Contacts of the strand formed by residues 286 - 291 (chain A) in PDB entry 3R68
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 ASP 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A ARG* 2.7 45.9 + - - -
267A ILE* 3.3 3.7 - - - +
268A ILE* 2.8 43.1 + - + +
282A LEU* 3.6 9.2 - - - +
283A LYS* 2.8 50.4 + - - +
284A ASN 3.6 0.8 - - - -
285A ASN* 1.3 76.0 - - - +
287A LEU* 1.3 60.5 + - - +
288A VAL 3.7 0.2 + - - -
319A VAL* 3.9 13.0 - - + +
320A LEU 3.7 3.4 - - - +
321A ASP* 4.1 1.0 - - - +
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Residues in contact with LEU 287 (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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265A GLY* 3.6 30.1 - - - +
266A GLN 3.5 18.4 - - - +
267A ILE* 4.2 8.9 - - + +
285A ASN 3.5 2.0 + - - -
286A ASP* 1.3 71.8 - - - +
288A VAL* 1.3 63.5 + - - +
289A VAL* 3.5 19.9 + - + +
319A VAL* 3.1 6.0 - - - -
320A LEU* 2.8 57.6 + - + +
322A LYS* 4.5 22.9 - - + +
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Residues in contact with VAL 288 (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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257A LEU* 3.9 15.9 - - + -
265A GLY* 5.1 1.9 - - - -
266A GLN* 2.9 26.5 + - + +
268A ILE* 3.7 34.8 - - + -
287A LEU* 1.3 74.3 - - - +
289A VAL* 1.3 64.6 + - - +
290A ALA 3.8 18.2 - - - +
291A VAL* 4.1 11.4 - - + -
296A VAL* 3.6 22.5 - - + +
297A GLU* 5.4 0.9 - - - +
304A VAL* 4.5 6.5 - - + +
308A ILE* 5.5 0.4 - - + -
317A LEU* 4.3 13.2 - - + -
318A LEU 3.8 5.2 - - - +
319A VAL* 4.1 7.2 - - + -
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Residues in contact with VAL 289 (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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4A ZN 4.3 4.0 - - - -
241A PRO* 5.7 1.6 - - + -
287A LEU* 3.5 28.9 + - + +
288A VAL* 1.3 78.1 - - - +
290A ALA* 1.3 62.2 + - - +
295A SER* 3.4 4.7 + - - -
296A VAL* 3.0 23.5 + - - -
297A GLU* 3.6 37.2 - - + +
318A LEU* 2.9 44.0 + - + +
319A VAL* 4.6 3.6 - - - +
320A LEU* 4.5 14.4 - - + -
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Residues in contact with ALA 290 (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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288A VAL* 3.8 3.1 - - - +
289A VAL* 1.3 78.3 - - - +
291A VAL* 1.3 68.7 - - - +
292A ASN 4.2 0.2 - - - -
293A GLY* 4.5 7.9 - - - +
294A LYS 3.1 24.9 - - - +
295A SER* 4.1 2.0 - - - -
296A VAL* 3.9 2.4 - - - +
316A THR 4.4 0.2 - - - -
317A LEU* 3.4 5.2 - - - -
318A LEU* 3.0 48.7 + - + +
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Residues in contact with VAL 291 (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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288A VAL* 4.1 9.9 - - + -
290A ALA* 1.3 78.3 - - - +
292A ASN* 1.3 83.7 + - - +
293A GLY 3.2 0.9 - - - -
294A LYS* 2.9 25.8 + - - +
296A VAL* 3.8 15.9 - - + -
304A VAL* 4.5 2.7 - - + -
307A MET* 3.7 32.8 - - + +
308A ILE* 3.8 21.3 - - + -
315A THR* 3.6 22.0 - - - +
316A THR 3.5 4.0 - - - -
317A LEU* 3.8 7.6 - - + -
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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