Contacts of the strand formed by residues 264 - 269 (chain K) in PDB entry 2ONM
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 ARG 264 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159K VAL* 4.2 21.3 - - + +
239K ASP 3.1 11.5 + - - +
240K LYS* 3.8 17.5 - - + +
241K VAL* 2.9 26.6 + - - +
262K LEU 3.8 0.6 + - - +
263K LYS* 1.3 75.0 - - - +
265K VAL* 1.3 61.8 + - - +
266K THR* 6.1 1.3 - - + -
483K GLN 3.9 6.7 + - - -
484K ALA* 3.8 18.8 + - - +
486K THR 2.9 29.0 + - - -
487K LYS* 4.2 15.9 - - - +
488K VAL* 5.1 1.2 - - - +
467L GLY 5.8 0.2 + - - -
473L SER* 4.3 26.3 - - - +
474L GLY* 4.2 16.5 - - - +
475L ARG* 4.6 13.5 - - - +
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Residues in contact with VAL 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241K VAL* 3.4 20.2 - - + +
253K ILE* 4.0 8.1 - - + -
254K GLN* 4.6 20.7 + - + +
257K ALA* 3.4 33.2 - - + -
263K LYS 3.5 4.7 + - - +
264K ARG* 1.3 81.5 - - - +
266K THR* 1.3 69.1 + - - +
267K LEU* 3.8 28.5 - - + -
473K SER* 4.0 10.6 + - - -
254L GLN* 4.8 7.9 - - - +
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Residues in contact with THR 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K LYS* 3.0 34.0 + - - +
241K VAL 3.3 4.1 + - - +
242K ALA* 3.4 10.2 - - - +
243K PHE 3.0 23.3 + - - +
264K ARG* 6.1 1.1 - - + -
265K VAL* 1.3 80.3 - - - +
267K LEU* 1.3 64.3 + - - +
268K GLU* 5.8 2.2 - - - -
473K SER* 3.9 13.7 - - - +
474K GLY* 4.6 12.1 - - - -
475K ARG 6.0 0.9 - - - +
476K GLU* 5.6 1.6 + - - -
484K ALA* 4.1 15.9 - - + -
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Residues in contact with LEU 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K PHE* 3.5 26.2 - - + -
250K GLY* 3.4 31.4 - - - +
253K ILE* 4.3 3.1 - - + -
254K GLN* 3.9 13.7 - - + +
265K VAL* 3.8 19.7 - - + -
266K THR* 1.3 83.8 - - - +
268K GLU* 1.3 66.4 + - - +
269K LEU* 3.6 14.1 - - + -
467K GLY 5.7 0.3 + - - -
471K SER 3.8 0.3 - - - +
472K GLY* 3.1 24.2 - - - -
473K SER* 3.3 22.1 + - - +
474K GLY 4.9 0.3 - - - +
262L LEU* 3.9 28.9 - - + -
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Residues in contact with GLU 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K MET* 6.1 0.2 - - - +
177K TRP* 4.8 4.2 - - - -
243K PHE 2.8 7.8 + - - +
244K THR* 3.2 34.1 - - + +
245K GLY 3.1 21.7 + - - +
266K THR* 5.8 2.2 - - - -
267K LEU* 1.3 76.7 - - - +
269K LEU* 1.3 65.7 + - - +
302K CYS* 5.8 1.4 - - - +
427K LEU* 4.4 7.3 - - - +
465K PHE* 3.6 30.8 - - - +
466K GLY* 3.5 24.6 - - - -
467K GLY 4.3 1.0 + - - -
471K SER 4.1 1.2 - - - +
473K SER 5.8 0.2 - - - +
474K GLY 4.6 4.0 - - - +
475K ARG 5.8 0.2 - - - -
476K GLU* 3.8 30.0 - - + +
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Residues in contact with LEU 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K PHE* 4.1 6.3 - - + -
245K GLY 3.4 7.4 - - - +
246K SER 3.5 23.3 - - - +
247K THR* 3.9 13.9 - - + +
250K GLY* 3.9 15.0 - - - -
267K LEU* 4.0 16.6 - - + -
268K GLU* 1.3 79.9 - - - +
270K GLY* 1.3 67.9 + - - +
302K CYS* 4.6 3.0 - - - +
427K LEU* 3.6 16.3 - - - +
470K MET 3.3 23.6 - - - +
471K SER 2.9 20.0 + - - +
472K GLY* 3.7 12.8 - - - +
262L LEU* 3.5 28.9 - - + -
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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