Contacts of the helix formed by residues 154 - 159 (chain B) in PDB entry 1IAX
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 ALA 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.1 42.6 + - + +
153B PRO* 1.3 80.6 - - - +
155B PHE* 1.3 52.8 + - - +
157B ARG* 3.0 15.2 + - - +
158B ASP* 2.7 52.2 + - - +
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Residues in contact with PHE 155 (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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131B ASN* 3.7 24.2 - - - -
147B VAL* 4.1 16.8 - - + -
151B TYR* 3.6 25.6 - + + -
152B TYR* 3.2 39.7 + + + +
153B PRO 2.9 0.2 - - - -
154B ALA* 1.3 78.8 - - - +
156B ASN* 1.3 64.3 + - - +
158B ASP* 4.1 2.0 - - + -
159B LEU* 2.8 63.1 + - + +
160B ARG 3.6 1.0 + - - -
167B LEU* 4.1 4.2 - - + +
203B ILE* 3.9 15.5 - - + -
205B THR* 3.8 23.8 - - + -
237B ASP* 3.9 16.4 - - - -
501B PLP 5.5 0.2 - - + -
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Residues in contact with ASN 156 (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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151B TYR* 2.6 32.1 + - - -
153B PRO* 3.0 34.5 + - - +
155B PHE* 1.3 76.1 - - - +
157B ARG* 1.3 55.7 + - - +
160B ARG* 3.1 56.4 + - - +
161B TRP* 4.2 0.9 + - - -
167B LEU* 3.9 1.2 - - - +
402B SER 5.1 0.6 + - - -
404B GLU* 4.4 14.9 + - - +
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Residues in contact with ARG 157 (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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92A TYR* 3.4 35.8 + - - -
303A LYS* 4.1 10.9 + - - +
306A SER* 3.4 14.9 + - - -
307A PHE* 4.7 6.5 - - + -
128B THR* 3.9 14.9 + - - +
153B PRO 4.2 0.6 + - - +
154B ALA* 3.0 16.5 + - - +
155B PHE 3.0 0.2 - - - -
156B ASN* 1.3 79.1 - - - +
158B ASP* 1.3 92.3 + - - +
159B LEU 3.4 0.2 - - - -
161B TRP* 2.5 68.5 + - + +
162B ARG 4.6 0.3 + - - -
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Residues in contact with ASP 158 (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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307A PHE* 4.3 8.7 - - - -
128B THR* 3.4 41.0 + - - +
131B ASN* 4.3 8.0 + - + -
132B GLU* 3.5 30.8 - - - +
152B TYR* 4.6 2.6 + - - -
154B ALA* 2.7 34.9 + - - +
155B PHE* 4.1 4.5 - - + +
157B ARG* 1.3 105.0 + - - +
159B LEU* 1.3 67.8 + - + +
161B TRP 4.7 0.3 + - - -
162B ARG 5.5 0.2 + - - -
163B THR* 4.5 0.7 - - - +
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Residues in contact with LEU 159 (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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131B ASN* 3.5 32.3 - - + -
135B ILE* 3.7 36.5 - - + +
155B PHE* 2.8 59.7 + - + +
158B ASP* 1.3 72.4 - - - +
160B ARG* 1.3 54.3 + - - +
163B THR* 2.4 28.2 + - - +
165B VAL* 3.9 6.5 - - + +
167B LEU* 4.0 25.6 - - + -
203B ILE* 4.1 23.6 - - + -
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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