Contacts of the helix formed by residues 146 - 154 (chain A) in PDB entry 1U5U
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PRO* 5.0 2.4 - - - +
145A TRP* 1.3 93.9 + - - +
147A SER* 1.3 65.0 + - - +
148A PRO* 3.3 17.0 - - - +
149A SER* 2.6 37.0 + - - -
150A LEU* 3.0 23.6 + - - +
339A PRO 3.4 9.9 - - - +
340A GLU* 3.0 28.1 + - - +
341A ASP 3.7 0.9 - - - +
342A TYR* 4.3 5.6 - - - -
344A SER* 3.3 11.9 - - - +
345A ILE* 3.5 12.5 - - - +
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 6.0 0.2 - - - -
45A LYS* 3.6 21.1 - - - +
49A PHE* 3.6 20.1 - - - -
146A ASN* 1.3 71.0 - - - +
148A PRO* 1.3 60.1 - - - +
150A LEU* 3.2 7.0 + - - +
151A GLU* 2.9 31.5 + - - +
339A PRO* 2.9 37.1 + - - -
344A SER* 3.5 3.4 + - - -
345A ILE* 4.4 0.2 - - - +
348A LEU* 4.4 14.6 - - - -
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Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASN* 3.3 21.8 - - - +
147A SER* 1.3 94.3 - - - +
149A SER* 1.3 60.5 + - - +
151A GLU* 3.2 25.0 + - - +
152A ASP* 3.3 16.7 + - - +
339A PRO* 3.4 13.0 - - + +
340A GLU* 4.3 16.6 - - + +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE 4.9 0.2 - - - +
144A PHE* 3.7 12.0 - - - +
145A TRP* 2.8 47.1 + - - -
146A ASN* 2.6 27.5 + - - -
148A PRO* 1.3 76.1 - - - +
150A LEU* 1.3 62.0 + - - +
152A ASP* 3.2 16.3 + - - +
153A PHE* 3.4 5.9 + - - +
165A TYR* 5.0 0.3 - - - -
172A TYR* 3.4 24.2 + - - -
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.6 37.0 - - + -
53A PHE* 5.6 4.3 - - + -
144A PHE* 3.7 44.2 - - + +
146A ASN 3.0 18.8 + - - +
147A SER 3.5 2.9 - - - +
149A SER* 1.3 77.3 + - - +
151A GLU* 1.3 64.2 + - - +
153A PHE* 3.0 18.4 + - + +
154A VAL* 3.1 18.6 + - + +
345A ILE* 4.5 0.4 - - + -
348A LEU* 4.3 10.5 - - + -
999A HEM 3.8 34.8 - - + -
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Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 2.7 31.7 + - - +
48A LYS* 2.7 33.5 + - - +
49A PHE* 3.7 12.5 - - + -
147A SER* 2.9 20.7 + - - +
148A PRO* 3.2 20.5 + - - +
150A LEU* 1.3 77.2 - - - +
152A ASP* 1.3 61.2 + - - +
154A VAL* 3.7 9.0 + - + +
155A PRO* 3.2 18.5 - - - +
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PRO 3.3 11.3 + - - +
149A SER* 3.2 10.0 + - - +
150A LEU 3.1 0.6 - - - -
151A GLU* 1.3 78.3 - - - +
153A PHE* 1.3 60.2 + - - +
155A PRO* 3.5 13.9 - - - +
156A VAL* 3.9 2.3 - - - +
165A TYR* 3.3 16.7 - - + +
168A LYS* 3.6 30.0 + - + +
172A TYR* 2.6 39.2 + - + +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.9 22.2 - - + -
107A LYS* 6.5 2.0 - - + -
143A ILE* 3.4 30.7 - - + -
144A PHE* 3.8 29.4 - + + -
149A SER 3.4 7.0 + - - +
150A LEU* 3.0 13.8 + - + +
152A ASP* 1.3 80.0 - - - +
154A VAL* 1.3 66.4 + - - +
156A VAL* 3.0 47.2 + - + +
165A TYR* 3.8 17.7 - + - +
176A LEU* 5.3 6.1 - - + -
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.1 26.0 - - + -
52A LEU* 4.7 17.7 - - + -
53A PHE* 5.4 9.4 - - + -
107A LYS* 5.5 1.7 + - - -
150A LEU* 3.1 25.0 + - + +
151A GLU* 3.8 8.3 - - + +
153A PHE* 1.3 78.8 - - - +
155A PRO* 1.3 69.8 - - + +
156A VAL 3.3 3.8 + - - +
157A GLU* 5.0 3.5 - - - +
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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