Contacts of the strand formed by residues 381 - 385 (chain O) in PDB entry 4R2G
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 GLU 381 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298O ARG* 3.1 41.8 + - - +
377O ASN* 3.8 1.6 + - - -
378O CYS 3.2 32.4 + - - +
379O GLY 3.5 1.8 + - - -
380O GLY* 1.3 79.3 - - - +
382O PHE* 1.3 63.8 + - - +
383O PHE* 3.5 8.7 + - + -
420O ILE* 3.9 19.7 - - + +
421O LYS 5.2 1.6 - - - +
422O GLN* 6.4 1.6 - - + -
438O PRO* 4.1 24.2 - - + +
443O ILE* 2.4 39.5 - - + +
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Residues in contact with PHE 382 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O TRP* 3.5 23.8 - + - -
116O LEU* 4.4 5.6 - - + -
376O PHE 3.7 6.1 - - - +
377O ASN* 3.1 26.2 - - + -
380O GLY 3.9 11.2 - - - -
381O GLU* 1.3 74.8 - - - +
383O PHE* 1.3 65.2 + - - +
384O TYR* 3.7 7.1 - - + -
420O ILE* 3.4 4.1 - - - +
421O LYS 3.1 43.7 + - - +
422O GLN* 5.0 2.2 - - + -
424O ILE* 3.6 32.5 - - + -
435O TYR* 3.5 53.6 - + + -
436O ALA 5.6 1.1 - - - -
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Residues in contact with PHE 383 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296O CYS* 4.0 4.7 - - + -
297O THR* 3.7 27.8 - - - -
298O ARG 3.5 21.8 - - - -
329O ALA* 4.4 3.4 - - + -
330O HIS 4.7 2.0 - - - -
375O SER* 3.5 4.5 - - - -
376O PHE* 2.9 62.7 + + + +
378O CYS* 3.6 21.8 - - + -
381O GLU* 3.6 15.0 - - + -
382O PHE* 1.3 75.2 - - - +
384O TYR* 1.3 64.5 + - - +
385O CYS* 3.8 12.1 - - - -
418O CYS* 4.1 7.4 - - + -
419O ARG 3.9 3.1 - - - -
420O ILE* 3.7 18.2 - - + -
443O ILE* 3.5 24.0 - - + -
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Residues in contact with TYR 384 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369O PRO* 3.4 22.2 - - + -
370O GLU* 2.4 64.9 + - + +
373O MET* 3.6 25.8 - - + +
374O HIS 3.8 3.1 - - - -
375O SER* 4.2 8.3 - - - -
382O PHE* 3.7 13.9 - - + -
383O PHE* 1.3 79.9 - - - +
385O CYS* 1.3 63.6 + - - +
386O ASN 4.0 0.2 + - - -
417O PRO 4.3 0.3 - - - +
418O CYS* 3.7 1.7 - - - +
419O ARG* 2.8 40.7 + - + +
421O LYS* 3.5 35.2 - - + +
424O ILE* 3.7 21.8 - - + +
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Residues in contact with CYS 385 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331O CYS* 2.6 32.5 - - + -
373O MET* 3.1 8.4 - - - +
374O HIS* 2.9 48.8 + - + +
376O PHE* 3.3 18.2 - - + -
383O PHE* 4.1 2.0 - - - -
384O TYR* 1.3 74.7 - - - +
386O ASN* 1.3 59.8 + - - +
416O LEU* 4.8 5.8 - - + -
417O PRO 3.8 0.4 - - - -
418O CYS* 2.1 43.7 - - - -
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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