Contacts of the helix formed by residues 155 - 165 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA* 6.3 0.2 - - - -
153D SER 3.5 5.0 + - - -
154D VAL* 1.3 71.8 - - - +
156D VAL* 1.3 60.5 + - - +
157D ARG* 3.1 52.0 + - - +
158D LEU* 2.7 56.2 + - + +
159D GLU 3.7 0.9 + - - -
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ARG* 4.3 26.5 - - - +
154D VAL 3.0 6.0 + - - +
155D ASP* 1.3 74.5 + - - +
157D ARG* 1.3 62.2 + - + +
159D GLU* 2.8 29.2 + - - +
160D HIS* 2.9 38.7 + - + +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 6.1 0.4 - - - +
74B PHE* 5.9 1.1 - - + -
76B PRO* 4.0 27.4 - - + +
77B GLN* 3.6 29.4 + - - +
78B ASP* 4.0 10.5 + - - +
80B ALA* 4.2 14.3 - - + +
155D ASP* 2.9 30.1 + - - +
156D VAL* 1.3 75.4 - - + +
158D LEU* 1.3 57.0 + - - +
160D HIS* 2.7 18.6 + - + +
161D VAL* 2.6 38.0 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA* 3.7 22.4 - - + +
81B LEU 3.8 12.6 - - - +
82B PHE* 3.3 39.5 - - + -
83B PRO* 3.9 12.8 - - + -
154D VAL* 4.2 1.8 - - + -
155D ASP* 2.7 47.4 + - + +
157D ARG* 1.3 73.0 - - - +
159D GLU* 1.3 55.3 + - - +
161D VAL 3.6 0.2 + - - -
162D ALA* 3.0 24.3 + - - +
176D VAL* 3.9 15.0 - - + +
180D LEU* 3.9 20.9 - - + -
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 3.5 11.1 + - - -
78D ARG* 2.7 49.5 + - - -
154D VAL* 3.8 9.1 - - + +
156D VAL* 2.8 16.1 + - + +
158D LEU* 1.3 78.2 - - - +
160D HIS* 1.3 68.4 + - - +
162D ALA* 3.2 3.1 + - - +
163D ARG* 3.1 29.1 + - - +
172D VAL* 3.5 26.2 - - + +
176D VAL* 4.2 8.5 - - + -
177D SER* 3.0 23.5 + - - +
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 4.0 12.6 + - - -
47B ILE* 3.1 52.0 - - + +
74B PHE* 5.4 6.7 - + + -
156D VAL* 2.9 36.6 + - + +
157D ARG* 2.7 31.2 + - + +
159D GLU* 1.3 72.2 - - - +
161D VAL* 1.3 63.9 + - + +
163D ARG* 3.0 14.3 + - - +
164D THR* 2.9 20.8 + - - -
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PHE* 4.5 15.0 - - + +
76B PRO* 4.2 17.0 - - + -
80B ALA* 3.5 25.1 - - + -
82B PHE* 3.9 11.4 - - + -
139B ARG* 4.3 16.2 - - - +
157D ARG* 2.6 20.7 + - + +
158D LEU 3.7 4.7 - - - +
160D HIS* 1.3 72.7 - - + +
162D ALA* 1.3 51.4 + - - +
164D THR* 2.7 16.4 + - + -
165D LEU* 2.7 56.8 + - + +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.1 3.6 - - + -
93B TYR* 3.1 35.5 - - + +
158D LEU 3.0 16.0 + - - +
159D GLU 3.2 6.3 + - - +
161D VAL* 1.3 79.7 - - - +
163D ARG* 1.3 61.0 + - - +
165D LEU 3.5 4.7 + - - -
167D SER* 2.8 24.8 + - - -
172D VAL* 4.0 8.3 - - + -
176D VAL* 3.5 18.6 - - + -
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Residues in contact with ARG 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 5.9 1.6 - - + -
66B PRO* 4.8 1.8 - - - +
67B PRO* 3.9 24.3 - - + +
68B GLU* 2.8 60.8 + - - +
2C ARG* 4.7 6.5 - - - +
159D GLU* 3.1 14.5 + - - +
160D HIS* 3.0 12.6 + - - +
162D ALA* 1.3 72.7 - - - +
164D THR* 1.3 57.9 + - - +
166D GLY* 2.7 21.3 + - - -
167D SER 3.3 13.5 - - - +
169D PRO* 2.8 46.7 - - - +
172D VAL* 3.5 14.8 - - + -
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Residues in contact with THR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 5.3 2.6 + - - +
47B ILE* 4.1 11.4 - - - +
67B PRO* 3.8 22.6 + - - +
68B GLU* 4.4 1.6 - - - +
70B ARG 4.8 2.4 - - - +
71B GLY 6.0 0.2 - - - -
72B ILE 3.8 23.6 - - - +
73B GLY* 4.8 0.9 - - - -
74B PHE* 3.7 34.3 - - + +
143B ILE* 4.9 4.0 - - + +
160D HIS 2.9 13.3 + - - -
161D VAL* 2.7 19.3 + - + +
163D ARG* 1.3 72.3 - - - +
165D LEU* 1.3 68.3 + - + +
166D GLY* 2.8 11.4 + - - -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLY* 6.4 0.9 - - - -
82B PHE* 4.0 7.0 - - + -
93B TYR* 3.2 47.7 - - + +
94B GLY* 3.2 28.6 + - - +
139B ARG* 4.2 23.6 - - + +
140B ALA* 5.5 2.7 - - - -
143B ILE* 3.1 31.4 - - + -
161D VAL* 2.7 38.2 + - + +
162D ALA 3.8 0.4 - - - -
163D ARG 3.2 0.4 - - - -
164D THR* 1.3 80.2 - - + +
166D GLY* 1.3 64.0 + - - +
167D SER* 3.7 1.1 - - - -
171D ARG* 5.4 0.3 + - - -
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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