Contacts of the strand formed by residues 467 - 474 (chain A) in PDB entry 5E9W
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 TYR 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 5.7 4.9 - - - -
285A PHE* 3.7 36.8 - + - +
288A HIS* 4.8 4.0 + + - -
318A THR* 3.3 9.6 - - - +
319A PRO* 3.3 41.5 - - + +
320A ASN* 4.3 2.6 - - - +
360A PHE* 3.9 29.5 - + - -
370A GLU* 4.4 8.0 + - - -
394A THR* 3.7 3.5 - - - -
395A PHE* 2.9 48.3 + + + +
463A ALA 4.3 8.7 - - - -
464A THR* 3.1 14.5 + - - +
465A SER 3.9 4.2 - - - +
466A ILE* 1.3 92.1 - - + +
468A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 468 (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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317A THR* 3.4 4.7 - - - -
318A THR* 3.0 54.8 + - + +
319A PRO 4.3 2.0 - - - +
320A ASN* 3.6 36.3 - - + +
321A SER 5.0 0.7 - - - +
373A VAL 6.1 0.7 - - - +
375A PHE* 4.2 22.4 - - + -
392A LYS* 3.9 24.5 - - + -
393A LYS 3.3 17.9 - - - +
394A THR* 4.0 2.7 - - - +
395A PHE* 3.6 5.5 - - - -
467A TYR* 1.3 75.0 - - - +
469A VAL* 1.3 75.9 + - - +
470A PHE* 4.1 9.6 - - + -
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Residues in contact with VAL 469 (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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179A MET* 4.1 14.1 - - + +
183A LEU* 4.7 11.0 - - + -
316A GLY 3.4 9.0 - - - +
317A THR* 3.9 7.6 - - + -
391A TYR* 4.0 12.8 - - + -
392A LYS* 3.4 2.8 - - - -
393A LYS* 2.7 43.7 + - + +
395A PHE* 3.3 30.7 - - + -
398A PHE* 3.5 37.9 - - + -
468A LEU* 1.3 77.5 - - - +
470A PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 470 (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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183A LEU* 4.6 4.3 - - - +
287A CYS* 3.7 30.1 - - - -
314A PHE* 3.6 31.4 - + - -
315A ILE* 3.4 5.7 - - - +
316A GLY* 2.9 63.5 + - - +
317A THR 3.8 3.1 - - - -
318A THR* 4.2 13.9 - - + -
375A PHE* 3.6 33.9 - + + -
378A LEU* 4.5 6.3 - - + -
391A TYR* 3.4 9.4 - - - +
468A LEU* 4.1 15.5 - - + -
469A VAL* 1.3 76.5 - - - +
471A ALA* 1.3 64.8 + - - +
472A PHE* 3.7 16.8 - + + -
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Residues in contact with ALA 471 (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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187A PHE* 3.3 40.2 - - + -
314A PHE 3.2 6.1 - - - -
315A ILE* 3.9 9.9 - - + -
389A LEU* 3.5 5.9 - - - +
390A VAL* 2.8 35.9 + - + +
391A TYR* 3.0 14.4 + - + +
470A PHE* 1.3 78.1 - - - +
472A PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 472 (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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313A TYR* 3.2 7.1 - - - +
314A PHE* 2.6 61.3 + + + +
375A PHE* 3.8 26.0 - + - -
378A LEU* 4.2 13.2 - - + -
379A ASN* 3.4 42.2 - - - -
382A ALA* 4.0 18.2 - - + -
387A MET* 3.6 22.2 - - + +
388A LYS* 3.5 5.6 - - - +
389A LEU* 3.6 23.8 - - + -
390A VAL* 3.8 3.6 - - - -
470A PHE* 3.7 22.0 - + - -
471A ALA* 1.3 73.9 - - - +
473A GLU* 1.3 60.1 + - - +
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Residues in contact with GLU 473 (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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194A LYS* 2.3 33.8 + - - -
311A GLY* 3.7 6.5 - - - +
312A GLY 3.4 9.0 - - - +
313A TYR* 3.8 14.4 + - + -
387A MET* 3.4 7.0 - - - -
388A LYS* 2.9 33.6 + - + +
390A VAL* 3.7 17.1 - - + +
472A PHE* 1.3 73.4 - - - +
474A LYS* 1.3 71.6 + - - +
475A GLN* 3.1 17.8 - - - +
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Residues in contact with LYS 474 (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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305A CYS 2.8 27.2 + - - -
306A GLU* 4.2 8.0 + - - +
308A LEU* 3.2 25.8 - - + +
309A SER 3.4 25.1 - - - +
310A PRO* 3.6 12.1 - - + -
311A GLY* 2.7 27.0 + - - -
312A GLY 2.8 14.3 + - - +
385A TYR* 2.7 25.3 + - - +
386A ASN* 3.7 18.7 - - + +
387A MET* 3.5 13.5 - - - +
473A GLU* 1.3 75.4 - - - +
475A GLN* 1.3 65.9 + - - +
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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