Contacts of the strand formed by residues 26 - 30 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASP* 1.3 80.0 - - - +
27B CYS* 1.3 70.5 + - - +
28B VAL* 3.5 12.1 - - + -
169B LEU* 3.3 39.7 - - + +
170B ARG* 5.0 4.5 - - + -
173B GLN* 2.7 29.4 + - + +
180B ILE* 3.7 30.2 - - + +
182B HIS* 2.8 44.6 + + + -
193B LEU* 3.5 31.5 - - + +
194B ALA* 3.3 2.3 - - - -
195B ASP* 2.8 34.3 + - - +
196B GLU 3.7 0.5 + - - -
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Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.7 32.8 - - - -
22B MET* 3.3 26.5 - - + -
23B GLY 5.6 0.2 - - - +
25B ASP* 3.6 5.5 + - - +
26B TYR* 1.3 77.0 - - - +
28B VAL* 1.3 86.1 + - - +
29B LEU 4.7 0.7 - - - -
180B ILE 2.8 17.3 + - - +
181B LEU* 3.8 7.4 - - + -
182B HIS 3.2 10.4 + - - -
196B GLU* 3.7 12.8 - - + +
198B ALA 4.6 4.0 - - - -
208B LYS* 4.0 17.9 - - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.5 26.0 - - + -
27B CYS* 1.3 90.6 - - - +
29B LEU* 1.3 66.9 + - - +
30B LEU* 4.8 2.5 - - + +
182B HIS* 3.1 25.4 - - + +
184B THR* 5.2 5.8 - - - +
189B GLU 4.8 1.8 - - - +
190B ALA* 3.7 30.7 - - + +
193B LEU* 4.6 3.6 - - + -
194B ALA* 3.6 22.4 - - + +
196B GLU 3.3 3.0 + - - -
197B VAL* 3.2 10.0 - - - +
198B ALA 3.0 18.2 + - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 5.6 1.1 - - + -
28B VAL* 1.3 73.5 - - - +
30B LEU* 1.3 61.2 + - - +
37B LYS* 4.4 6.1 - - + -
40B PHE* 4.0 20.4 - - + -
181B LEU* 3.4 26.5 - - + -
182B HIS 3.0 8.1 + - - -
183B VAL* 3.4 35.2 - - + +
184B THR 3.2 24.9 + - - +
198B ALA* 3.4 24.5 - - + +
199B VAL 4.5 0.4 - - - +
200B MET* 3.8 35.9 - - + -
205B ILE* 4.4 8.3 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.8 2.2 + - + -
29B LEU* 1.3 74.1 - - - +
31B GLY* 1.3 58.0 + - - +
37B LYS* 4.8 1.1 - - - -
184B THR* 3.2 5.6 - - - +
185B HIS 3.8 6.1 - - - -
186B ASP 3.5 43.7 - - - +
187B LEU* 3.4 25.1 - - + +
190B ALA* 3.8 23.6 - - + -
197B VAL* 4.1 12.8 - - + -
198B ALA 2.9 9.6 + - - +
199B VAL* 3.2 6.8 - - + +
200B MET* 2.7 27.0 + - - +
211B LEU* 4.6 0.4 - - + -
225B PHE* 3.5 15.0 - - + -
226B LEU* 3.7 16.2 - - + -
229B 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