Contacts of the helix formed by residues 168 - 176 (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 SER 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU* 3.9 7.8 - - - -
2C ARG* 4.9 9.6 - - - -
166D GLY 4.3 0.2 - - - -
167D SER* 1.3 74.4 - - - +
169D PRO* 1.3 78.9 - - - +
170D LEU* 3.7 10.3 + - - +
171D ARG* 2.8 42.8 + - - +
172D VAL* 2.8 12.0 + - - +
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Residues in contact with PRO 169 (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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68B GLU* 4.0 4.7 - - - +
2C ARG* 4.3 24.5 - - + +
5C PHE* 4.3 14.4 - - + -
74D TYR* 5.2 2.8 + - - -
163D ARG* 2.8 33.5 - - + +
168D SER* 1.3 88.8 - - - +
170D LEU* 1.3 61.9 + - + +
172D VAL* 3.5 7.9 + - + +
173D PHE* 3.0 24.1 + - - +
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Residues in contact with LEU 170 (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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5C PHE* 3.1 55.3 - - + -
168D SER* 3.0 9.6 - - - +
169D PRO* 1.3 78.0 - - + +
171D ARG* 1.3 67.9 + - + +
173D PHE* 3.4 4.7 + - - +
174D PHE* 3.1 49.8 - - + -
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Residues in contact with ARG 171 (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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96B ARG* 4.0 36.5 + - - +
97B ASN* 5.2 10.3 + - - +
165D LEU 5.4 0.2 + - - -
166D GLY 3.2 21.2 + - - -
167D SER* 2.9 29.3 + - - +
168D SER* 2.8 31.8 + - - +
170D LEU* 1.3 79.2 - - + +
172D VAL* 1.3 61.6 + - - +
174D PHE* 3.1 3.4 + - - +
175D THR* 2.3 33.8 + - - +
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Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TYR* 4.4 2.2 - - - -
74D TYR* 5.3 2.7 - - - +
159D GLU* 3.5 44.0 - - + +
162D ALA* 4.0 12.3 - - + -
163D ARG* 3.5 29.6 - - + -
167D SER* 3.5 8.0 + - - +
168D SER 2.8 22.6 + - - +
169D PRO* 3.5 7.9 - - + +
171D ARG* 1.3 72.4 - - - +
173D PHE* 1.3 59.1 + - - +
175D THR* 4.0 2.9 - - - -
176D VAL* 2.6 41.4 + - + -
177D SER* 3.2 6.4 + - - +
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Residues in contact with PHE 173 (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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5C PHE* 3.9 17.7 - + + -
9C LEU* 4.9 11.9 - - + -
70D THR* 4.4 10.5 - - + -
71D PRO* 5.3 2.0 - - + -
74D TYR* 3.4 58.3 + + + +
151D PHE* 3.8 5.4 - + - -
169D PRO 3.0 10.5 + - - +
170D LEU 3.4 9.9 - - - +
172D VAL* 1.3 80.3 - - - +
174D PHE* 1.3 87.8 + + - +
177D SER* 3.3 7.5 - - - -
178D LEU* 2.7 73.0 + - + +
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Residues in contact with PHE 174 (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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5C PHE* 3.9 5.8 - + - -
8C LEU* 6.3 1.8 - - + -
170D LEU* 3.1 41.7 - - + +
171D ARG* 3.1 6.6 + - - +
173D PHE* 1.3 103.3 - + - +
175D THR* 1.3 60.8 + - - +
178D LEU* 3.9 21.1 - - + +
179D PRO* 3.1 16.9 - - - +
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Residues in contact with THR 175 (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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84B HIS* 3.1 16.3 + - - -
85B LEU* 5.6 1.0 - - + +
93B TYR* 4.2 24.2 + - + -
167D SER* 4.9 0.2 + - - -
171D ARG* 2.3 37.8 + - - +
172D VAL* 3.8 1.2 + - - -
174D PHE* 1.3 77.5 - - - +
176D VAL* 1.3 60.7 + - - +
179D PRO* 3.0 18.8 - - - +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 4.6 8.7 - - + -
84B HIS* 4.4 6.5 - - + -
93B TYR* 3.8 16.4 - - + +
154D VAL* 4.7 0.9 - - + -
158D LEU* 3.9 29.2 - - + +
159D GLU* 4.2 7.2 - - + -
162D ALA* 3.5 28.9 - - + -
172D VAL* 2.6 21.4 + - + +
175D THR* 1.3 78.9 - - - +
177D SER* 1.3 70.7 + - - +
179D PRO* 3.3 1.3 - - - +
180D LEU* 3.1 43.4 + - + +
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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