Contacts of the strand formed by residues 196 - 201 (chain G) 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 GLU 196 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1G MET* 5.3 6.1 - - - +
23G GLY* 3.7 19.1 + - - -
25G ASP* 4.2 11.2 - - - +
26G TYR 3.8 1.4 + - - -
27G CYS* 3.8 8.2 - - + -
28G VAL 3.3 13.1 + - - -
194G ALA* 2.9 17.5 - - - +
195G ASP* 1.3 87.3 + - + +
197G VAL* 1.3 64.0 + - - +
208G LYS* 3.1 40.8 + - - +
209G GLY* 3.1 17.1 - - - +
210G LYS* 5.0 4.9 - - + +
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Residues in contact with VAL 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL 3.2 10.3 - - - +
30G LEU* 4.0 22.2 - - + -
190G ALA* 4.2 8.5 - - + +
194G ALA* 3.2 20.0 - - + -
196G GLU* 1.3 81.7 - - - +
198G ALA* 1.3 75.3 + - - +
199G VAL* 4.3 0.4 - - + -
208G LYS* 3.1 6.0 - - - -
209G GLY 2.6 33.6 + - - +
210G LYS* 5.3 0.2 - - - -
211G LEU* 4.0 24.2 - - + +
214G LEU* 3.7 25.9 - - + +
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Residues in contact with ALA 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G PHE* 4.0 24.5 - - + -
27G CYS* 4.8 2.1 - - - -
28G VAL 3.1 6.6 + - - +
29G LEU* 3.4 21.1 - - + -
30G LEU 2.9 21.0 + - - -
197G VAL* 1.3 76.4 - - - +
199G VAL* 1.3 72.8 + - - +
205G ILE* 4.1 15.5 - - + -
207G GLU 3.4 5.8 - - - -
208G LYS* 3.9 7.4 - - + +
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Residues in contact with VAL 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 3.1 14.6 - - + +
197G VAL* 4.3 3.6 - - + -
198G ALA* 1.3 84.7 - - - +
200G MET* 1.3 65.8 + - - +
201G LEU* 4.4 10.5 - - + -
205G ILE* 3.6 3.4 - - - +
206G VAL* 3.0 27.5 + - - +
207G GLU 3.0 16.5 + - - +
214G LEU* 4.1 15.9 - - + -
222G VAL* 4.0 39.9 - - + -
225G PHE* 4.3 17.5 - - + -
226G LEU* 4.7 5.6 - - + -
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Residues in contact with MET 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G LEU* 4.5 6.5 - - + -
18G VAL* 4.8 0.4 - - + -
29G LEU* 3.9 24.4 - - + +
30G LEU 2.7 13.8 + - - +
31G GLY* 3.4 15.1 - - - -
32G PRO* 3.6 1.7 - - - +
35G ALA* 2.9 33.7 - - + +
36G GLY* 3.1 31.9 - - - +
37G LYS* 3.8 8.1 - - + -
40G PHE* 4.3 10.1 - - + -
198G ALA 4.3 0.2 - - - -
199G VAL* 1.3 73.4 - - - +
201G LEU* 1.3 73.6 + - - +
203G GLY* 3.5 20.9 - - - +
204G ARG 3.4 9.4 - - - +
205G ILE* 3.5 23.6 - - + -
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Residues in contact with LEU 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PRO* 3.4 26.7 - - + -
35G ALA* 4.3 2.2 - - - -
199G VAL* 4.1 13.7 + - + -
200G MET* 1.3 84.8 - - - +
202G ASN* 1.3 76.0 + - - +
203G GLY 3.5 0.2 - - - -
204G ARG* 2.9 21.9 + - - +
206G VAL* 3.9 16.3 - - + +
221G GLU* 3.4 57.7 - - + +
222G VAL* 4.5 1.8 - - - +
225G PHE* 4.9 9.9 - - + -
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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