Contacts of the strand formed by residues 242 - 247 (chain A) in PDB entry 1OBC
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.4 47.2 + - + +
234A PHE 3.3 9.9 - - - +
235A PRO* 3.9 29.2 - - + +
240A GLU 3.6 9.1 + - - +
241A VAL* 1.3 82.1 - - - +
243A ILE* 1.3 65.0 + - - +
244A PRO* 3.4 12.1 - - - +
409A GLY 3.3 23.8 + - - -
410A LEU* 4.5 10.7 - - - +
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ILE 3.3 3.8 - - - +
233A LEU* 4.4 0.2 - - - -
234A PHE* 2.7 39.9 + - - +
236A VAL* 3.5 27.8 - - + -
241A VAL* 4.7 1.3 - - + -
242A ARG* 1.3 70.8 - - - +
244A PRO* 1.3 76.2 - - + +
245A VAL* 4.3 5.8 - - + +
259A LEU* 4.4 13.9 - - + -
261A LEU* 4.0 19.7 - - + -
265A HIS* 5.1 1.8 - - - +
267A LEU* 3.6 22.9 - - + -
271A LEU* 3.9 16.6 - - + -
322A ILE* 4.1 13.0 - - + -
336A ALA* 3.9 19.5 - - + -
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Residues in contact with PRO 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLU* 3.8 24.2 - - + +
232A ILE 3.4 6.5 - - - +
233A LEU* 3.7 17.3 - - + -
241A VAL* 5.8 1.3 - - + -
242A ARG 3.4 10.1 - - - +
243A ILE* 1.3 86.8 - - + +
245A VAL* 1.3 57.5 + - - +
265A HIS* 5.5 6.7 + - - +
267A LEU* 5.7 2.7 - - + -
334A THR* 2.6 30.7 + - + -
336A ALA* 3.9 6.1 - - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ALA 3.6 0.9 - - - +
231A GLU* 3.1 4.2 - - - -
232A ILE* 2.8 47.6 + - + +
234A PHE* 3.7 18.6 - - + -
243A ILE* 4.3 11.0 - - + +
244A PRO* 1.3 80.6 - - - +
246A PHE* 1.3 62.8 + - - +
247A THR* 5.3 0.7 - - + -
259A LEU* 4.3 11.7 - - + -
334A THR* 3.4 7.9 - - - -
336A ALA* 3.5 18.2 - - + +
337A ILE* 3.7 21.8 - - - +
338A MET* 3.9 22.0 - - + +
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY* 4.5 0.4 - - - -
230A ALA 3.5 9.9 - - - -
231A GLU* 4.4 2.2 - - + +
245A VAL* 1.3 77.4 - - - +
247A THR* 1.3 77.2 + - - +
248A THR* 3.8 17.9 - - + -
332A TYR* 4.1 15.7 - + - -
333A GLY* 4.1 16.8 - - - -
334A THR* 3.8 6.7 + - + +
336A ALA 3.8 6.9 + - - +
337A ILE* 4.9 2.4 - - - +
338A MET 5.6 0.2 + - - -
414A ARG* 3.8 46.2 - - - +
416A THR* 3.4 34.8 - - + -
1815A NVA 4.1 1.0 - - - +
1816A 2AD 3.4 55.0 - + + -
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Residues in contact with THR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY* 3.3 1.6 - - - -
230A ALA 2.9 37.3 + - - +
232A ILE* 4.0 17.3 - - + -
245A VAL* 5.2 1.8 - - + +
246A PHE* 1.3 78.5 - - - +
248A THR* 1.3 61.6 + - - +
249A ARG* 2.9 21.0 + - - +
250A PRO* 4.0 11.1 - - + +
338A MET* 3.8 28.7 - - + +
1815A NVA 2.9 23.6 + - - -
1816A 2AD 3.3 7.4 + - - -
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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