Contacts of the helix formed by residues 117 - 126 (chain A) in PDB entry 1U1L
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 GLU 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASP* 4.2 11.1 - - - +
116A THR* 1.3 80.7 - - - +
118A GLU* 1.3 61.9 + - - +
119A HIS* 2.9 35.5 + - + +
120A HIS* 2.8 31.7 + - - +
121A LEU* 3.5 2.3 + - - +
136A ILE* 3.6 7.4 - - - +
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Residues in contact with GLU 118 (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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117A GLU* 1.3 72.9 - - - +
119A HIS* 1.3 63.2 + - - +
121A LEU* 3.0 6.9 + - - +
122A ARG* 3.0 33.5 + - - +
134A ILE* 3.0 53.1 - - + +
135A GLU* 5.0 0.9 - - - -
136A ILE* 3.6 15.3 + - + +
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Residues in contact with HIS 119 (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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117A GLU* 2.9 42.5 + - + +
118A GLU* 1.3 78.7 - - - +
120A HIS* 1.3 95.1 + + - +
122A ARG* 3.5 11.6 + - - +
123A ASP* 3.0 39.8 + - - +
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Residues in contact with HIS 120 (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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115A ASP* 3.7 9.7 + - - -
116A THR* 3.7 11.0 - - + -
117A GLU* 2.8 38.5 + - - +
119A HIS* 1.3 112.9 + + - +
121A LEU* 1.3 61.1 + - - +
123A ASP* 3.5 11.0 + - - +
124A TYR* 3.6 8.8 + - - +
170A VAL* 4.1 12.9 - - + +
171A ASN* 3.5 45.1 + - + +
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Residues in contact with LEU 121 (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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109A VAL* 4.4 13.2 - - + -
112A ILE* 4.9 3.6 - - + -
116A THR* 4.6 3.8 - - + -
117A GLU 4.3 3.1 - - - +
118A GLU* 3.0 7.7 + - - +
120A HIS* 1.3 76.3 - - - +
122A ARG* 1.3 57.9 + - - +
124A TYR* 3.2 2.3 + - - +
125A PHE* 2.8 62.3 + - + +
134A ILE* 3.5 33.7 - - + -
136A ILE* 3.8 26.2 - - + -
149A ALA* 4.0 15.7 - - + -
151A VAL* 4.5 8.3 - - + -
170A VAL* 3.9 19.1 - - + -
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Residues in contact with ARG 122 (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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118A GLU* 3.0 22.5 + - - +
119A HIS* 3.9 10.8 - - - +
121A LEU* 1.3 76.8 - - - +
123A ASP* 1.3 65.0 + - - +
126A GLU* 2.8 65.8 + - + +
131A ILE* 4.0 28.8 + - + +
132A GLU 5.8 2.6 + - - -
133A VAL* 6.3 0.4 - - - +
134A ILE* 3.5 31.0 - - + +
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Residues in contact with ASP 123 (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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119A HIS* 3.0 31.5 + - - +
120A HIS* 3.9 7.1 - - - +
121A LEU 3.3 0.4 - - - -
122A ARG* 1.3 77.6 - - - +
124A TYR* 1.3 58.5 + - - +
127A GLN* 5.1 10.3 - - - +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A HIS 3.6 4.1 + - - +
121A LEU 3.2 6.0 + - - +
122A ARG 3.0 0.4 - - - -
123A ASP* 1.3 81.7 - - - +
125A PHE* 1.3 95.4 + + - +
126A GLU 3.6 0.4 - - - -
127A GLN* 4.0 14.0 + - - +
128A TYR* 2.8 42.2 + + - -
167A TYR 3.6 6.1 + - - -
168A HIS* 2.5 42.4 + - + -
169A THR* 3.3 36.8 - - - +
170A VAL* 4.0 13.5 - - + -
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Residues in contact with PHE 125 (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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107A ILE* 3.5 24.5 - - + -
109A VAL* 3.8 12.8 - - + -
121A LEU* 2.8 52.4 + - + +
124A TYR* 1.3 101.5 - + - +
126A GLU* 1.3 65.5 + - - +
127A GLN 3.0 2.9 - - - -
128A TYR* 2.9 20.7 + + - +
131A ILE* 3.9 15.3 - - + -
151A VAL* 4.2 10.1 - - + -
153A PHE* 3.7 14.0 - + + -
162A ILE* 3.7 31.0 - - + -
170A VAL* 4.1 11.7 - - + -
175A CYS* 4.9 0.4 - - - -
177A VAL* 3.8 18.6 - - + -
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Residues in contact with GLU 126 (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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122A ARG* 2.8 62.2 + - + +
125A PHE* 1.3 76.2 - - - +
127A GLN* 1.3 63.0 + - + +
128A TYR 3.0 1.4 + - - -
129A GLY* 3.1 23.1 + - - +
131A ILE* 3.5 18.4 - - + +
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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