Contacts of the strand formed by residues 264 - 269 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473K SER* 3.8 29.3 - - - +
474K GLY* 5.0 8.9 - - - +
475K ARG* 5.7 4.2 - - - +
159L VAL* 4.1 19.1 - - + +
239L ASP 3.1 9.4 + - - +
240L LYS* 3.9 17.5 - - + +
241L VAL 2.9 26.2 + - - -
262L LEU 5.2 0.4 - - - +
263L LYS* 1.3 77.1 - - - +
265L VAL* 1.3 61.8 + - - +
266L THR* 6.2 0.9 - - + -
483L GLN 3.6 4.2 + - - -
484L ALA* 2.9 34.3 + - - +
486L THR 2.9 31.1 + - - +
487L LYS* 4.4 11.3 - - - +
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Residues in contact with VAL 265 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254K GLN* 4.4 9.3 - - - +
241L VAL* 3.4 19.3 - - + +
253L ILE* 4.2 5.6 - - + -
254L GLN* 4.5 20.2 + - + +
257L ALA* 3.4 32.5 - - + -
263L LYS 3.6 5.1 + - - +
264L ARG* 1.3 82.4 - - - +
266L THR* 1.3 69.4 + - - +
267L LEU* 3.8 32.1 - - + -
473L SER* 4.1 10.6 + - - +
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Residues in contact with THR 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L LYS* 3.0 30.1 + - - +
241L VAL 3.3 4.8 + - - +
242L ALA* 3.5 10.7 - - - +
243L PHE 3.0 22.5 + - - -
264L ARG* 6.2 0.7 - - + -
265L VAL* 1.3 79.6 - - - +
267L LEU* 1.3 65.2 + - - +
473L SER* 3.8 14.8 - - - +
474L GLY* 4.5 12.8 - - - -
475L ARG 5.5 1.1 - - - +
484L ALA* 4.1 19.5 - - + -
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Residues in contact with LEU 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262K LEU* 4.1 18.4 - - + -
243L PHE* 3.5 26.9 - - + -
250L GLY* 3.6 30.1 - - - +
253L ILE* 4.4 3.1 - - + -
254L GLN* 3.7 22.4 - - + +
265L VAL* 3.8 19.5 - - + -
266L THR* 1.3 81.6 - - - +
268L GLU* 1.3 60.6 + - - +
269L LEU* 3.6 11.7 - - + -
467L GLY 5.7 0.9 + - - -
471L SER 3.7 0.7 - - - +
472L GLY* 3.1 30.5 - - - -
473L SER* 3.3 23.8 + - - +
474L GLY 5.0 1.4 - - - +
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Residues in contact with GLU 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L MET* 5.2 2.4 - - - +
177L TRP* 5.2 4.0 - - - -
243L PHE 2.8 8.2 + - - +
244L THR* 3.3 34.1 - - - +
245L GLY 3.2 20.3 + - - +
267L LEU* 1.3 74.4 - - - +
269L LEU* 1.3 73.0 + - - +
302L CYS* 3.5 22.6 - - - +
427L LEU* 3.6 15.9 - - + +
465L PHE* 3.8 22.9 - - + +
466L GLY* 5.6 3.1 - - - -
471L SER 4.1 1.1 - - - -
476L GLU* 3.5 28.1 - - + +
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Residues in contact with LEU 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262K LEU* 3.6 27.4 - - + -
243L PHE* 4.0 7.0 - - + -
245L GLY 3.4 7.4 - - - +
246L SER 3.6 20.4 - - - +
247L THR* 3.6 22.4 - - + +
250L GLY* 4.0 11.4 - - - -
267L LEU* 3.9 20.2 - - + -
268L GLU* 1.3 92.1 - - - +
270L GLY* 1.3 68.8 + - - +
302L CYS* 4.5 1.7 - - - +
427L LEU* 3.5 8.0 - - - +
470L MET 3.2 22.7 - - - +
471L SER 2.9 21.0 + - - +
472L GLY* 4.0 5.2 - - - +
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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
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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