Contacts of the helix formed by residues 155 - 165 (chain H) in PDB entry 2ONK
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 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ALA* 6.2 0.4 - - - -
153H SER 3.5 5.2 + - - -
154H VAL* 1.3 71.7 - - - +
156H VAL* 1.3 60.7 + - - +
157H ARG* 3.1 51.1 + - - +
158H LEU* 2.7 56.0 + - + +
159H GLU 3.7 0.9 + - - -
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Residues in contact with VAL 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H ARG* 4.0 37.2 - - - +
154H VAL 3.0 4.9 + - - +
155H ASP* 1.3 73.5 + - - +
157H ARG* 1.3 64.8 + - + +
159H GLU* 2.8 24.1 + - + +
160H HIS* 2.9 36.5 + - + +
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Residues in contact with ARG 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F PRO* 3.8 34.4 - - + +
77F GLN* 3.3 34.9 + - - +
78F ASP* 3.6 17.4 + - - +
80F ALA* 3.9 7.0 - - + +
155H ASP* 2.9 30.4 + - - +
156H VAL* 1.3 75.9 - - + +
158H LEU* 1.3 56.4 + - - +
160H HIS* 2.7 19.3 + - + +
161H VAL* 2.7 36.0 + - - +
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ALA* 3.4 26.5 - - + +
81F LEU 3.3 28.9 - - - +
82F PHE* 3.3 22.5 - - + -
83F PRO* 3.8 11.2 - - + -
154H VAL* 4.2 2.0 - - + -
155H ASP* 2.7 45.9 + - + +
157H ARG* 1.3 72.3 - - - +
159H GLU* 1.3 54.3 + - - +
161H VAL* 3.6 0.5 + - - +
162H ALA* 3.1 22.9 + - - +
176H VAL* 3.9 15.0 - - + -
180H LEU* 3.9 20.6 - - + -
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Residues in contact with GLU 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H TYR* 3.0 19.9 + - - -
78H ARG* 3.2 40.8 + - - -
151H PHE* 5.8 0.2 - - - -
154H VAL* 3.8 9.6 - - + +
156H VAL* 2.8 14.2 + - + +
158H LEU* 1.3 77.7 - - - +
160H HIS* 1.3 69.2 + - - +
162H ALA* 3.2 3.3 + - - +
163H ARG* 3.1 28.4 + - - +
172H VAL* 3.5 26.7 - - + +
176H VAL* 4.2 9.2 - - + -
177H SER* 3.0 23.4 + - - +
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Residues in contact with HIS 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F GLU* 3.3 26.7 + - + -
47F ILE* 3.3 44.7 - - + +
74F PHE* 4.5 12.8 - + + -
156H VAL* 2.9 36.0 + - + +
157H ARG* 2.7 30.2 + - + +
159H GLU* 1.3 72.6 - - + +
161H VAL* 1.3 63.4 + - - +
163H ARG* 3.0 8.4 + - - +
164H THR* 2.9 19.1 + - - -
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Residues in contact with VAL 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F PHE* 4.2 12.3 - - + +
76F PRO* 3.4 25.4 - - + -
80F ALA* 3.0 33.2 - - + +
82F PHE* 4.4 1.8 - - + -
139F ARG* 3.7 30.1 - - - +
157H ARG 2.7 14.1 + - - +
158H LEU 3.7 4.9 - - - +
160H HIS* 1.3 71.3 - - - +
162H ALA* 1.3 53.2 + - - +
164H THR* 2.7 13.3 + - - -
165H LEU* 2.7 49.4 + - + +
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Residues in contact with ALA 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PHE* 3.7 11.2 - - + -
93F TYR* 3.7 14.6 - - - +
158H LEU 3.1 15.3 + - - +
159H GLU 3.4 6.3 - - - +
161H VAL* 1.3 79.4 - - - +
163H ARG* 1.3 60.6 + - - +
165H LEU* 3.5 8.2 + - - +
167H SER* 2.8 24.8 + - - -
172H VAL* 4.0 8.7 - - + -
176H VAL* 3.5 26.9 - - + -
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Residues in contact with ARG 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F GLY 5.2 0.4 + - - -
47F ILE* 4.9 8.6 - - + +
67F PRO* 3.4 41.4 - - + +
68F GLU* 2.6 36.5 + - - -
159H GLU* 3.1 14.5 + - - +
160H HIS* 3.0 12.3 + - - +
162H ALA* 1.3 73.8 - - - +
164H THR* 1.3 58.4 + - - +
166H GLY* 2.7 26.7 + - - -
167H SER 3.3 14.8 + - - +
169H PRO* 2.8 38.1 - - - +
172H VAL* 3.5 14.4 - - + -
2I ARG* 3.8 15.6 - - - +
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Residues in contact with THR 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA* 4.8 4.4 + - - +
47F ILE* 4.1 6.6 - - - +
67F PRO* 3.8 15.3 - - - +
70F ARG 4.9 2.8 - - - +
72F ILE 3.5 19.3 - - - +
73F GLY* 4.2 1.8 - - - -
74F PHE* 2.7 63.2 - - + +
143F ILE* 4.8 2.4 - - - +
160H HIS 2.9 13.3 + - - -
161H VAL* 2.7 13.7 + - - +
163H ARG* 1.3 72.7 - - - +
165H LEU* 1.3 65.4 + - + +
166H GLY 2.8 10.6 + - - -
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F GLY* 5.8 1.1 - - - -
74F PHE 5.4 1.8 - - - +
82F PHE* 4.3 6.1 - - + -
93F TYR* 3.9 25.9 - - + +
94F GLY* 3.3 26.8 - - - +
97F ASN* 5.8 0.7 + - - -
139F ARG* 3.4 47.8 - - + +
140F ALA* 4.6 6.3 - - - +
143F ILE* 3.4 30.9 - - + +
161H VAL* 2.7 31.4 + - + +
162H ALA 3.8 6.2 - - - +
163H ARG 3.2 0.6 - - - -
164H THR* 1.3 81.1 - - + +
166H GLY* 1.3 62.9 + - - +
167H SER* 3.7 2.1 - - - -
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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