Contacts of the helix formed by residues 100 - 116 (chain B) in PDB entry 1UN0
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B SER* 3.1 13.7 + - - +
99B ASP* 1.3 75.1 - - - +
101B MET* 1.3 66.9 + - - +
102B GLN* 3.3 25.0 + - - +
103B GLU* 3.0 32.9 + - + +
104B GLN* 3.2 13.8 + - - +
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Residues in contact with MET 101 (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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99B ASP 3.4 7.6 + - - +
100B ASP* 1.3 73.6 + - - +
102B GLN* 1.3 62.3 + - - +
104B GLN* 3.4 28.3 - - - +
105B LEU* 3.2 23.0 + - - +
142B ASN 5.2 6.1 - - - +
143B GLN* 4.4 9.4 - - - +
144B PRO* 3.8 37.7 - - + -
147B LEU* 4.9 4.1 - - - +
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Residues in contact with GLN 102 (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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100B ASP* 3.1 20.0 + - - +
101B MET* 1.3 80.4 - - - +
103B GLU* 1.3 66.9 + - - +
105B LEU* 3.8 11.7 + - - +
106B SER* 3.4 23.2 + - - +
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Residues in contact with GLU 103 (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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95B GLN* 3.7 32.2 + - + +
98B SER* 3.7 25.4 - - - +
100B ASP* 3.0 20.2 + - + +
102B GLN* 1.3 81.7 + - - +
104B GLN* 1.3 60.6 + - - +
105B LEU 3.2 1.8 - - - -
106B SER* 3.2 8.0 + - - -
107B ALA* 2.9 32.1 + - - +
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Residues in contact with GLN 104 (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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95B GLN 4.0 6.2 + - - -
96B LEU* 4.2 3.1 - - - +
98B SER 3.1 28.7 + - - +
99B ASP* 4.1 9.5 + - - +
100B ASP 3.2 11.9 + - - +
101B MET* 3.4 36.3 - - - +
103B GLU* 1.3 76.6 - - - +
105B LEU* 1.3 56.0 + - - +
107B ALA* 3.7 3.5 - - - +
108B THR* 3.0 33.1 + - - -
134B ARG* 3.2 17.8 - - - +
138B PHE* 3.7 28.0 - - + -
143B GLN* 5.0 0.9 - - - +
147B LEU* 4.0 11.8 - - + +
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Residues in contact with LEU 105 (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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101B MET 3.2 12.9 + - - +
102B GLN* 3.9 14.1 - - - +
103B GLU 3.2 0.6 - - - -
104B GLN* 1.3 77.5 - - - +
106B SER* 1.3 67.5 + - - +
107B ALA 3.1 0.2 + - - -
108B THR* 3.2 2.1 + - - -
109B VAL* 3.0 35.3 + - + +
146B MET* 3.6 28.7 - - + +
147B LEU* 3.5 42.5 - - + +
150B GLU* 4.5 8.5 - - + -
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Residues in contact with SER 106 (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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95B GLN* 3.3 20.8 + - - -
102B GLN* 3.4 18.5 + - - +
103B GLU* 3.2 11.5 + - - -
105B LEU* 1.3 79.0 - - - +
107B ALA* 1.3 60.7 + - - +
109B VAL* 3.4 8.2 + - - +
110B LYS* 3.2 28.6 + - - +
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Residues in contact with ALA 107 (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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92B MET* 4.1 5.4 - - - +
95B GLN* 3.7 17.0 - - + +
96B LEU* 3.5 41.1 - - + +
103B GLU 2.9 16.4 + - - +
104B GLN 3.7 1.1 - - - +
106B SER* 1.3 73.8 - - - +
108B THR* 1.3 66.2 + - - +
109B VAL 3.0 1.8 - - - -
110B LYS* 3.0 16.9 + - - +
111B PHE* 3.1 17.9 + - + -
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Residues in contact with THR 108 (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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96B LEU* 3.4 9.8 - - - +
104B GLN 3.0 7.5 + - - -
105B LEU 3.2 4.0 + - - -
107B ALA* 1.3 77.7 - - - +
109B VAL* 1.3 56.5 + - - +
111B PHE* 3.6 4.8 + - - +
112B ARG* 3.0 25.3 + - - +
135B LEU* 4.0 8.2 - - + +
138B PHE* 3.0 34.0 - - + -
147B LEU* 4.2 7.9 - - + -
150B GLU* 3.5 13.2 - - + +
