Contacts of the helix formed by residues 143 - 150 (chain B) in PDB entry 1YAA
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 HIS 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B LEU* 4.2 10.9 - - + +
135B LEU* 4.0 19.0 - - + +
139B THR* 2.8 26.4 + - + -
140B TRP* 3.3 37.0 + + + +
142B ASN* 1.3 78.5 - - - +
144B MET* 1.3 63.4 + - - +
146B ILE* 3.4 8.4 + - + +
147B PHE* 3.0 35.6 + + - -
187B VAL* 3.7 23.8 - - + +
189B HIS* 3.6 15.5 - + - -
222B ASP* 2.7 32.1 + - - +
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Residues in contact with MET 144 (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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135B LEU* 3.9 21.6 - - + +
139B THR* 5.5 0.4 - - + +
140B TRP 4.7 1.6 + - - -
141B ALA 4.9 4.9 + - - +
142B ASN 3.4 0.4 - - - -
143B HIS* 1.3 78.7 - - - +
145B ALA* 1.3 58.3 - - - +
147B PHE* 3.3 2.8 + - - +
148B GLU* 2.9 61.6 + - + +
154B THR* 3.7 20.9 - - - +
155B ALA 5.9 1.6 - - - +
156B THR* 6.5 1.3 - - - -
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Residues in contact with ALA 145 (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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289A LYS* 4.8 18.2 - - + -
293A SER* 3.9 11.4 - - - -
141B ALA 5.3 2.2 + - - +
142B ASN* 3.4 22.4 + - - +
143B HIS 3.4 0.4 - - - -
144B MET* 1.3 76.8 - - - +
146B ILE* 1.3 59.9 + - - +
148B GLU* 4.4 5.8 - - - +
149B ASN* 2.8 35.2 + - - +
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Residues in contact with ILE 146 (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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293A SER* 3.6 25.8 - - - +
109B THR* 3.9 11.7 - - + -
112B LEU* 3.5 44.6 - - + +
113B HIS* 4.1 6.3 + - + +
116B ALA* 3.8 2.0 - - + +
140B TRP* 3.6 22.2 - - + -
142B ASN* 3.1 40.2 + - - +
143B HIS* 3.7 9.9 - - + +
144B MET 3.3 0.4 - - - -
145B ALA* 1.3 77.6 - - - +
147B PHE* 1.3 64.3 + - + +
149B ASN* 3.7 4.3 + - - +
150B GLN* 3.7 19.4 - - - +
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Residues in contact with PHE 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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112B LEU* 4.5 17.3 - - + -
116B ALA* 3.8 27.4 - - + -
119B PHE* 4.6 6.5 - + - -
133B VAL* 3.7 35.2 - - + -
135B LEU* 4.3 8.5 - - + -
143B HIS* 3.0 36.1 - + - -
144B MET 3.3 1.9 + - - +
145B ALA 3.2 0.4 - - - -
146B ILE* 1.3 76.8 - - + +
148B GLU* 1.3 62.7 + - - +
149B ASN 3.2 1.8 - - - -
150B GLN* 3.2 17.0 + - - +
151B GLY 3.6 0.2 + - - -
152B LEU* 3.3 27.6 + - + +
154B THR* 3.9 18.4 - - + -
185B ILE* 5.7 0.2 - - + -
187B VAL* 3.8 24.9 - - + -
220B LEU* 4.2 18.4 - - + -
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Residues in contact with GLU 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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144B MET* 2.9 45.7 + - + +
145B ALA* 4.2 4.3 - - - +
147B PHE* 1.3 73.1 - - - +
149B ASN* 1.3 59.1 + - - +
150B GLN 3.0 6.8 + - - -
151B GLY* 3.3 10.8 + - - +
152B LEU 3.9 17.5 - - - +
153B LYS* 5.4 0.5 - - - -
154B THR* 3.5 22.9 + - + +
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Residues in contact with ASN 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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117A LYS* 2.9 43.4 + - - +
121A LYS* 5.7 3.6 - - - -
289A LYS* 5.2 2.9 - - - +
290A ILE* 4.5 8.7 + - - +
293A SER* 3.2 21.6 + - - +
294A GLU* 3.3 25.7 + - - +
145B ALA 2.8 18.6 + - - +
146B ILE 3.8 5.6 - - - +
147B PHE 3.2 0.6 - - - -
148B GLU* 1.3 77.7 - - - +
150B GLN* 1.3 86.7 + - - +
151B GLY 3.5 0.6 + - - -
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Residues in contact with GLN 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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117A LYS* 4.5 3.9 + - - +
150A GLN* 5.9 0.2 + - - -
294A GLU* 4.1 1.7 + - - +
113B HIS* 3.5 22.7 + - - +
116B ALA* 3.6 32.1 - - + +
117B LYS* 3.2 37.4 - - - +
120B SER* 3.3 32.1 + - - +
146B ILE 3.7 6.1 - - - +
147B PHE 3.2 6.7 + - - +
148B GLU 3.0 0.6 - - - -
149B ASN* 1.3 115.2 + - - +
151B GLY* 1.3 59.1 + - - +
152B LEU* 3.3 2.2 - - + -
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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