Contacts of the strand formed by residues 244 - 251 (chain L) in PDB entry 2HOD
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 244 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152L ASP* 2.8 42.1 + - - +
192L THR* 5.0 1.1 - - + +
236L ILE* 2.9 34.4 - - + +
237L SER* 3.5 20.2 - - - +
239L GLN* 3.3 9.9 + - + -
242L ILE* 3.0 17.5 + - + +
243L PRO* 1.3 73.4 - - - +
245L ALA* 1.3 59.3 + - - +
246L LEU 3.9 0.2 - - - -
264L MET* 3.1 10.9 + - - +
265L PHE* 2.8 48.9 + - + +
386L ILE* 4.3 13.0 - - + -
387L ILE* 2.9 33.9 - - - -
388L PRO* 3.0 29.4 - - + -
389L PHE* 4.3 0.4 - - - -
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Residues in contact with ALA 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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191L TRP* 3.7 4.9 - - + -
244L TYR* 1.3 69.7 - - - +
246L LEU* 1.3 63.7 + - - +
261L ASP* 5.7 4.5 - - + +
262L TYR 3.4 13.9 - - - +
263L ALA* 4.9 0.4 - - - -
264L MET 4.7 0.7 - - - +
265L PHE* 4.9 0.2 - - - -
386L ILE* 4.5 0.4 - - - -
387L ILE* 2.6 43.1 + - + +
389L PHE* 3.4 40.0 - - + +
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Residues in contact with LEU 246 (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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194L PHE* 4.1 14.8 - - + -
244L TYR 3.8 4.0 + - - -
245L ALA* 1.3 72.3 - - - +
247L ARG* 1.3 65.5 + - - +
248L VAL* 4.5 12.3 - - + -
261L ASP* 3.1 4.0 - - - +
262L TYR* 2.7 57.9 + - + +
265L PHE* 3.2 51.5 - - + +
276L LEU* 5.9 0.2 - - + -
278L TYR* 6.1 1.1 - - + -
290L PHE* 4.9 14.8 - - + -
384L MET* 5.2 3.1 - - + -
385L LYS 3.4 17.7 - - - +
386L ILE* 3.4 13.5 - - + -
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Residues in contact with ARG 247 (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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191L TRP* 3.5 42.2 - - + +
245L ALA 3.7 1.0 + - - -
246L LEU* 1.3 75.0 - - - +
248L VAL* 1.3 84.3 + - - +
249L GLU* 4.8 9.1 + - + -
259L THR* 3.1 36.7 + - - +
260L ALA 4.1 2.9 - - - -
261L ASP* 3.1 25.2 + - - +
384L MET* 3.5 0.3 - - - -
385L LYS* 2.9 52.2 + - + +
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Residues in contact with VAL 248 (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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246L LEU* 4.5 16.8 - - + -
247L ARG* 1.3 87.1 - - - +
249L GLU* 1.3 65.4 + - - +
250L LEU* 3.6 16.5 - - + +
259L THR* 3.1 6.5 - - - -
260L ALA* 3.0 40.1 + - + +
262L TYR* 5.8 1.3 - - + -
290L PHE* 6.4 1.1 - - + -
344L LEU* 3.5 30.5 - - + -
369L TRP* 5.2 17.5 - - + -
383L THR 3.7 4.5 - - - +
384L MET* 4.3 17.0 - - + -
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Residues in contact with GLU 249 (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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247L ARG* 4.8 9.3 + - + +
248L VAL* 1.3 74.8 - - - +
250L LEU* 1.3 74.1 + - - +
257L THR* 6.0 2.5 - - + -
258L SER 3.9 13.0 - - - +
259L THR* 4.6 7.6 - - - +
381L LYS 5.5 0.2 - - - -
382L THR* 3.6 4.2 - - - -
383L THR* 3.1 48.2 + - + +
385L LYS* 3.3 34.7 + - - -
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Residues in contact with LEU 250 (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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248L VAL* 3.6 24.0 - - + +
249L GLU* 1.3 98.6 - - - +
251L GLU* 1.3 60.5 + - - +
257L THR* 2.9 26.4 - - - +
258L SER* 3.3 24.9 + - - +
286L ALA* 4.8 2.2 - - + -
344L LEU* 4.4 6.5 - - + -
369L TRP* 3.2 41.5 - - + +
372L TRP* 3.4 27.5 - - + -
379L MET* 3.5 18.4 - - + -
381L LYS 3.8 4.0 - - - -
382L THR* 4.0 9.6 - - - +
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Residues in contact with GLU 251 (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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250L LEU* 1.3 73.2 - - - +
252L ASP* 1.3 60.7 - - - +
255L GLY 4.1 11.5 - - - +
257L THR* 3.4 18.6 - - + +
379L MET* 2.8 8.7 - - - +
380L LYS* 2.6 46.4 + - + +
381L LYS* 2.8 63.2 + - + +
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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