Contacts of the helix formed by residues 121 - 130 (chain D) in PDB entry 5UHE
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 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D ASP 4.2 1.0 + - - -
120D LEU* 1.3 74.9 - - - +
122D PRO* 1.3 63.6 - - + +
123D LYS* 4.4 3.1 - - + +
124D ASP* 3.1 30.8 + - + +
125D LEU* 2.6 37.0 + - - +
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Residues in contact with PRO 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 4.5 3.4 - - + -
112D SER* 4.0 27.4 - - - +
115D GLY 5.8 0.2 - - - -
116D TYR* 5.5 9.6 - - + -
120D LEU 3.5 6.3 - - - +
121D ALA* 1.3 83.6 - - + +
123D LYS* 1.3 61.5 + - - +
125D LEU* 3.1 17.8 + - + +
126D GLU* 3.2 16.6 + - - +
22H T 6.1 1.8 - - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ALA* 3.3 3.5 - - + +
122D PRO* 1.3 76.5 - - - +
124D ASP* 1.3 67.8 + - - +
126D GLU* 3.5 29.2 + - + +
127D LYS* 3.5 47.5 + - - +
223F ALA 4.9 7.1 + - - -
225F ALA* 6.2 3.6 - - - +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 5.2 2.1 - - + +
121D ALA* 3.1 29.5 + - + +
123D LYS* 1.3 78.5 - - - +
125D LEU* 1.3 65.2 + - - +
127D LYS* 3.5 15.2 + - - +
128D ILE* 3.1 26.8 + - - +
234D LEU* 3.2 36.2 - - + +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 3.8 22.7 - - + -
112D SER* 4.5 5.6 - - - +
114D LEU* 3.6 18.4 - - + -
115D GLY* 3.5 32.1 - - - +
118D LEU* 5.4 1.3 - - + -
120D LEU* 3.8 28.5 - - + +
121D ALA 2.6 18.2 + - - +
122D PRO* 3.1 8.9 + - + +
124D ASP* 1.3 75.3 - - - +
126D GLU* 1.3 56.7 + - - +
128D ILE* 3.5 4.6 + - + +
129D ILE* 3.0 35.3 + - + +
261D ILE* 3.5 31.0 - - + -
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 3.3 25.2 - - + -
108D LYS* 3.7 22.7 + - - -
122D PRO 3.2 12.1 + - - +
123D LYS* 3.6 29.5 + - + +
124D ASP 3.2 0.2 - - - -
125D LEU* 1.3 72.5 - - - +
127D LYS* 1.3 63.9 - - + +
128D ILE 2.9 5.1 + - - -
129D ILE 3.2 0.2 + - - -
130D TYR* 2.9 33.9 + - + +
387D ARG* 3.7 35.5 + - - +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 3.5 44.5 - - - +
124D ASP* 3.5 22.4 + - - +
126D GLU* 1.3 78.6 - - + +
128D ILE* 1.3 55.2 + - - +
132D ALA* 2.7 28.0 + - + -
133D ALA* 2.5 46.9 + - + +
234D LEU* 4.5 2.5 - - + -
236D VAL* 4.9 14.5 - - + +
222F THR* 4.5 10.9 - - - +
223F ALA* 4.0 30.1 + - + +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 4.3 10.1 - - + -
124D ASP 3.1 17.0 - - - +
125D LEU* 3.5 22.4 - - + +
126D GLU 2.9 1.2 + - - -
127D LYS* 1.3 75.3 - - - +
129D ILE* 1.3 68.0 + - - +
131D PHE* 3.0 13.0 + - - -
133D ALA 3.6 8.9 - - - +
135D VAL* 3.6 44.0 - - + -
234D LEU* 3.6 27.8 - - + -
257D GLY 3.3 17.2 + - - +
260D SER* 3.9 5.4 - - - +
261D ILE* 3.6 22.4 - - + -
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR* 3.4 28.7 - - + +
107D PHE* 3.4 34.1 - - + -
114D LEU* 4.6 3.4 - - + -
125D LEU* 3.0 16.2 + - + +
128D ILE* 1.3 78.3 - - - +
130D TYR* 1.3 75.4 + - + +
131D PHE* 3.1 23.2 - - - -
257D GLY* 3.7 10.5 - - - -
258D ALA* 4.0 3.1 + - + -
261D ILE* 3.6 21.8 - - + -
375D GLN* 3.5 35.2 - - - +
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Residues in contact with TYR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 5.0 0.7 - - - +
107D PHE* 3.9 22.0 - + - -
126D GLU* 2.9 20.5 + - - +
129D ILE* 1.3 96.7 - - + +
131D PHE* 1.3 70.3 + - - +
132D ALA* 3.3 6.7 + - + +
372D ARG* 3.1 25.1 - - + +
375D GLN* 3.7 17.3 + - + -
376D GLU* 3.6 26.9 - - + +
379D ASP* 2.2 32.4 + - - +
387D ARG* 3.1 63.8 - - - +
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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