Contacts of the helix formed by residues 110 - 128 (chain A) in PDB entry 5UDJ
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 ARG 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLU* 4.2 9.3 + - - -
72A LEU* 3.7 22.4 - - - +
76A LYS* 5.9 3.2 - - - +
105A TYR* 2.9 43.5 + - + +
108A MET* 4.0 25.8 - - + +
109A GLY* 1.3 75.9 - - - +
111A LEU* 1.3 58.7 + - - +
112A ALA 3.3 2.2 - - - -
113A GLU* 2.9 48.8 + - - +
114A ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 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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10A VAL* 5.0 13.7 - - + +
106A TYR* 3.6 46.2 - - + +
109A GLY* 3.1 22.1 + - - +
110A ARG* 1.3 72.4 - - - +
112A ALA* 1.3 65.8 + - - +
114A ALA* 3.4 4.7 + - + +
115A GLN* 3.1 22.3 + - - +
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Residues in contact with ALA 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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110A ARG 3.3 0.6 - - - -
111A LEU* 1.3 78.5 - - - +
113A GLU* 1.3 63.5 + - + +
115A GLN* 3.3 7.8 + - - +
116A THR* 3.0 23.2 + - - -
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Residues in contact with GLU 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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105A TYR* 3.9 24.7 + - + -
110A ARG* 2.9 59.5 + - - +
112A ALA* 1.3 78.0 - - + +
114A ALA* 1.3 66.3 + - - +
116A THR* 3.1 19.5 + - - +
117A TYR* 3.1 20.5 + - + -
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Residues in contact with ALA 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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10A VAL* 5.1 9.0 - - + -
14A LEU* 5.3 1.1 - - + -
102A ALA* 3.4 29.1 - - + +
105A TYR* 3.7 6.4 - - - +
106A TYR* 3.8 22.2 - - + +
110A ARG 3.0 10.3 + - - +
111A LEU* 3.6 12.1 - - + +
112A ALA 3.3 0.2 - - - -
113A GLU* 1.3 74.7 - - - +
115A GLN* 1.3 63.4 + - - +
117A TYR* 3.1 5.4 + - - +
118A LEU* 3.0 25.8 + - - +
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Residues in contact with GLN 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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9A GLN* 6.2 0.2 - - - +
10A VAL* 3.7 26.3 - - + +
111A LEU 3.1 13.8 + - - +
112A ALA* 3.6 9.4 - - - +
114A ALA* 1.3 76.6 - - - +
116A THR* 1.3 62.1 + - - +
118A LEU* 3.2 22.8 + - - +
119A ASP* 2.9 58.2 + - - +
134A TYR* 4.5 6.9 + - - -
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Residues in contact with THR 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 3.0 15.2 + - - -
113A GLU* 3.1 14.9 + - - +
115A GLN* 1.3 76.3 - - - +
117A TYR* 1.3 65.8 + - + +
119A ASP* 3.2 11.3 + - - +
120A LYS* 3.0 39.1 + - + +
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Residues in contact with TYR 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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79A GLU* 4.5 5.9 + - - -
98A TRP* 3.6 37.7 - + + +
101A PHE* 3.6 41.6 - + + -
102A ALA* 3.9 9.2 - - + +
105A TYR* 3.6 29.3 + + - -
113A GLU* 3.1 25.5 + - + +
114A ALA 3.1 6.0 + - - +
116A THR* 1.3 83.6 - - + +
118A LEU* 1.3 65.3 + - - +
120A LYS* 3.2 23.7 + - + +
121A VAL* 3.1 28.1 + - - +
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Residues in contact with LEU 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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10A VAL* 4.3 22.2 - - + +
13A SER* 3.9 38.4 - - - +
14A LEU* 4.1 9.2 - - + -
17A LEU* 4.0 30.1 - - + -
102A ALA* 4.3 1.7 - - + +
114A ALA 3.0 18.1 + - - +
115A GLN* 3.6 32.8 - - - +
117A TYR* 1.3 73.7 - - - +
119A ASP* 1.3 58.6 + - - +
121A VAL* 3.2 6.0 + - - +
122A GLU 2.9 23.9 + - - -
134A TYR* 3.5 23.3 - - + +
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Residues in contact with ASP 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 GLN* 2.9 47.0 + - - +
