Contacts of the strand formed by residues 264 - 269 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473I SER* 4.3 23.6 - - - +
474I GLY* 4.6 15.3 - - - +
475I ARG* 5.8 4.2 - - - +
159J VAL* 4.5 17.1 - - + +
239J ASP 3.2 9.3 + - - +
240J LYS* 3.9 20.6 - - + +
241J VAL* 2.9 26.7 + - - +
262J LEU 3.8 0.9 + - - +
263J LYS* 1.3 76.0 - - - +
265J VAL* 1.3 62.9 + - - +
266J THR* 6.2 0.4 - - + -
483J GLN 3.4 8.3 + - - -
484J ALA* 3.3 28.0 + - - +
486J THR 2.7 32.1 + - - +
487J LYS* 5.1 7.3 - - - +
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Residues in contact with VAL 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I GLN* 5.5 1.3 - - - +
241J VAL* 3.4 18.6 - - + +
253J ILE* 4.3 7.0 - - + +
254J GLN* 4.1 28.0 + - - +
257J ALA* 3.4 33.9 - - + -
263J LYS 3.6 5.3 + - - +
264J ARG* 1.3 81.4 - - - +
266J THR* 1.3 69.2 + - - +
267J LEU* 3.8 29.7 + - + +
473J SER* 5.0 8.3 + - - -
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Residues in contact with THR 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J LYS* 3.2 28.3 + - - +
241J VAL 3.3 4.7 + - - +
242J ALA* 3.5 15.9 - - - +
243J PHE 3.0 25.5 + - - +
264J ARG* 6.2 0.4 - - + -
265J VAL* 1.3 78.9 - - - +
267J LEU* 1.3 65.9 + - - +
268J GLU* 5.3 7.3 + - - +
473J SER 3.8 14.4 - - - +
474J GLY* 4.4 12.6 - - - -
475J ARG 5.5 0.7 - - - +
476J GLU* 5.6 1.2 + - - -
484J ALA* 4.1 16.6 - - + +
485J TYR* 5.3 0.5 + - - -
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Residues in contact with LEU 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262I LEU* 3.9 26.0 - - + -
243J PHE* 3.5 26.7 - - + -
250J GLY* 3.5 30.1 - - - +
253J ILE* 4.3 3.1 - - + -
254J GLN* 3.7 20.6 - - - +
265J VAL* 3.8 17.3 - - + -
266J THR* 1.3 80.9 - - - +
268J GLU* 1.3 65.6 - - - +
269J LEU* 3.7 9.0 - - + -
467J GLY 5.7 0.3 + - - -
472J GLY* 3.1 30.5 - - - -
473J SER* 3.2 22.6 + - - +
474J GLY 5.0 0.2 - - - +
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Residues in contact with GLU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J LYS* 4.5 0.4 - - - +
242J ALA* 6.5 0.4 - - + -
243J PHE 2.8 11.3 + - - +
244J THR* 3.2 36.9 - - + +
245J GLY 3.1 21.0 + - - -
266J THR* 5.3 6.2 + - - +
267J LEU* 1.3 80.2 - - - +
269J LEU* 1.3 65.0 + - - +
302J CYS* 5.8 1.3 - - - +
427J LEU* 5.2 3.8 - - + +
465J PHE* 4.1 11.2 - - + +
466J GLY* 4.1 19.8 - - - -
467J GLY 4.8 1.4 + - - -
471J SER 4.1 2.1 - - - +
473J SER 5.0 1.3 - - - -
474J GLY 4.3 6.9 - - - +
475J ARG 4.3 3.5 - - - -
476J GLU* 2.9 45.8 + - - +
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Residues in contact with LEU 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262I LEU* 3.7 22.2 - - + -
243J PHE* 3.9 8.5 - - + -
245J GLY 3.3 7.4 - - - +
246J SER 3.4 25.1 - - - +
247J THR* 3.7 22.7 - - + +
250J GLY* 3.9 14.6 - - - -
267J LEU* 4.1 13.2 - - + -
268J GLU* 1.3 78.4 - - - +
270J GLY* 1.3 68.6 + - - +
302J CYS* 4.6 3.5 - - - +
427J LEU* 3.5 16.5 - - - +
470J MET 3.2 23.3 - - - +
471J SER* 3.0 21.0 + - - +
472J GLY* 3.9 9.4 - - - +
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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