* 4.4 11.0 - - + +
153A LYS* 2.8 57.0 + - - +
168A TYR* 4.4 4.3 - - - -
192A THR 3.3 24.9 - - - -
193A GLN* 3.3 34.8 - - - -
196A ALA* 3.4 29.2 - - + -
197A LEU* 5.5 1.6 - - + -
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Residues in contact with ASN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.8 16.7 - - + -
143A THR* 4.4 15.4 - - - +
146A THR* 3.7 17.9 + - - +
147A HIS* 3.4 15.4 + - - +
148A GLN 3.3 0.4 - - - -
149A PHE* 1.3 75.0 - - - +
151A PHE* 1.3 62.2 + - - +
153A LYS* 5.0 6.4 + - - +
154A ASN* 2.9 41.6 + - - +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.4 8.7 - - + -
67A VAL* 3.9 24.2 - - + -
89A ILE* 5.8 0.4 - - + -
117A TRP* 3.4 39.9 - + + -
121A ALA* 4.4 11.0 - - + -
132A ILE* 3.9 25.4 - - + -
134A TYR* 3.4 42.6 - + + -
147A HIS 3.5 1.4 + - - -
148A GLN 3.3 6.4 + - - +
150A ASN* 1.3 80.5 - - - +
152A ILE* 1.3 62.9 + - + +
155A HIS* 2.8 48.8 + - + -
156A ALA* 3.1 23.6 + - + -
159A LEU* 4.7 3.6 - - + -
166A LEU* 4.6 0.9 - - + -
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 5.8 0.7 - - + -
148A GLN* 2.8 33.8 + - + +
149A PHE* 4.0 9.2 - - + +
151A PHE* 1.3 80.8 - - + +
153A LYS* 1.4 62.7 + - + +
156A ALA* 3.4 21.5 + - + +
157A PHE* 3.5 6.9 + - - +
166A LEU* 3.8 26.7 - - + -
168A TYR* 3.7 44.6 - - + -
196A ALA 5.3 1.1 - - - +
197A LEU* 3.9 19.5 - - + -
200A ALA* 3.8 21.7 - - + +
202A PHE* 3.9 6.5 - - + -
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 2.8 44.5 + - - +
150A ASN* 4.3 6.5 + - - +
152A ILE* 1.4 75.6 - - + +
154A ASN* 1.3 66.9 + - - +
157A PHE* 4.8 5.4 - - - +
158A ARG* 5.8 0.5 + - - +
196A ALA* 4.1 16.8 - - + +
199A GLU* 4.2 29.5 + - + +
200A ALA* 3.9 32.9 - - + +
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Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 5.5 2.2 - - - -
150A ASN* 2.9 34.6 + - - +
153A LYS* 1.3 81.6 - - - +
155A HIS* 1.4 84.9 + - + +
158A ARG* 3.4 17.3 - - - +
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Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.7 29.9 + + - -
118A GLU 4.9 2.2 + - - -
121A ALA* 3.6 26.2 - - + +
122A PRO* 3.8 26.6 - - + +
151A PHE* 2.8 24.2 + + + +
153A LYS 3.5 0.8 - - - -
154A ASN* 1.4 97.6 + - + +
156A ALA* 1.4 64.7 + - - +
157A PHE 3.3 2.5 - - - -
158A ARG* 3.2 24.9 + - - +
159A LEU* 2.9 44.6 + - + +
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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