Contacts of the strand formed by residues 386 - 393 (chain A) in PDB entry 2ODP
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 LEU 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A HIS* 3.2 13.7 - - + +
351A ILE* 4.2 8.1 - - + -
369A VAL 5.2 0.2 - - - +
372A ILE* 3.9 22.2 - - + -
373A ARG* 3.8 32.8 - - + +
376A LEU* 3.9 15.0 - - + -
378A ILE* 3.5 23.2 - - + +
383A ASN 3.3 4.2 + - - +
384A ASP 3.3 1.2 - - - -
385A TYR* 1.3 81.3 - - - +
387A ASP* 1.3 76.0 + - - +
388A ILE* 4.1 24.2 - - + -
408A SER* 4.3 3.0 + - - +
410A LYS* 2.8 26.9 + - - -
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Residues in contact with ASP 387 (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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224A LYS 2.8 44.4 + - - +
225A ILE* 5.0 0.3 - - - -
349A HIS 3.0 10.6 + - - +
350A ALA* 3.3 8.5 - - + +
351A ILE 2.8 31.8 + - - -
384A ASP* 4.1 9.4 - - - +
386A LEU* 1.3 74.4 - - - +
388A ILE* 1.3 60.7 + - - +
389A TYR* 3.7 19.3 - - + -
408A SER* 3.6 3.8 - - - -
410A LYS* 2.9 22.6 + - - -
415A HIS* 2.9 15.3 + - - +
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Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 5.0 5.4 - - + -
351A ILE* 3.4 24.9 - - + +
353A LEU* 3.9 25.8 - - + -
369A VAL* 3.9 39.9 - - + -
372A ILE* 5.4 1.8 - - + -
386A LEU* 4.1 23.6 - - + -
387A ASP* 1.3 78.8 - - - +
389A TYR* 1.3 64.1 + - - +
406A LEU* 3.5 22.2 - - + +
407A GLY* 3.2 3.5 - - - -
408A SER* 2.8 40.1 + - - +
415A HIS* 3.3 7.6 - - - -
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Residues in contact with TYR 389 (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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224A LYS* 3.3 29.6 + - - +
225A ILE* 3.8 17.2 + - + -
350A ALA* 5.5 0.4 - - + -
351A ILE 2.7 18.1 + - - +
352A ILE* 3.4 21.1 - - + -
353A LEU* 2.8 30.8 + - - +
387A ASP* 3.7 17.0 - - + -
388A ILE* 1.3 75.6 - - - +
390A ALA* 1.3 60.5 + - - +
391A ILE* 4.2 5.2 - - + -
407A GLY* 5.0 0.2 - - - -
413A GLU* 4.3 1.2 + - - -
414A ARG 3.6 14.5 + - - -
415A HIS* 3.3 44.1 + + - -
417A PHE* 4.1 7.9 - + - -
432A MET* 3.7 41.3 + - + +
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Residues in contact with ALA 390 (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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353A LEU* 3.5 10.1 - - + +
389A TYR* 1.3 73.4 - - - +
391A ILE* 1.3 61.4 + - - +
403A LEU* 3.6 42.7 - - + +
406A LEU* 3.8 23.3 - - + -
407A GLY* 4.4 1.1 - - - +
415A HIS 3.1 7.1 + - - -
416A ALA* 3.3 6.4 - - - +
417A PHE 3.2 22.3 + - - +
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Residues in contact with ILE 391 (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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260A MET* 5.0 1.1 - - - -
352A ILE* 3.9 22.2 - - + -
353A LEU 2.9 7.5 + - - -
354A LEU* 3.3 20.3 - - + +
355A THR 3.2 22.5 + - - -
389A TYR* 4.4 3.6 - - + -
390A ALA* 1.3 83.3 - - - +
392A GLY* 1.3 68.0 + - - +
393A VAL* 3.6 11.7 + - + +
403A LEU* 4.2 1.4 - - - +
417A PHE* 3.4 22.4 - - + +
419A LEU* 3.9 25.1 - - + -
425A LEU* 4.2 16.6 - - + -
432A MET* 4.2 27.8 - - + -
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Residues in contact with GLY 392 (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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355A THR 3.2 18.2 - - - -
391A ILE* 1.3 71.4 - - - +
393A VAL* 1.3 60.0 + - - -
394A GLY 4.1 1.3 + - - +
396A LEU* 4.9 2.7 - - - -
398A VAL* 4.2 19.1 - - - +
403A LEU* 3.7 7.1 - - - +
417A PHE 3.1 10.1 + - - -
418A ILE* 3.5 7.6 - - - +
419A LEU 2.9 25.6 + - - +
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Residues in contact with VAL 393 (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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249A ASP* 5.1 0.9 - - - +
252A ILE* 3.9 12.3 - - + +
253A PHE* 3.3 32.8 - - + -
256A SER* 3.7 24.7 - - - +
354A LEU* 4.0 25.4 - - + -
391A ILE* 3.6 11.3 + - + -
392A GLY* 1.3 74.3 - - - -
394A GLY* 1.3 62.3 + - - +
396A LEU* 3.4 6.1 - - - +
419A LEU* 3.2 11.2 - - + +
421A ASP 3.6 31.9 - - - +
422A THR* 4.5 0.4 - - - -
425A LEU* 4.6 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