151B ALA* 3.4 36.8 - - + +
154B ALA* 4.7 1.0 - - + +
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Residues in contact with VAL 109 (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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105B LEU* 3.0 37.4 + - + +
106B SER* 3.6 8.7 - - - +
107B ALA 3.0 1.0 - - - -
108B THR* 1.3 74.5 - - - +
110B LYS* 1.3 66.0 + - - +
112B ARG* 3.6 20.3 + - - +
113B GLN* 3.1 36.2 + - - +
150B GLU* 3.8 30.3 - - + +
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Residues in contact with LYS 110 (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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88B GLU* 4.3 23.8 - - - +
92B MET* 3.8 25.6 - - + -
95B GLN* 3.3 35.9 + - - +
106B SER* 3.2 13.8 + - - +
107B ALA* 3.0 10.4 + - - +
109B VAL* 1.3 80.4 - - - +
111B PHE* 1.3 61.5 + - - +
113B GLN* 3.1 16.3 + - - +
114B ILE* 3.1 29.1 + - + +
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Residues in contact with PHE 111 (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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89B LEU* 4.6 9.4 - - + -
92B MET* 3.5 49.3 - - + +
93B THR* 4.2 8.3 - - - -
96B LEU* 3.8 27.1 - - + -
107B ALA 3.1 20.3 + - - -
108B THR* 3.7 8.7 - - - +
110B LYS* 1.3 73.4 - - - +
112B ARG* 1.3 65.4 + - - +
113B GLN 3.1 0.2 + - - -
114B ILE* 3.2 4.3 - - + +
115B LEU* 3.0 35.4 + - + +
126B VAL* 3.5 44.0 - - + -
129B ALA* 5.2 0.9 - - + -
131B VAL* 3.6 25.6 - - + -
135B LEU* 5.1 5.6 - - + -
154B ALA* 4.9 4.5 - - + -
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Residues in contact with ARG 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 THR 3.0 16.4 + - - +
109B VAL* 3.8 16.8 + - - +
111B PHE* 1.3 78.5 - - - +
113B GLN* 1.3 78.1 + - - +
115B LEU* 3.7 3.3 - - - +
116B SER* 2.9 30.3 + - - -
150B GLU* 2.6 42.9 + - - +
153B TRP* 3.5 68.3 - - + -
154B ALA* 4.0 19.9 - - + +
157B ASN* 3.9 0.5 + - - -
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Residues in contact with GLN 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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109B VAL* 3.1 29.9 + - - +
110B LYS* 3.1 19.4 + - - +
111B PHE 3.1 0.8 - - - -
112B ARG* 1.3 96.7 - - - +
114B ILE* 1.3 68.8 + - + +
115B LEU 3.1 1.8 - - - -
116B SER* 3.2 15.2 + - - +
117B ARG* 3.6 6.6 + - - +
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Residues in contact with ILE 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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89B LEU* 4.1 13.5 - - + -
92B MET* 4.0 24.7 - - + -
110B LYS* 3.1 15.1 + - + +
111B PHE* 3.2 12.6 - - - +
113B GLN* 1.3 79.7 - - + +
115B LEU* 1.3 63.7 + - - +
117B ARG* 3.2 20.4 + - - +
122B PRO* 2.9 34.9 - - + +
126B VAL* 3.8 26.7 - - + -
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Residues in contact with LEU 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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111B PHE* 3.0 26.7 + - + +
112B ARG 3.7 6.5 - - - +
113B GLN 3.1 0.2 - - - -
114B ILE* 1.3 79.6 - - - +
116B SER* 1.3 57.9 + - - +
117B ARG 3.2 1.9 + - - +
121B PRO* 3.8 17.8 - - - +
122B PRO* 4.2 3.8 - - - +
123B ILE* 4.1 22.9 - - + +
126B VAL* 3.8 36.3 - - + -
135B LEU* 5.4 0.7 - - + -
154B ALA* 3.4 39.0 - - + +
157B ASN* 3.9 21.3 - - + +
158B ILE* 4.1 21.5 - - + -
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Residues in contact with SER 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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118A GLU* 4.9 10.3 + - - +
112B ARG* 2.9 23.9 + - - -
113B GLN* 3.2 9.8 + - - -
114B ILE 3.1 0.8 - - - -
115B LEU* 1.3 74.8 - - - +
117B ARG* 1.3 67.6 + - - +
118B GLU* 3.2 4.2 + - - +
153B TRP* 4.1 11.9 + - - -
157B ASN* 3.0 19.9 + - - +
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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