Contacts of the helix formed by residues 146 - 155 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B GLU 3.6 7.7 + - - +
143B THR* 3.2 21.7 + - - +
145B HIS* 1.3 88.7 - - + +
147B HIS* 1.4 68.9 + - - +
148B GLN* 3.2 4.7 - - - -
149B PHE* 3.0 38.4 + - + +
150B ASN* 3.7 10.0 + - - -
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Residues in contact with HIS 147 (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* 3.7 12.6 + - + +
118B GLU* 5.9 1.8 - - - +
134B TYR* 2.7 33.5 + + - +
136B THR* 3.1 23.8 + - - -
137B TYR* 4.1 9.5 + - - +
138B PRO* 3.6 28.7 - - + +
139B LEU 5.5 0.9 - - - +
143B THR* 3.2 34.4 + - + +
146B THR* 1.4 75.1 + - - +
148B GLN* 1.3 64.1 + - + +
149B PHE 3.3 1.0 + - - -
150B ASN* 3.3 24.1 + - - +
151B PHE 3.5 7.3 + - - -
169B CYS 5.2 1.3 - - - -
170B ASN* 3.1 39.8 + - + -
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Residues in contact with GLN 148 (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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134B TYR* 3.6 32.8 - - + -
145B HIS 3.8 11.2 + - - +
146B THR 3.7 1.3 - - - -
147B HIS* 1.3 80.8 + - + +
149B PHE* 1.3 72.7 + - + +
151B PHE* 3.2 3.6 + - - +
152B ILE* 2.8 41.5 + - + +
168B TYR* 3.7 25.2 - - + -
169B CYS 5.2 1.3 - - - +
170B ASN* 2.9 39.5 + - - +
173B SER* 5.3 0.6 + - - -
174B TRP* 4.2 1.8 - - - +
193B GLN* 3.0 26.7 + - - +
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Residues in contact with PHE 149 (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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145B HIS 3.5 16.2 - - - -
146B THR* 3.0 31.8 + - + +
148B GLN* 1.3 84.2 - - + +
150B ASN* 1.3 61.5 + - - +
152B ILE* 4.0 11.2 - - + +
153B LYS* 2.9 56.2 + - - +
168B TYR* 4.5 3.6 - - - -
192B THR 3.3 25.8 - - - -
193B GLN* 3.3 35.0 - - - -
196B ALA* 3.4 26.2 - - + -
197B LEU* 5.5 1.1 - - + -
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Residues in contact with ASN 150 (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* 3.7 16.5 - - + -
143B THR* 4.7 11.7 - - - +
146B THR* 3.8 16.5 + - - -
147B HIS* 3.3 16.2 + - - +
149B PHE* 1.3 75.9 - - - +
151B PHE* 1.4 62.3 + - - +
153B LYS* 5.0 6.9 + - - +
154B ASN* 3.0 39.8 + - - +
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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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65B LEU* 4.4 8.5 - - + -
67B VAL* 3.9 24.5 - - + -
89B ILE* 5.8 0.4 - - + -
117B TRP* 3.3 40.3 - + + -
121B ALA* 4.4 11.0 - - + -
132B ILE* 3.9 24.9 - - + -
134B TYR* 3.4 42.2 - + + -
147B HIS 3.5 1.2 + - - -
148B GLN 3.2 6.7 + - - +
150B ASN* 1.4 77.7 - - - +
152B ILE* 1.4 63.9 + - + +
155B HIS* 2.8 49.5 + - + -
156B ALA* 3.1 22.6 + - + -
159B LEU* 4.6 3.6 - - + -
166B LEU* 4.9 1.1 - - + -
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Residues in contact with ILE 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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134B TYR* 5.8 0.9 - - + -
148B GLN* 2.8 34.9 + - + +
149B PHE* 3.3 9.2 + - + +
151B PHE* 1.4 78.3 - - + +
153B LYS* 1.3 64.1 + - + +
156B ALA* 3.4 22.4 + - - +
157B PHE* 3.5 6.9 + - - +
166B LEU* 3.8 29.2 - - + -
168B TYR* 3.8 43.5 - - + -
196B ALA 5.3 1.3 - - - +
197B LEU* 3.8 19.5 - - + -
200B ALA* 3.8 21.2 - - + +
202B PHE* 4.0 5.6 - - + -
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Residues in contact with LYS 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 PHE* 2.9 43.9 + - - +
150B ASN* 4.3 7.3 + - - +
152B ILE* 1.3 75.3 - - + +
154B ASN* 1.3 67.1 + - - +
155B HIS 3.7 0.2 + - - -
157B PHE* 4.8 5.7 - - - +
158B ARG* 5.9 0.2 - - - +
196B ALA* 4.1 17.3 - - - +
199B GLU* 4.2 32.0 + - + +
200B ALA* 3.9 33.2 - - + +
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Residues in contact with ASN 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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117B TRP* 5.7 0.6 - - + -
150B ASN* 3.0 31.0 + - - +
153B LYS* 1.3 80.3 - - - +
155B HIS* 1.3 83.8 + - + +
158B ARG* 3.4 17.7 - - - -
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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
----------------------------------------------------------
117B TRP* 3.7 29.6 + + - -
118B GLU 4.9 1.8 + - - -
121B ALA* 3.6 17.5 - - + +
122B PRO* 3.7 36.0 - - + +
151B PHE* 2.8 25.9 + + + +
153B LYS 3.5 1.4 - - - -
154B ASN* 1.3 97.3 + - + +
156B ALA* 1.4 58.0 + - - +
157B PHE 3.3 2.0 - - - -
158B ARG* 3.2 23.2 + - - +
159B LEU* 2.9 49.8 + - + +
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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