Contacts of the helix formed by residues 155 - 165 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ALA* 6.4 0.2 - - - -
153C SER 3.5 4.8 + - - -
154C VAL* 1.3 72.0 - - - +
156C VAL* 1.3 60.7 + - - +
157C ARG* 3.1 51.1 + - - +
158C LEU* 2.7 55.6 + - + +
159C GLU 3.7 0.7 + - - -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 4.0 36.6 - - - +
154C VAL 3.0 5.5 + - - +
155C ASP* 1.3 74.5 + - - +
157C ARG* 1.3 63.5 + - + +
159C GLU* 2.8 24.1 + - - +
160C HIS* 2.9 36.5 + - + +
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 5.9 0.9 - - - +
74A PHE* 5.8 0.4 - - + -
76A PRO* 4.0 34.3 - - + +
77A GLN* 3.5 32.4 + - - +
78A ASP* 4.1 11.2 + - - +
80A ALA* 4.3 3.8 - - + -
155C ASP* 2.9 29.9 + - - +
156C VAL* 1.3 77.0 - - + +
158C LEU* 1.3 55.4 + - - +
160C HIS* 2.7 19.2 + - + +
161C VAL* 2.7 38.1 + - - +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ALA* 3.5 36.1 - - + +
81A LEU 3.6 17.7 - - - +
82A PHE* 3.4 24.9 - - + -
83A PRO* 4.1 9.2 - - + -
154C VAL* 4.2 2.2 - - + -
155C ASP* 2.7 46.8 + - + +
157C ARG* 1.3 72.0 - - - +
159C GLU* 1.3 56.0 + - - +
161C VAL* 3.6 0.3 + - - +
162C ALA* 3.0 23.2 + - - +
176C VAL* 3.9 13.9 - - + -
180C LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C TYR* 3.1 19.0 + - - -
78C ARG* 3.1 39.7 + - - -
151C PHE* 5.8 0.2 - - - -
154C VAL* 3.8 10.4 - - + +
156C VAL* 2.8 15.4 + - + +
158C LEU* 1.3 78.2 - - - +
160C HIS* 1.3 68.5 + - - +
162C ALA* 3.2 3.7 + - - +
163C ARG* 3.1 28.7 + - - +
172C VAL* 3.5 26.6 - - + +
176C VAL* 4.2 9.6 - - + -
177C SER* 3.0 23.6 + - - +
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Residues in contact with HIS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.5 23.6 + - - -
47A ILE* 3.0 46.6 - - + +
74A PHE* 4.8 9.0 - + + -
156C VAL* 2.9 36.3 + - + +
157C ARG* 2.7 30.4 + - + +
159C GLU* 1.3 73.3 - - + +
161C VAL* 1.3 64.0 + - - +
163C ARG* 3.0 10.6 + - - +
164C THR* 2.9 21.0 + - - -
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.1 16.2 - - + +
76A PRO* 3.5 24.0 - - + -
80A ALA* 3.2 30.1 - - + +
82A PHE* 4.5 1.8 - - + -
139A ARG* 3.9 22.4 - - - +
157C ARG 2.7 15.7 + - - +
158C LEU* 3.7 4.9 - - - +
160C HIS* 1.3 71.5 - - - +
162C ALA* 1.3 52.7 + - - +
164C THR* 2.7 13.3 + - - -
165C LEU* 2.7 55.1 + - + +
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.8 10.8 - - + -
93A TYR* 3.6 18.7 - - - +
158C LEU 3.0 15.8 + - - +
159C GLU 3.4 6.3 - - - +
161C VAL* 1.3 81.8 - - - +
163C ARG* 1.3 60.5 + - - +
165C LEU* 3.5 5.7 + - - -
167C SER* 2.8 25.1 + - - -
172C VAL* 4.0 8.5 - - + -
176C VAL* 3.5 26.7 - - + -
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Residues in contact with ARG 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 5.6 3.5 - - - +
66A PRO* 4.3 0.4 - - - +
67A PRO* 3.4 35.2 - - + +
68A GLU* 2.5 48.4 + - - +
159C GLU* 3.1 14.7 + - - +
160C HIS* 3.0 13.6 + - - +
162C ALA* 1.3 72.9 - - - +
164C THR* 1.3 58.2 + - - +
166C GLY* 2.7 27.0 + - - -
167C SER 3.3 14.4 - - - +
169C PRO* 2.8 42.7 - - - +
172C VAL* 3.5 15.3 - - + -
2D ARG* 4.2 10.5 - - - +
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Residues in contact with THR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.7 5.6 + - - +
47A ILE* 4.0 7.6 - - - +
67A PRO* 3.6 17.4 - - - +
70A ARG 4.8 3.1 - - - +
71A GLY 5.5 0.2 - - - -
72A ILE* 3.6 19.6 - - + +
73A GLY 4.1 0.2 - - - -
74A PHE* 3.1 58.7 - - + +
143A ILE* 4.7 2.6 - - - +
160C HIS 2.9 14.0 + - - -
161C VAL 2.7 14.3 + - - +
163C ARG* 1.3 72.9 - - - +
165C LEU* 1.3 65.2 + - + +
166C GLY* 2.8 11.2 + - - -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY* 5.7 1.3 - - - -
74A PHE 5.4 2.9 - - - +
82A PHE* 4.3 5.8 - - + -
93A TYR* 4.0 23.5 - - + +
94A GLY* 3.2 27.7 - - - +
139A ARG* 3.5 47.3 - - + +
140A ALA* 4.6 6.3 - - - -
143A ILE* 3.3 31.4 - - + +
161C VAL* 2.7 33.7 + - + +
162C ALA 3.8 5.8 - - - +
163C ARG 3.2 0.4 - - - -
164C THR* 1.3 80.0 - - + +
166C GLY* 1.3 62.0 + - - +
167C SER* 3.7 2.2 - - - -
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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