Contacts of the helix formed by residues 141 - 147 (chain B) in PDB entry 5AO4
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 PHE 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ILE* 3.5 6.3 - - + +
136B ILE* 3.5 32.3 - - + +
138B THR* 3.2 18.2 + - - +
140B GLN* 1.3 78.7 - - - +
142B GLN* 1.3 56.7 + - - +
143B ARG 2.9 5.2 - - - -
144B LEU* 3.0 31.7 + - + +
165B PHE* 3.3 45.5 - + - -
168B SER* 3.5 26.9 - - - -
169B LEU* 3.9 7.6 - - + -
204B LEU* 3.3 43.5 - - + -
205B CYS* 5.0 6.3 - - - -
208B LEU* 3.9 17.3 - - + -
244B LEU* 4.1 5.1 - - + +
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Residues in contact with GLN 142 (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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155A TYR* 4.4 8.5 - - - -
448A ILE* 4.6 4.8 + - - +
449A GLU* 3.6 45.5 + - + +
451A ARG* 5.3 6.9 + - - +
136B ILE* 3.8 12.2 + - - +
137B ASP* 4.1 13.9 + - - -
138B THR 2.8 24.4 + - - +
139B PRO 4.5 1.3 - - - +
141B PHE* 1.3 67.1 - - - +
143B ARG* 1.3 60.5 + - - +
144B LEU 3.0 6.6 + - - -
145B ARG* 3.1 43.2 + - - +
146B TYR* 3.2 16.6 + - + +
165B PHE* 3.7 28.8 - - - -
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Residues in contact with ARG 143 (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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432A TYR* 5.5 0.9 - - - +
449A GLU* 5.8 0.9 - - - -
139B PRO 3.2 21.2 + - - +
140B GLN 3.4 14.6 + - - +
141B PHE 2.9 0.4 - - - -
142B GLN* 1.3 78.2 - - - +
144B LEU* 1.3 75.2 + - - +
145B ARG 3.2 2.1 + - - -
146B TYR* 3.4 22.1 + - - -
147B ILE* 3.8 8.9 - - - +
208B LEU 2.8 27.5 + - - -
210B HIS 3.0 24.7 + - - -
211B GLY* 4.5 0.8 - - - -
240B MET* 4.4 6.3 - - - +
419B TYR* 3.1 44.4 + - - -
420B THR* 3.3 31.1 + - - +
422B LEU 3.5 17.4 + - - -
423B THR* 3.7 15.1 - - + +
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Residues in contact with LEU 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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140B GLN 4.7 0.7 - - - +
141B PHE* 3.0 22.4 + - + +
143B ARG* 1.3 101.6 - - - +
145B ARG* 1.3 58.0 + - - +
146B TYR 3.1 5.9 + - - -
147B ILE* 3.8 16.9 + - + -
163B ASN* 3.6 1.2 - - - +
164B ARG* 3.5 20.9 + - + +
165B PHE* 2.9 35.7 + - - +
168B SER* 3.5 24.5 - - - +
204B LEU 5.3 0.2 - - - +
207B ASP 3.6 27.1 - - - +
208B LEU* 3.8 22.7 - - + +
210B HIS* 5.5 0.2 - - + -
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Residues in contact with ARG 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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154A TYR* 3.0 55.3 + - + -
155A TYR* 3.5 48.4 + - - +
158A PRO* 5.1 4.0 - - - +
451A ARG* 5.3 3.0 - - - +
142B GLN* 3.1 43.7 + - - +
144B LEU* 1.3 78.5 - - - +
146B TYR* 1.3 70.8 + - + +
163B ASN* 2.4 28.7 + - - -
165B PHE* 3.3 47.0 - - + -
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Residues in contact with TYR 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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148A LYS* 6.2 1.6 - - - -
154A TYR* 6.0 1.1 - + - -
155A TYR* 3.4 23.8 + - - -
427A PHE* 3.3 26.6 - + - -
428A LEU* 3.7 34.8 - - + -
431A LEU* 4.5 4.7 - - + +
432A TYR* 4.2 10.5 - - - -
449A GLU* 4.7 12.9 + - - +
142B GLN* 3.2 22.6 + - + +
143B ARG* 3.4 18.1 + - - -
144B LEU 3.1 1.0 - - - -
145B ARG* 1.3 94.7 - - + +
147B ILE* 1.3 61.5 + - - +
163B ASN* 4.2 2.0 - - - +
423B THR* 3.6 17.9 - - + +
424B ASP* 3.0 33.9 + - + +
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Residues in contact with ILE 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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143B ARG* 3.8 30.3 - - - +
144B LEU* 3.8 14.6 + - + +
145B ARG 3.6 2.6 + - - -
146B TYR* 1.3 83.7 - - - +
148B LYS* 1.3 64.5 + - - +
163B ASN* 3.1 4.7 - - - -
164B ARG* 3.0 38.0 + - + +
210B HIS* 3.1 28.0 - - + +
211B GLY 3.3 24.0 - - - +
213B PHE 4.2 1.6 - - - +
214B SER* 3.6 23.3 - - - +
422B LEU 4.9 0.9 - - - +
423B THR* 4.5 9.4 - - + -
424B ASP* 3.4 4.5 - - - +
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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