Contacts of the helix formed by residues 112 - 120 (chain A) in PDB entry 1U5Q
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A SER* 1.3 71.8 - - - +
113A SER* 1.3 62.5 + - - +
115A LEU* 3.0 20.5 + - + +
116A LEU* 3.1 16.9 + - - +
123A LEU* 5.4 0.4 - - + +
131A VAL* 4.5 12.3 - - + -
154A ALA* 3.2 17.4 + - + +
157A ILE* 2.8 22.3 + - + +
159A LEU* 3.8 10.0 - - + +
218A LEU* 3.7 24.7 - - + +
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Residues in contact with SER 113 (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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111A SER* 3.4 9.4 - - - -
112A ALA* 1.3 75.9 - - - +
114A ASP* 1.3 66.5 + - - +
116A LEU* 3.0 11.6 + - - +
117A GLU* 2.9 34.6 + - - +
154A ALA* 3.3 10.2 + - - +
155A GLY* 3.5 24.9 - - - -
217A GLU* 4.8 5.1 + - - -
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Residues in contact with ASP 114 (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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110A GLY* 3.4 7.7 - - - -
111A SER* 2.8 42.7 + - - +
113A SER* 1.3 77.7 + - - +
115A LEU* 1.3 58.8 + - + +
117A GLU* 3.1 8.5 + - - +
118A VAL* 2.9 28.4 + - - +
312A MET* 3.1 32.0 - - + +
314A LYS* 3.1 35.7 + - - -
315A ILE* 4.2 7.6 - - + -
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Residues in contact with LEU 115 (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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110A GLY* 5.6 4.5 - - - -
111A SER 3.5 14.1 - - - +
112A ALA* 3.0 14.9 + - + +
114A ASP* 1.3 81.8 - - + +
116A LEU* 1.3 59.8 + - - +
118A VAL* 3.4 3.9 + - - +
119A HIS* 3.3 33.6 + - + +
123A LEU* 4.3 18.8 - - + +
131A VAL* 5.2 1.3 - - + -
159A LEU* 3.9 23.3 - - + -
293A LEU* 3.2 38.1 - - + -
294A ILE* 5.6 4.7 - - + -
297A THR* 3.5 33.2 - - + +
315A ILE* 6.0 1.8 - - + -
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Residues in contact with LEU 116 (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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112A ALA 3.1 13.8 + - - +
113A SER* 3.0 10.4 + - - +
115A LEU* 1.3 75.0 - - - +
117A GLU* 1.3 58.6 + - + +
120A LYS* 3.0 28.9 + - - -
121A LYS 3.7 21.5 + - - +
122A PRO* 4.2 2.2 - - + -
123A LEU* 4.2 14.1 - - + -
154A ALA* 4.2 6.5 - - + -
217A GLU* 3.5 34.5 - - + +
218A LEU* 3.7 38.1 - - + +
221A ARG* 4.1 25.0 + - + +
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Residues in contact with GLU 117 (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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113A SER* 2.9 22.3 + - - +
114A ASP* 3.1 17.6 + - - +
116A LEU* 1.3 76.9 - - + +
118A VAL* 1.3 64.8 + - - +
120A LYS* 2.9 37.4 + - - +
221A ARG* 5.4 1.8 - - - +
312A MET* 4.3 22.2 - - + +
49B ARG 5.3 2.1 - - - +
50B ASN* 4.8 14.8 - - + +
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Residues in contact with VAL 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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114A ASP 2.9 11.5 + - - +
115A LEU 3.4 3.8 + - - +
117A GLU* 1.3 77.7 - - - +
119A HIS* 1.3 67.3 + - + +
120A LYS* 4.5 3.3 - - - +
297A THR* 4.1 14.1 - - + +
300A ALA* 3.7 30.6 - - + +
301A VAL* 3.6 29.6 - - + +
304A LEU* 4.9 16.4 - - + +
312A MET* 3.2 38.8 - - + -
315A ILE* 4.7 0.2 - - + -
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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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115A LEU* 3.3 27.6 + - + +
118A VAL* 1.3 79.1 - - + +
120A LYS* 1.3 72.4 + - - +
121A LYS* 3.0 29.1 + - + +
122A PRO 5.9 0.2 - - - +
123A LEU* 5.1 3.8 - - + -
293A LEU* 5.1 1.8 - - + -
296A ARG* 3.5 59.5 + - + +
297A THR* 3.0 28.5 + - - +
300A ALA* 3.7 19.5 - - + +
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Residues in contact with LYS 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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116A LEU 3.0 13.7 + - - -
117A GLU* 2.9 31.3 + - - +
118A VAL 4.5 3.4 - - - +
119A HIS* 1.3 78.7 - - - +
121A LYS* 1.3 64.1 + - - +
221A ARG* 3.2 29.7 + - - +
310A ARG* 5.4 7.0 - - - +
50B ASN* 3.1 31.3 + - - +
51B SER* 4.4 4.7 - - - -
52B GLU* 2.8 42.6 + - + +
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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