Contacts of the helix formed by residues 108 - 120 (chain A) in PDB entry 2ONF
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 LYS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A MSE 3.5 29.6 + - + +
66A GLY 4.7 4.0 + - - -
67A ILE* 3.9 26.0 - - + -
104A GLU 5.0 5.2 - - - -
105A ASP* 3.0 26.8 + - - +
107A GLU* 1.3 89.7 - - + +
109A ILE* 1.3 59.8 + - - +
110A PRO 3.5 1.3 - - - -
111A ARG* 3.4 4.2 + - - +
112A ALA* 3.0 25.1 + - - +
140A EDO 3.7 25.8 - - - -
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Residues in contact with ILE 109 (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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58A PHE* 3.9 18.4 - - + -
67A ILE* 3.9 23.3 - - + -
99A ILE* 4.1 8.3 - - + -
101A VAL* 3.9 24.2 - - + -
105A ASP 3.6 11.9 - - - +
106A LYS* 3.1 12.0 + - - +
108A LYS* 1.3 74.9 - - - +
110A PRO* 1.4 69.8 - - + +
112A ALA* 4.2 1.3 - - - -
113A MSE 2.8 35.6 + - + +
136A TYR* 3.6 28.7 - - + -
138A PHE* 4.0 21.1 - - + -
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Residues in contact with PRO 110 (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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106A LYS 3.4 12.8 - - - +
107A GLU* 3.6 14.1 - - - +
108A LYS 3.6 0.4 - - - -
109A ILE* 1.4 88.6 - - + +
111A ARG* 1.3 56.5 + - - +
113A MSE 3.9 2.8 - - + +
114A GLN* 3.0 28.4 + - - +
136A TYR* 3.5 21.3 - - + +
138A PHE* 5.8 0.4 - - + -
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Residues in contact with ARG 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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65A MSE 4.3 5.8 - - + -
107A GLU 5.3 0.2 + - - -
108A LYS 3.4 2.2 + - - +
109A ILE 3.2 0.6 - - - -
110A PRO* 1.3 77.6 - - - +
112A ALA* 1.3 58.7 + - - +
114A GLN* 2.7 40.4 + - - +
115A LEU* 2.9 59.6 + - + +
140A EDO 3.9 38.1 + - - +
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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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58A PHE* 3.5 25.1 - - + -
61A PHE* 4.6 8.1 - - + +
62A LYS 5.5 0.9 - - - +
65A MSE 3.9 16.9 - - - +
67A ILE* 3.8 20.2 - - + -
108A LYS 3.0 17.5 + - - +
109A ILE* 3.1 4.5 + - - +
111A ARG* 1.3 76.3 - - - +
113A MSE 1.3 57.8 + - - +
115A LEU* 3.5 4.1 + - - +
116A ALA* 2.9 29.1 + - - +
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Residues in contact with MSE 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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54A LEU* 4.8 4.6 - - + +
58A PHE* 3.7 14.8 - - + -
72A TRP* 3.5 34.5 - - + -
97A VAL* 4.2 10.5 - - + -
99A ILE* 3.8 5.6 - - + -
109A ILE* 2.8 37.9 + - + +
110A PRO* 3.9 3.1 - - + +
112A ALA* 1.3 70.8 - - - +
114A GLN* 1.3 65.0 + - - +
116A ALA* 3.8 4.2 - - - +
117A GLU* 3.0 26.7 + - - +
134A VAL* 3.7 29.8 - - + +
136A TYR* 3.8 31.9 - - + -
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Residues in contact with GLN 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 PRO 3.0 19.8 + - - +
111A ARG* 2.7 39.9 + - - +
113A MSE 1.3 75.1 - - - +
115A LEU* 1.3 68.5 + - - +
117A GLU* 3.8 4.1 - - - +
118A LYS* 2.9 57.8 + - + +
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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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61A PHE* 3.7 34.9 - - + -
65A MSE 4.3 15.0 - - + -
111A ARG* 2.9 53.4 + - + +
112A ALA 3.7 3.1 - - - +
114A GLN* 1.3 93.3 - - - +
116A ALA* 1.3 65.9 + - - +
118A LYS* 3.3 1.3 + - + +
119A TYR* 3.0 54.4 + - + +
142A EDO 5.4 1.3 - - - +
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Residues in contact with ALA 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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54A LEU* 3.9 15.2 - - + +
57A THR* 3.6 12.6 - - - +
58A PHE* 3.6 38.8 - - + +
61A PHE* 4.1 2.2 - - - -
112A ALA 2.9 18.2 + - - +
113A MSE 3.8 6.5 - - - +
114A GLN 3.4 0.2 - - - -
115A LEU* 1.3 74.3 - - - +
117A GLU* 1.3 57.8 + - - +
120A CYS* 3.0 32.9 + - - +
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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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54A LEU* 3.8 12.3 - - + +
113A MSE 3.0 17.4 + - - +
114A GLN* 4.0 3.9 - - - +
116A ALA* 1.3 75.4 - - - +
118A LYS* 1.3 62.2 + - - +
119A TYR 3.5 0.3 + - - -
120A CYS* 3.7 2.2 + - - -
123A SER* 3.6 8.0 - - - +
127A ARG* 2.9 30.9 + - - +
132A GLU* 3.6 43.7 - - - +
134A VAL* 3.7 29.3 + - + +
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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 GLN* 2.9 38.9 + - - +
115A LEU* 3.3 5.2 + - - +
117A GLU* 1.3 76.9 - - - +
119A TYR* 1.3 91.6 + - + +
124A ARG* 3.0 25.7 + - - +
127A ARG* 3.3 17.2 + - - +
85B GLU* 4.4 13.3 + - - -
86B LYS* 4.8 8.3 - - - +
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Residues in contact with TYR 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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57A THR* 3.9 16.0 + - + +
61A PHE* 3.5 20.4 - + + -
115A LEU* 3.0 43.1 + - + +
118A LYS* 1.3 103.7 + - + +
120A CYS* 1.3 67.1 + - - +
121A PHE* 3.1 6.2 + - - +
124A ARG* 3.3 33.7 + - - +
142A EDO 3.7 19.8 + - - +
85B GLU 3.7 1.1 + - - -
86B LYS* 3.1 50.0 - - - -
87B GLY* 3.7 11.7 - - - -
88B PHE* 4.3 6.6 + - - +
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Residues in contact with CYS 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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50A LEU* 4.2 5.6 - - - -
53A CYS* 3.5 24.2 - - - -
54A LEU* 3.7 21.3 - - - -
57A THR* 3.5 14.3 - - - +
116A ALA 3.0 20.2 + - - +
117A GLU* 3.9 1.6 - - - +
118A LYS 3.5 0.6 - - - +
119A TYR* 1.3 75.7 - - - +
121A PHE* 1.3 60.2 + - - +
122A ILE 3.7 0.2 - - - -
123A SER* 3.1 39.0 + - - +
124A ARG* 2.9 27.5 + - - +
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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