116A THR* 3.5 10.7 - - - +
117A TYR 3.2 0.2 - - - -
118A LEU* 1.3 77.7 - - - +
120A LYS* 1.3 57.3 + - + +
122A GLU* 3.3 15.4 + - - +
123A ASN* 2.9 29.9 + - - +
134A TYR* 5.1 1.6 + - - -
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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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79A GLU* 6.0 0.2 - - - -
98A TRP* 3.5 50.3 - - + +
116A THR* 3.0 25.7 + - + +
117A TYR* 3.2 34.5 + - + +
119A ASP* 1.3 77.5 - - + +
121A VAL* 1.3 60.9 + - - +
123A ASN* 3.4 8.0 + - - +
124A ILE* 3.3 26.5 + - - +
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Residues in contact with VAL 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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17A LEU* 3.9 23.3 - - + -
95A LEU* 4.2 23.1 - - + +
98A TRP* 3.8 31.6 - - + -
99A GLY* 4.4 2.7 - - - +
117A TYR 3.1 13.7 + - - +
118A LEU 3.6 6.1 - - - +
120A LYS* 1.3 72.4 - - - +
122A GLU* 1.3 66.9 + - - +
124A ILE* 3.1 4.0 + - - +
125A CYS* 2.9 29.2 + - - -
134A TYR* 3.6 28.5 - - + +
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Residues in contact with GLU 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 LEU 2.9 16.5 + - - +
119A ASP* 3.6 15.2 - - - +
120A LYS 3.3 0.2 - - - -
121A VAL* 1.3 77.3 - - - +
123A ASN* 1.3 61.9 + - - +
125A CYS* 3.2 2.6 + - - +
126A LYS* 2.9 26.5 + - + +
133A ARG* 3.3 55.0 + - + +
134A TYR* 3.8 16.7 + - + -
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Residues in contact with ASN 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 ASP 2.9 16.6 + - - +
120A LYS* 3.6 8.6 + - - +
121A VAL 3.2 0.2 - - - -
122A GLU* 1.3 77.2 - - - +
124A ILE* 1.3 74.4 + - - +
126A LYS* 3.4 5.2 + - - +
127A LYS* 3.0 31.6 + - - +
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Residues in contact with ILE 124 (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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92A VAL* 5.1 2.9 - - + -
95A LEU* 3.8 25.6 - - + -
98A TRP* 3.5 25.4 - - + -
120A LYS 3.3 12.3 + - - +
121A VAL 3.1 7.0 + - - +
123A ASN* 1.3 88.9 - - - +
125A CYS* 1.3 67.4 + - - +
127A LYS* 3.3 19.7 + - + +
128A LEU* 3.1 44.7 + - + +
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Residues in contact with CYS 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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95A LEU* 4.3 2.0 - - - -
121A VAL* 2.9 21.4 + - - -
122A GLU 3.7 2.7 - - - +
124A ILE* 1.3 76.0 - - - +
126A LYS* 1.3 59.7 + - - +
128A LEU 3.6 0.2 + - - -
129A SER 3.4 1.7 + - - -
130A ASN* 2.9 53.7 + - + +
132A PHE 3.5 11.7 - - - +
133A ARG* 3.3 26.0 - - - +
134A TYR* 4.0 17.0 - - - -
136A MET* 4.0 22.0 - - - -
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Residues in contact with LYS 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 GLU* 2.9 19.7 + - + +
123A ASN* 3.8 6.5 - - - +
125A CYS* 1.3 75.9 - - - +
127A LYS* 1.3 67.1 + - - +
129A SER* 3.0 16.6 + - - +
130A ASN 5.5 0.9 - - - -
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Residues in contact with LYS 127 (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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123A ASN* 3.0 22.0 + - - +
124A ILE* 3.3 23.2 + - + +
126A LYS* 1.3 76.8 - - - +
128A LEU* 1.3 74.1 + - + +
129A SER* 3.5 3.8 + - - -
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Residues in contact with LEU 128 (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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92A VAL* 4.4 12.6 - - + -
124A ILE* 3.1 36.4 + - + +
125A CYS 4.3 1.8 - - - +
126A LYS 3.1 0.2 - - - -
127A LYS* 1.3 91.3 - - + +
129A SER* 1.3 69.9 + - - +
130A ASN* 3.1 2.5 + - - -
136A MET* 3.8 31.3 - - + +
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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