Contacts of the strand formed by residues 389 - 395 (chain B) in PDB entry 2O1X
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 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B ASP* 4.5 5.6 - - - +
341B ARG* 2.6 68.4 + - + +
342B THR* 3.6 9.8 - - - +
388B MET* 1.3 78.6 + - - +
390B PRO* 1.3 65.9 - - - +
391B VAL* 3.5 1.4 + - - +
416B ASN* 3.1 44.6 + - - +
467B ALA 4.7 1.0 + - - -
468B GLN* 3.1 57.4 + - - +
469B THR* 5.0 3.1 - - - -
470B HIS* 3.5 19.3 + - - +
471B ASP* 4.4 9.7 + - - -
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Residues in contact with PRO 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ARG 4.3 0.2 - - - -
343B PHE* 3.2 14.8 - - + +
345B VAL* 5.4 0.9 - - + -
380B ALA* 3.2 44.6 - - + +
383B MET* 4.1 12.1 - - - -
384B ALA* 3.8 7.6 - - + +
388B MET* 3.3 10.7 - - + +
389B ARG* 1.3 89.5 - - - +
391B VAL* 1.3 59.6 + - - +
392B VAL 4.0 0.7 - - - -
416B ASN 3.2 18.3 - - - +
417B VAL* 3.6 10.0 - - + +
418B THR* 3.2 22.7 + - - +
468B GLN* 4.4 0.7 - - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 4.1 19.3 - - + -
332B VAL* 4.7 4.3 - - + -
342B THR* 4.5 7.6 - - + -
343B PHE 2.7 11.4 + - - +
344B VAL* 3.3 13.2 - - + +
345B VAL* 3.1 22.8 + - - -
389B ARG 3.5 1.1 + - - +
390B PRO* 1.3 71.2 - - - +
392B VAL* 1.3 67.8 + - - +
393B ALA 3.6 0.7 + - - -
418B THR* 3.1 17.7 - - + +
420B CYS* 3.9 23.3 - - - -
464B LEU* 4.5 5.8 - - + -
468B GLN* 3.6 37.7 - - + +
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL* 3.7 11.7 - - + +
347B PRO* 5.4 0.2 - - + -
376B ALA* 4.1 19.7 - - + +
377B VAL* 4.3 15.3 - - + -
380B ALA* 3.4 33.2 - - + -
390B PRO 4.0 0.4 - - - -
391B VAL* 1.3 71.4 - - - +
393B ALA* 1.3 62.4 + - - +
394B ILE* 3.7 24.0 + - + +
417B VAL* 3.8 9.2 - - + -
418B THR 2.8 9.6 + - - +
419B PHE* 3.4 23.1 - - + +
420B CYS 2.9 26.2 + - - +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B PHE* 4.0 22.4 - - + -
344B VAL* 4.4 3.4 - - + -
345B VAL 2.9 11.2 + - - +
346B THR* 3.8 4.6 + - - -
347B PRO* 3.1 24.4 - - - +
349B MET* 5.7 0.2 - - - +
353B SER* 4.5 11.4 + - - -
355B LEU* 3.9 28.7 - - + -
391B VAL 3.6 1.2 + - - -
392B VAL* 1.3 71.4 - - - +
394B ILE* 1.3 59.5 + - - +
420B CYS* 3.5 7.9 - - - +
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B PRO* 3.7 16.6 - - + -
349B MET* 6.4 1.1 - - - -
353B SER* 4.8 2.1 + - - -
373B GLU* 3.5 33.9 - - + -
376B ALA* 5.3 0.4 - - + -
377B VAL* 5.0 4.7 - - + -
392B VAL* 4.0 22.7 - - + +
393B ALA* 1.3 76.2 - - - +
395B TYR* 1.3 78.2 + - - +
398B PHE* 4.2 4.3 - - + -
399B LEU* 3.7 44.2 - - + +
419B PHE* 4.5 2.0 - - + -
420B CYS 3.0 8.5 + - - -
421B ILE* 3.0 37.3 - - + -
422B ASP* 3.1 4.2 + - - +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B MET* 4.2 20.6 - - + +
352B GLY* 3.2 27.4 + - - -
353B SER* 3.8 19.1 - - - -
394B ILE* 1.3 78.4 - - - +
396B SER* 1.3 66.1 + - - +
397B THR* 4.3 5.4 - - - +
398B PHE* 3.1 41.4 + + + +
399B LEU* 2.9 20.6 + - - +
421B ILE* 4.2 0.2 - - - -
422B ASP* 3.1 21.1 - - + +
423B ARG* 3.2 53.3 + - + -
434B HIS* 5.8 4.3 - + - -
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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
------------------------------------------------------------
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