Contacts of the helix formed by residues 113 - 120 (chain B) in PDB entry 2ONL
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 LEU 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA 3.8 0.6 + - - -
112B ASP* 1.3 70.0 - - - +
114B ASN* 1.3 66.6 + - - +
116B ILE* 3.0 25.4 + - + -
117B VAL* 3.0 21.6 + - + +
122B LEU* 4.8 8.3 - - + -
130B LEU* 4.0 27.1 - - + -
134B ILE* 5.6 0.9 - - + -
153B PRO* 3.1 26.0 + - + +
156B LEU* 3.0 28.5 + - + +
158B VAL* 3.6 27.8 - - + +
164B LEU* 4.1 5.6 - - + -
212B ILE* 5.8 2.9 - - + -
216B LEU* 5.0 17.7 - - + -
372D ILE* 5.8 0.2 - - + -
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Residues in contact with ASN 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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112B ASP* 2.7 21.1 + - - +
113B LEU* 1.3 72.1 - - - +
115B ASN* 1.3 61.6 + - - +
117B VAL* 3.1 17.1 + - - +
118B LYS* 3.1 39.1 + - - +
152B LYS* 6.0 0.2 - - - +
153B PRO* 3.0 20.3 + - - +
154B SER* 3.5 30.3 - - - +
188B TYR* 5.1 3.8 + - - -
215B GLU* 4.8 8.1 - - - +
362D THR* 4.4 12.0 + - - +
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Residues in contact with ASN 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 ALA* 4.5 13.4 - - + +
112B ASP* 3.0 26.3 + - - +
114B ASN* 1.3 79.2 - - - +
116B ILE* 1.3 65.4 + - - +
118B LYS* 2.9 38.2 + - - +
119B CYS* 3.4 12.8 + - - +
364D ARG 4.0 11.9 + - - +
365D VAL* 5.0 0.2 - - - -
366D ASP 4.7 3.5 + - - -
367D TYR* 3.3 44.2 + - - +
369D GLN* 6.5 0.2 - - - -
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Residues in contact with ILE 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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111B ALA* 3.1 27.1 - - + +
112B ASP 3.0 26.6 + - - +
113B LEU* 3.0 24.7 + - + +
115B ASN* 1.3 78.3 - - - +
117B VAL* 1.3 59.6 + - - +
119B CYS* 3.4 5.4 + - - +
120B GLN* 2.9 42.6 + - - +
122B LEU* 4.3 13.2 - - + -
158B VAL* 4.2 6.7 - - + +
370D ILE* 3.6 39.3 - - + +
372D ILE* 4.3 16.4 - - + -
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Residues in contact with VAL 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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113B LEU* 3.0 12.3 + - + +
114B ASN* 3.1 16.1 + - - +
116B ILE* 1.3 74.6 - - - +
118B LYS* 1.3 67.7 + - + +
119B CYS 2.8 9.8 + - - -
120B GLN 3.0 20.6 + - - +
122B LEU* 4.1 21.1 - - + -
215B GLU* 5.5 12.1 - - + +
216B LEU* 4.5 22.0 - - + +
219B GLY* 5.9 6.7 - - - +
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Residues in contact with LYS 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 ASN* 3.1 50.6 + - - +
115B ASN* 2.9 27.6 + - - +
117B VAL* 1.3 81.0 - - + +
119B CYS* 1.3 57.2 + - - +
235D LEU* 3.4 32.0 - - - +
236D GLY* 5.8 0.2 - - - -
240D TYR* 4.7 6.4 + - + +
362D THR 4.3 9.3 + - - -
363D MET* 4.1 13.5 + - - +
364D ARG 4.1 4.2 + - - -
365D VAL* 2.9 48.7 - - + +
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Residues in contact with CYS 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 ASN 3.8 10.8 - - - +
116B ILE* 3.4 4.9 + - - -
117B VAL 2.9 0.4 - - - -
118B LYS* 1.3 81.9 - - + +
120B GLN* 1.3 62.3 + - - +
365D VAL* 6.0 1.3 - - + -
369D GLN 5.5 3.4 - - - -
370D ILE 4.6 14.4 - - - -
371D LYS* 3.1 46.1 + - - +
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Residues in contact with GLN 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 ILE* 2.9 17.3 + - - +
117B VAL* 3.0 20.4 + - - +
119B CYS* 1.3 88.0 - - - +
121B LYS* 1.3 69.7 + - - +
122B LEU* 3.5 15.1 + - + +
126B HIS* 4.1 15.3 - - - -
370D ILE 4.2 2.4 - - - +
371D LYS* 3.8 15.2 - - - +
372D ILE* 2.9 55.5 + - - +
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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