Contacts of the helix formed by residues 149 - 156 (chain Q) in PDB entry 5A31
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 ASN 149 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102Q CYS 5.4 0.6 + - - -
103Q TYR* 3.7 27.5 - - - +
104Q HIS 3.3 21.2 + - - +
105Q PRO* 2.9 8.2 + - - +
107Q VAL 3.5 9.7 + - - +
108Q ASP* 5.5 0.6 - - - -
109Q THR* 5.9 4.8 - - - +
147Q PRO* 4.4 1.3 - - - -
148Q LEU* 1.3 79.1 - - - +
150Q THR* 1.3 58.6 + - - +
151Q HIS* 3.1 12.8 + - - +
152Q ALA* 2.9 21.8 + - - +
153Q ALA* 3.0 26.5 + - - +
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Residues in contact with THR 150 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Q PRO* 4.4 20.4 - - + +
148Q LEU 4.3 1.3 + - - -
149Q ASN* 1.3 71.8 + - - +
151Q HIS* 1.3 68.1 + - - +
153Q ALA* 3.3 6.7 + - + +
154Q GLU* 2.9 38.3 + - - +
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Residues in contact with HIS 151 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q TYR* 2.6 32.6 + - + -
149Q ASN* 3.1 8.4 + - - +
150Q THR* 1.3 82.5 + - - +
152Q ALA* 1.3 56.4 + - - +
154Q GLU* 3.2 9.8 + - - +
155Q LEU* 2.9 42.7 + - + +
165Q TYR* 4.1 27.3 + + - -
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Residues in contact with ALA 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q TYR* 3.2 32.7 + - + -
104Q HIS 3.6 31.0 - - - +
105Q PRO* 3.6 2.0 - - - -
149Q ASN* 2.9 17.6 + - - +
151Q HIS* 1.3 77.8 - - - +
153Q ALA* 1.3 58.6 + - - +
155Q LEU 4.4 0.4 - - - +
156Q TRP* 2.9 30.7 + - - +
162Q PHE* 3.5 8.6 - - + -
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Residues in contact with ALA 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Q PRO* 3.9 17.6 - - + +
144Q ILE* 4.1 28.0 - - + +
147Q PRO* 3.9 22.4 - - + -
149Q ASN 3.0 17.2 + - - +
150Q THR* 3.3 6.7 + - - +
152Q ALA* 1.3 79.1 - - - +
154Q GLU* 1.3 63.3 + - + +
156Q TRP* 3.5 12.5 + - - +
157Q LYS* 4.5 1.7 + - - +
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Residues in contact with GLU 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Q THR* 2.9 28.0 + - - +
151Q HIS* 3.7 8.2 - - - +
153Q ALA* 1.3 78.6 - - + +
155Q LEU* 1.3 63.0 + - - +
156Q TRP 3.5 0.3 + - - -
157Q LYS* 3.4 34.3 + - - +
158Q ASN* 5.0 0.7 + - - -
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Residues in contact with LEU 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q TYR* 3.6 20.0 - - + +
151Q HIS* 2.9 25.2 + - + +
152Q ALA 3.9 2.0 - - - +
153Q ALA 3.3 0.2 - - - -
154Q GLU* 1.3 74.2 - - - +
156Q TRP* 1.3 65.2 + - - +
157Q LYS 3.1 3.1 - - - -
158Q ASN* 2.9 29.8 + - + +
161Q ALA* 4.0 22.0 - - + +
162Q PHE* 3.8 27.0 - - + +
165Q TYR* 4.0 21.5 - - + -
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Residues in contact with TRP 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Q THR* 6.2 0.2 - - - -
73Q VAL* 3.8 22.0 - - + -
74Q TYR* 4.0 8.1 - + - -
105Q PRO* 4.4 5.4 - - + -
139Q LEU 3.6 18.6 - - - -
140Q GLY* 3.6 13.9 - - - -
142Q PRO* 3.4 30.4 - - + +
144Q ILE* 4.0 24.5 - - + -
152Q ALA 2.9 16.4 + - - +
153Q ALA 3.5 10.1 - - - +
154Q GLU 3.3 0.6 - - - -
155Q LEU* 1.3 76.3 - - - +
157Q LYS* 1.3 61.6 + - - +
158Q ASN 3.0 6.0 + - - -
159Q PRO* 3.9 12.5 - - - +
162Q PHE* 3.7 48.1 - + - +
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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