Contacts of the strand formed by residues 413 - 421 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332K ASN* 4.2 10.5 - - + +
333K ILE 3.9 7.4 + - - +
334K SER* 4.8 2.6 - - - +
335K ARG* 5.3 0.2 + - - -
411K ASN* 3.3 15.7 - - - +
412K ASP* 1.3 78.6 - - - +
414K ILE* 1.3 73.2 + - - +
415K ILE* 3.8 22.8 + - + +
513K NAG 4.9 12.4 + - + +
1V NAG 4.1 22.6 + - - +
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Residues in contact with ILE 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K CYS 3.6 0.9 - - - +
332K ASN* 3.3 4.0 - - - -
333K ILE* 2.7 81.7 + - + +
334K SER 4.4 4.0 - - - +
335K ARG* 3.2 47.3 - - + +
338K TRP* 5.6 2.7 - - + -
389K GLN* 3.4 48.7 - - + +
390K LEU* 4.3 11.9 - - + -
411K ASN 4.6 0.2 - - - -
412K ASP 3.9 1.0 + - - -
413K THR* 1.3 73.9 - - - +
415K ILE* 1.3 59.4 + - - +
416K LEU* 4.3 5.6 - - + +
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Residues in contact with ILE 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J PHE* 4.1 45.0 + - + +
330K HIS* 3.8 22.9 - - + -
331K CYS 3.3 3.6 - - - +
332K ASN* 3.2 20.9 - - - +
389K GLN* 3.2 22.3 + - - +
413K THR* 3.8 12.8 + - + +
414K ILE* 1.3 79.4 - - - +
416K LEU* 1.3 64.9 + - - +
417K PRO* 3.7 3.9 - - - +
1V NAG 3.6 34.5 - - - -
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Residues in contact with LEU 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294K ILE* 4.5 5.4 - - + -
330K HIS* 3.1 7.7 - - - -
331K CYS* 2.8 57.1 + - + +
333K ILE* 4.4 12.6 - - + -
374K HIS* 5.4 4.5 - - + +
385K CYS* 4.8 7.9 - - + -
386K ASN 3.3 28.0 - - - +
387K SER* 4.7 0.9 - - - -
389K GLN* 4.3 18.8 - - + +
390K LEU* 4.2 38.1 - - + -
414K ILE* 4.8 6.5 - - + +
415K ILE* 1.3 78.9 - - - +
417K PRO* 1.3 71.9 - - - +
418K CYS* 3.7 0.7 - - - -
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Residues in contact with PRO 417 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J PHE* 4.4 18.6 - - + +
328K GLN* 3.9 17.0 - - - +
329K ALA 4.1 3.1 - - - +
384K TYR 4.1 0.3 - - - +
385K CYS* 3.4 1.2 - - - -
386K ASN* 2.9 53.9 + - + +
389K GLN* 4.1 11.4 - - - +
415K ILE 3.7 7.6 - - - +
416K LEU* 1.3 85.4 - - + +
418K CYS* 1.3 58.8 + - - +
515K NAG 5.5 0.2 - - - +
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Residues in contact with CYS 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K GLN* 4.2 10.4 + - - +
329K ALA* 2.9 33.7 + - + +
330K HIS* 3.9 5.6 - - - -
331K CYS* 3.5 13.0 - - - -
383K PHE* 3.9 13.2 - - + -
384K TYR 3.5 4.9 - - - +
385K CYS* 2.0 48.2 - - - -
416K LEU 3.7 6.7 - - - -
417K PRO* 1.3 74.7 - - - +
419K ARG* 1.3 69.2 + - - +
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Residues in contact with ARG 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369K PRO* 6.4 0.2 - - - +
373K MET* 3.7 28.3 - - - +
383K PHE* 3.6 1.4 - - - -
384K TYR* 2.9 38.5 + - + +
418K CYS* 1.3 78.5 - - - +
420K ILE* 1.3 72.6 + - - +
421K LYS* 5.1 14.8 - - + +
515K NAG 3.4 29.9 + - - +
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Residues in contact with ILE 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K ARG* 3.5 35.2 - - + -
329K ALA* 4.5 6.7 - - + -
381K GLU* 3.3 23.1 - - + +
382K PHE 3.3 15.7 - - - +
383K PHE* 3.8 35.7 - - + -
419K ARG* 1.3 82.8 - - - +
421K LYS* 1.3 73.6 + - - +
422K GLN* 5.5 2.9 - - + +
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Residues in contact with LYS 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369K PRO* 3.7 27.5 - - - +
370K GLU* 4.8 2.5 + - - +
373K MET* 5.3 1.8 - - - +
381K GLU* 5.1 0.5 - - - +
382K PHE* 3.1 22.5 + - - +
384K TYR* 3.5 42.8 - - + +
419K ARG* 5.1 16.1 - - + +
420K ILE* 1.3 87.0 - - - +
422K GLN* 1.3 71.8 + - - +
423K ILE 4.0 13.7 + - - +
424K ILE* 3.8 17.3 - - + -
432K LYS* 6.1 0.6 - - - +
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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