Contacts of the strand formed by residues 26 - 30 (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 TYR 26 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ASP* 1.3 79.2 - - - +
27G CYS* 1.3 69.8 + - - +
28G VAL* 3.5 12.8 - - + -
169G LEU* 3.2 41.1 - - + +
170G ARG* 4.8 4.7 - - - -
173G GLN* 2.6 30.0 + - + +
180G ILE* 3.7 30.9 - - + +
182G HIS* 2.8 44.7 + - + -
193G LEU* 3.5 31.1 - - + +
194G ALA* 3.4 2.4 - - - -
195G ASP* 2.8 34.8 + - - +
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Residues in contact with CYS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G PHE* 3.7 31.9 - - - -
22G MET* 3.3 26.0 - - + -
23G GLY 5.6 0.4 - - - +
25G ASP* 3.6 4.9 + - - +
26G TYR* 1.3 76.4 - - - +
28G VAL* 1.3 86.1 + - - +
180G ILE 2.8 16.4 + - - +
181G LEU* 3.8 8.5 - - + -
182G HIS 3.2 10.2 + - - -
196G GLU* 3.8 14.6 - - + +
198G ALA* 4.8 3.4 - - - -
208G LYS* 4.1 17.0 - - - +
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G TYR* 3.5 25.4 - - + -
27G CYS* 1.3 88.7 - - - +
29G LEU* 1.3 67.6 + - - +
30G LEU* 4.8 2.7 - - + +
182G HIS* 3.1 26.2 - - + +
184G THR* 5.2 4.7 - - - +
189G GLU 4.8 1.3 - - - +
190G ALA* 3.7 31.0 - - + +
193G LEU* 4.5 4.3 - - + -
194G ALA* 3.5 22.7 - - + +
196G GLU 3.3 3.8 + - - -
197G VAL* 3.2 9.5 - - - +
198G ALA 3.1 17.9 + - - -
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Residues in contact with LEU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G PHE* 5.6 0.7 - - + -
28G VAL* 1.3 73.3 - - - +
30G LEU* 1.3 63.6 + - - +
37G LYS* 4.4 5.4 - - + -
40G PHE* 4.0 20.0 - - + -
181G LEU* 3.3 27.6 - - + -
182G HIS 3.0 9.1 + - - +
183G VAL* 3.3 36.6 - - + +
184G THR 3.2 23.8 + - - +
198G ALA* 3.4 25.1 - - + +
199G VAL 4.6 0.2 - - - +
200G MET* 3.9 35.0 - - + -
205G ILE* 4.4 9.2 - - + -
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Residues in contact with LEU 30 (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* 3.8 1.9 + - + -
29G LEU* 1.3 74.1 - - - +
31G GLY* 1.3 52.7 + - - +
37G LYS* 4.8 1.1 - - - -
184G THR* 3.3 4.9 - - - +
185G HIS 3.9 5.2 - - - -
186G ASP 3.5 43.3 - - - +
187G LEU* 3.5 28.3 - - + +
190G ALA* 3.7 23.8 - - + -
197G VAL* 4.0 14.6 - - + -
198G ALA 2.9 9.4 + - - +
199G VAL* 3.1 6.2 - - + +
200G MET* 2.7 33.3 + - - +
211G LEU* 4.5 0.9 - - + -
225G PHE* 3.5 12.3 - - + -
226G LEU* 3.7 16.6 - - + -
229G ARG* 4.3 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
------------------------------------------------------------
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