Contacts of the strand formed by residues 240 - 245 (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 LYS 240 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159L VAL* 4.0 19.3 - - + -
161L VAL 3.2 3.0 + - - -
162L CYS* 3.3 5.1 - - + -
163L GLY 2.6 32.6 + - - -
238L VAL* 3.2 7.2 + - - +
239L ASP* 1.3 80.7 - - - +
241L VAL* 1.3 57.6 + - - +
242L ALA* 3.4 19.8 - - - +
263L LYS* 4.3 1.6 - - - -
264L ARG* 3.4 25.4 - - + +
266L THR* 3.0 34.3 + - - +
484L ALA* 3.1 40.1 - - - +
485L TYR* 3.9 27.7 + - + -
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Residues in contact with VAL 241 (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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163L GLY 3.2 11.7 - - - +
165L ILE* 4.2 13.9 - - + -
232L ILE* 3.9 25.1 - - + +
233L ALA* 4.0 15.9 - - - -
238L VAL* 5.0 0.7 - - + -
240L LYS* 1.3 77.4 + - - +
242L ALA* 1.3 60.7 + - - +
253L ILE* 3.5 30.7 - - + +
257L ALA* 5.3 0.2 - - + -
263L LYS* 3.8 14.3 - - + +
264L ARG 2.9 7.1 + - - +
265L VAL* 3.4 19.4 - - + -
266L THR* 3.3 20.8 + - - +
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Residues in contact with ALA 242 (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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162L CYS* 6.5 0.2 - - + -
163L GLY 2.8 11.7 + - - +
164L GLN* 3.6 3.9 - - + -
165L ILE* 3.0 28.1 + - - +
178L LYS* 3.7 18.3 - - + -
240L LYS* 3.4 20.8 - - - +
241L VAL* 1.3 73.0 - - - +
243L PHE* 1.3 61.2 + - - +
266L THR* 3.5 11.4 - - - +
485L TYR* 3.5 17.9 - - + +
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Residues in contact with PHE 243 (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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165L ILE* 3.7 21.5 - - + -
178L LYS* 5.1 0.6 - - - -
241L VAL 4.0 0.6 - - - -
242L ALA* 1.3 73.9 - - - +
244L THR* 1.3 68.1 + - - +
245L GLY* 3.3 20.9 - - - -
246L SER 3.5 17.7 - - - -
249L ILE* 3.5 21.3 - - + -
250L GLY* 3.8 17.5 - - - -
253L ILE* 3.9 25.1 - - + -
266L THR 3.0 7.4 + - - +
267L LEU* 3.5 19.1 - - + -
268L GLU* 2.8 25.6 + - - +
269L LEU* 4.0 5.2 - - + -
512L ADP 3.3 48.7 - - - -
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Residues in contact with THR 244 (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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165L ILE 3.3 8.7 + - - +
166L ILE 4.2 1.2 - - - -
167L PRO* 3.2 46.7 - - + +
174L MET* 3.9 11.2 - - - -
178L LYS* 2.8 29.0 + - - -
243L PHE* 1.3 83.3 + - - +
245L GLY* 1.3 59.8 + - - +
268L GLU* 3.3 40.7 - - - +
302L CYS* 6.0 2.5 - - + -
476L GLU* 5.4 0.2 - - - +
512L ADP 4.3 1.4 - - - +
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Residues in contact with GLY 245 (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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167L PRO* 4.8 5.4 - - - -
243L PHE* 3.3 13.2 - - - -
244L THR* 1.3 75.2 - - - +
246L SER* 1.3 65.9 + - - -
268L GLU 3.2 7.4 + - - +
269L LEU* 3.4 20.3 - - - -
270L GLY* 3.5 6.4 + - - -
401L PHE* 5.8 5.3 - - - -
512L ADP 3.7 9.2 - - - -
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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