Contacts of the strand formed by residues 413 - 421 (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 THR 413 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332O ASN* 4.4 16.3 + - - +
333O ILE 3.8 10.8 + - - -
334O SER* 4.9 2.0 - - - +
411O ASN* 4.3 11.2 + - - +
412O ASP* 1.3 79.3 - - + +
414O ILE* 1.3 62.8 + - - +
415O ILE* 3.6 9.4 + - + +
513O NAG 4.6 9.4 + - - +
1R NAG 4.1 29.1 + - - +
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Residues in contact with ILE 414 (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 3.5 1.4 - - - +
332O ASN* 3.4 4.3 - - - +
333O ILE* 2.7 50.2 + - + +
334O SER 4.7 0.2 - - - +
335O ARG* 3.6 60.6 - - + +
338O TRP* 4.5 12.3 - - + -
389O GLN* 3.5 30.1 - - + +
390O LEU* 4.2 17.5 - - + -
411O ASN* 5.2 0.7 - - - -
413O THR* 1.3 70.9 - - - +
415O ILE* 1.3 63.1 + - - +
416O LEU* 3.7 20.8 - - + +
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Residues in contact with ILE 415 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D SER* 3.6 70.2 - - + +
330O HIS* 3.9 17.5 - - + -
331O CYS 3.5 2.0 - - - -
332O ASN* 2.9 18.6 - - - +
389O GLN* 3.0 26.5 + - - +
413O THR* 3.6 10.6 + - + +
414O ILE* 1.3 74.9 - - - +
416O LEU* 1.3 64.6 + - - +
417O PRO* 3.9 1.7 - - - +
1R NAG 3.7 24.2 - - - +
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Residues in contact with LEU 416 (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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294O ILE* 4.8 4.3 - - + -
330O HIS* 3.3 3.8 - - - +
331O CYS* 2.8 58.8 + - + +
333O ILE* 4.1 22.7 - - + -
374O HIS* 5.5 2.9 - - + -
385O CYS* 4.8 6.7 - - + -
386O ASN 3.2 30.5 - - - +
387O SER* 4.7 1.8 - - - -
389O GLN* 4.3 10.5 - - + -
390O LEU* 4.1 23.3 - - + +
414O ILE* 3.7 27.6 - - + +
415O ILE* 1.3 75.9 - - - +
417O PRO* 1.3 67.6 - - - +
418O CYS* 3.7 1.2 - - - -
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Residues in contact with PRO 417 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D PHE* 4.2 23.5 - - + +
328O GLN* 4.1 14.4 - - - +
329O ALA 4.1 3.8 - - - +
384O TYR 4.3 0.7 - - - +
385O CYS* 3.8 0.2 - - - -
386O ASN* 3.1 47.6 + - + +
389O GLN* 4.2 10.5 - - - +
415O ILE 3.9 6.5 - - - +
416O LEU* 1.3 84.1 - - + +
418O CYS* 1.3 58.9 + - - +
419O ARG* 6.1 0.2 - - - -
515O NAG 5.4 4.3 - - - +
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Residues in contact with CYS 418 (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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328O GLN* 3.6 14.5 + - - +
329O ALA* 2.8 41.3 + - + +
330O HIS* 3.8 5.4 - - - -
331O CYS* 3.5 9.4 - - - -
383O PHE* 4.1 8.1 - - + -
384O TYR 3.7 3.8 - - - -
385O CYS* 2.1 52.3 - - - +
416O LEU 3.7 6.3 - - - -
417O PRO* 1.3 75.8 - - - +
419O ARG* 1.3 68.0 + - - +
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Residues in contact with ARG 419 (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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328O GLN* 5.4 3.4 - - - +
373O MET* 4.0 28.2 - - - +
383O PHE* 3.9 0.2 - - - -
384O TYR* 2.8 44.1 + - + +
417O PRO 6.1 0.4 - - - -
418O CYS* 1.3 78.5 - - - +
420O ILE* 1.3 68.8 + - - +
421O LYS* 5.6 10.1 - - + +
515O NAG 5.0 13.2 + - - +
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Residues in contact with ILE 420 (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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298O ARG* 3.4 41.7 - - + -
329O ALA* 3.8 10.5 - - + -
381O GLU* 3.9 22.2 - - + +
382O PHE 3.4 13.0 - - - +
383O PHE* 3.7 30.3 - - + -
384O TYR* 4.7 0.4 - - - +
419O ARG* 1.3 81.3 - - - +
421O LYS* 1.3 79.2 + - - +
422O GLN* 5.8 2.5 - - + -
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Residues in contact with LYS 421 (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* 4.7 15.5 - - - +
370O GLU* 5.6 0.2 - - - +
373O MET* 5.9 2.7 - - - -
381O GLU* 5.2 1.0 - - - +
382O PHE* 3.1 33.0 + - - +
384O TYR* 3.5 38.3 - - + +
419O ARG* 5.6 10.5 - - + +
420O ILE* 1.3 85.7 - - - +
422O GLN* 1.3 67.9 + - - +
423O ILE 4.0 16.2 + - - +
424O ILE* 3.8 15.5 - - + -
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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