Contacts of the helix formed by residues 111 - 121 (chain B) in PDB entry 1UK0
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.4 27.0 - - + +
41B SER 4.5 6.3 - - - +
42B LYS* 3.4 46.1 + - - +
43B ARG* 5.1 1.2 + - - -
45B ILE* 5.7 0.2 - - + -
107B LEU 2.7 20.9 + - - +
108B LEU* 3.6 15.7 + - + +
109B ASP 3.3 0.8 - - - -
110B ILE* 1.3 73.7 - - - +
112B VAL* 1.3 65.7 + - - +
114B TYR* 4.5 4.9 - - + -
115B SER* 2.9 53.2 + - - -
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Residues in contact with VAL 112 (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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108B LEU 3.7 9.1 + - - +
109B ASP* 2.4 28.5 + - - +
111B GLU* 1.3 79.7 - - - +
113B ALA* 1.3 73.5 + - - +
115B SER* 4.5 3.4 - - - -
116B LEU* 2.6 47.9 + - + +
210B GLY* 3.7 13.2 - - - -
213B SER* 3.2 21.1 - - - +
214B GLN* 3.8 20.2 - - - +
217B ARG* 5.2 3.6 - - - +
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Residues in contact with ALA 113 (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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15B ILE 4.1 11.4 - - - +
16B PHE* 4.6 5.1 - - - +
21B MET* 3.7 22.2 - - + -
109B ASP 2.9 10.7 + - - +
110B ILE* 3.3 1.9 + - - +
112B VAL* 1.3 80.4 - - - +
114B TYR* 1.4 51.8 - - - +
116B LEU* 2.8 16.1 + - - +
117B LEU* 2.9 22.7 + - - +
206B THR 3.6 20.4 - - - +
209B ALA* 4.3 19.5 - - + -
210B GLY 4.7 2.4 - - - +
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Residues in contact with TYR 114 (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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18B VAL* 5.3 8.3 - - + -
21B MET* 3.3 16.0 - - - +
37B LEU* 3.3 63.9 - - + -
38B GLY* 3.9 22.5 - - - -
40B LEU* 5.9 3.6 - - + -
110B ILE* 3.2 17.7 - - + +
111B GLU* 4.1 5.8 - - + +
113B ALA* 1.4 71.9 - - - +
115B SER* 1.4 59.6 + - - +
116B LEU 3.1 0.3 + - - -
117B LEU* 3.5 5.6 + - - +
118B ARG* 2.7 82.9 + - + +
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Residues in contact with SER 115 (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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42B LYS* 5.7 2.6 - - - -
111B GLU* 2.9 40.6 + - - -
112B VAL* 3.1 5.4 + - - -
114B TYR* 1.4 82.0 - - - +
116B LEU* 1.4 71.9 + - - +
118B ARG 3.8 0.7 - - - +
119B GLY* 3.3 18.9 + - - +
120B GLY 4.2 0.3 + - - -
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Residues in contact with LEU 116 (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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16B PHE* 4.3 14.1 - - + -
112B VAL* 2.6 44.6 + - + +
113B ALA 3.2 2.9 - - - +
115B SER* 1.4 79.8 - - - +
117B LEU* 1.3 70.6 + - - +
120B GLY* 3.2 15.8 - - - -
135B LYS* 3.7 45.4 + - + +
136B LEU* 4.7 1.3 - - + -
137B LYS* 6.4 0.2 - - + -
209B ALA* 4.1 18.4 - - + +
213B SER* 3.8 21.3 - - - +
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Residues in contact with LEU 117 (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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16B PHE* 3.3 42.5 - - + +
18B VAL* 3.3 34.1 - - + -
113B ALA 2.9 12.8 + - - +
114B TYR* 4.3 3.4 - - - +
116B LEU* 1.3 81.5 - - - +
118B ARG* 1.4 69.9 + - + +
120B GLY* 2.8 20.3 + - - -
121B SER 3.5 8.0 + - - +
132B ASN* 4.0 11.7 - - - +
135B LYS* 3.7 9.4 + - - +
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Residues in contact with ARG 118 (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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114B TYR* 2.7 58.4 + - + +
117B LEU* 1.4 84.1 - - + +
119B GLY* 1.3 68.8 + - - +
120B GLY 2.8 2.1 + - - -
121B SER 4.3 6.9 + - - +
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Residues in contact with GLY 119 (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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115B SER* 3.3 15.1 + - - +
118B ARG* 1.3 81.6 - - - +
120B GLY* 1.4 61.8 - - - +
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Residues in contact with GLY 120 (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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116B LEU 3.2 14.9 + - - -
117B LEU 2.8 10.1 + - - -
118B ARG 2.8 4.2 + - - -
119B GLY* 1.4 78.6 - - - +
121B SER* 1.4 59.8 + - - -
135B LYS* 3.6 19.8 - - - +
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Residues in contact with SER 121 (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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117B LEU* 3.5 8.1 + - - +
118B ARG 4.7 5.4 - - - +
119B GLY 4.0 0.2 - - - -
120B GLY* 1.4 73.2 - - - +
122B ASP* 1.3 65.0 + - - +
123B ASP* 2.7 38.3 + - - +
128B PRO* 5.7 0.9 - - - -
131B VAL* 3.2 40.1 - - - +
132B ASN* 5.6 0.4 - - - -
135B LYS* 3.8 5.5 - - - +
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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