Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 1UIR
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 ASP 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A THR* 2.8 27.9 + - - +
31A PRO* 4.6 0.9 - - - +
32A PHE* 3.8 19.5 - - + +
33A GLN* 3.0 24.1 - - - +
108A ASP* 3.0 10.6 + - - +
109A ILE* 1.3 81.6 - - + +
111A GLY* 1.3 62.9 + - - +
112A GLU* 3.2 12.6 + - - +
113A LEU* 3.0 30.7 + - + +
114A VAL* 3.2 24.6 + - - +
138A ILE* 4.5 0.7 - - - -
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Residues in contact with GLY 111 (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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32A PHE* 5.4 0.6 - - - -
109A ILE 3.5 5.7 + - - -
110A ASP* 1.3 70.6 + - - +
112A GLU* 1.3 65.3 + - - +
114A VAL* 3.3 4.7 + - - +
115A GLU* 3.0 27.3 + - - +
138A ILE* 3.6 33.7 - - - +
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Residues in contact with GLU 112 (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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29A LYS 3.7 12.6 - - - +
30A THR* 3.6 20.1 - - + +
31A PRO* 3.5 21.1 - - + +
35A TYR* 4.7 8.0 + - - +
110A ASP* 3.2 8.4 + - - +
111A GLY* 1.3 77.5 - - - +
113A LEU* 1.3 62.2 + - - +
115A GLU* 3.2 11.1 + - + +
116A VAL* 3.1 25.6 + - + +
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Residues in contact with LEU 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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30A THR* 4.1 3.6 - - + +
33A GLN* 3.6 20.2 - - + +
35A TYR* 4.2 16.6 - - + -
47A LEU* 4.9 9.6 - - + -
49A LEU* 3.7 40.2 - - + -
87A GLY* 5.7 10.1 - - - +
108A ASP* 5.3 4.5 - - - +
110A ASP* 3.0 30.0 + - + +
112A GLU* 1.3 74.9 - - - +
114A VAL* 1.3 67.0 + - + +
116A VAL* 2.9 27.8 + - + +
117A ALA* 3.0 12.9 + - + +
121A MET* 6.5 0.4 - - - -
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Residues in contact with VAL 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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87A GLY* 4.1 18.8 - - - +
106A MET* 4.6 4.0 - - + -
108A ASP* 3.9 19.5 - - + +
110A ASP 3.2 14.1 + - - +
111A GLY* 3.5 8.5 - - - +
113A LEU* 1.3 77.2 - - + +
115A GLU* 1.3 58.5 + - - +
117A ALA* 3.1 3.8 + - - +
118A LYS* 2.9 50.6 + - + +
129A PHE* 4.1 14.8 - - + -
136A LEU* 4.0 16.2 - - + -
138A ILE* 4.0 15.7 - - + -
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Residues in contact with GLU 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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111A GLY 3.0 17.7 + - - +
112A GLU* 3.3 14.6 - - + +
114A VAL* 1.3 76.8 - - + +
116A VAL* 1.3 65.0 + - + +
118A LYS* 3.3 29.1 + - - +
119A ARG* 3.0 27.0 + - - +
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Residues in contact with VAL 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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26A ALA* 5.2 2.9 - - + -
35A TYR* 3.6 50.7 - - + +
37A LEU* 5.3 4.5 - - + -
47A LEU* 5.4 5.2 - - + -
112A GLU* 3.1 20.9 + - + +
113A LEU* 2.9 18.7 + - + +
115A GLU* 1.3 76.5 - - - +
117A ALA* 1.3 59.9 + - - +
120A HIS* 2.8 50.8 + - + +
121A MET* 5.1 7.9 - - - -
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Residues in contact with ALA 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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87A GLY 3.8 20.4 - - - +
88A GLU* 3.9 20.9 - - + +
113A LEU* 3.0 10.3 + - + +
114A VAL 3.1 8.5 + - - +
116A VAL* 1.3 75.5 - - - +
118A LYS* 1.3 61.1 + - + +
121A MET* 2.7 55.7 + - + +
125A HIS* 3.5 3.4 - - + -
129A PHE* 5.3 0.7 - - + -
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Residues in contact with LYS 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 VAL* 2.9 31.6 + - + +
115A GLU* 3.6 30.5 + - - +
117A ALA* 1.3 77.0 - - - +
119A ARG* 1.3 58.9 + - - +
121A MET 4.6 0.2 + - - -
122A PRO* 4.7 2.9 - - - +
125A HIS* 3.2 26.0 + - + +
129A PHE* 3.7 45.3 - - + +
136A LEU* 3.9 16.4 - - - +
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Residues in contact with ARG 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 GLU* 3.0 16.6 + - - +
118A LYS* 1.3 80.0 - - - +
120A HIS* 1.3 101.9 + - + +
122A PRO* 4.5 5.2 - - - +
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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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25A ILE* 3.7 22.5 - - + +
26A ALA* 4.2 21.8 - - + +
37A LEU* 3.5 23.5 - - + +
45A LYS* 2.9 25.8 + - - +
116A VAL* 2.8 32.4 + - + +
119A ARG* 1.3 123.9 + - + +
121A MET* 1.3 64.3 + - - +
122A PRO* 3.2 6.3 - - - -
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Residues in contact with MET 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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37A LEU* 4.0 15.0 - - + -
47A LEU* 3.8 32.5 - - + -
55A SER* 5.1 0.2 - - - -
88A GLU* 3.7 20.6 - - + -
113A LEU* 6.5 0.4 - - - -
116A VAL* 4.5 4.9 - - - +
117A ALA* 2.7 45.2 + - + +
120A HIS* 1.3 79.3 - - - +
122A PRO* 1.3 64.9 - - - +
123A GLU* 3.1 8.1 - - - -
124A TRP* 3.0 64.7 + - + +
125A HIS* 3.2 11.1 - - - -
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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