Contacts of the strand formed by residues 387 - 394 (chain B) 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 MET 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B CYS* 3.7 28.7 - - + -
308B LEU* 3.6 21.3 - - + -
314B PHE* 3.9 6.3 - - + -
379B ASN 5.2 0.3 - - - +
382B ALA* 3.3 31.2 + - + +
383B LYS* 3.9 22.9 + - - +
385B TYR 3.6 15.7 - - - +
386B ASN* 1.3 78.7 - - - +
388B LYS* 1.3 60.2 + - - +
472B PHE* 3.6 27.9 - - + +
473B GLU 3.3 23.1 - - - -
474B LYS* 3.5 22.0 - - - +
475B GLN* 4.7 1.1 - - - -
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Residues in contact with LYS 388 (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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387B MET* 1.3 74.8 - - - +
389B LEU* 1.3 67.7 + - - +
472B PHE* 3.3 4.3 - - - -
473B GLU* 2.7 38.3 + - + +
475B GLN* 3.4 30.5 + - + +
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Residues in contact with LEU 389 (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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375B PHE* 3.8 23.6 - - + -
379B ASN* 3.4 21.7 + - - +
388B LYS* 1.3 76.0 - - - +
390B VAL* 1.3 61.5 + - - +
391B TYR* 3.5 29.2 - - - +
392B LYS* 4.4 11.7 - - + +
471B ALA 3.5 8.5 - - - +
472B PHE* 3.6 28.5 - - + -
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 4.3 12.6 - - + -
190B LYS* 5.1 7.2 - - - +
313B TYR* 4.1 13.7 - - + -
389B LEU* 1.3 76.2 - - - +
391B TYR* 1.3 78.4 + - + +
471B ALA* 2.7 22.6 + - + +
472B PHE 4.0 2.7 - - - -
473B GLU* 3.6 38.4 - - + +
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Residues in contact with TYR 391 (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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183B LEU* 3.3 12.4 - - + +
186B GLU* 3.0 37.1 + - - -
187B PHE* 3.2 27.1 - + - -
389B LEU* 3.5 13.6 - - - +
390B VAL* 1.3 95.1 - - + +
392B LYS* 1.3 62.8 + - - +
393B LYS* 3.1 42.4 - - + +
398B PHE* 3.4 8.3 - + - -
401B GLU* 6.1 1.3 - - - -
469B VAL* 3.8 23.8 - - + -
470B PHE* 3.4 1.9 - - - -
471B ALA* 3.0 31.1 + - + -
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Residues in contact with LYS 392 (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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320B ASN* 5.2 5.3 + - - +
322B PHE* 5.7 6.1 - - - -
375B PHE* 3.5 54.9 - - + +
389B LEU* 4.3 7.7 - - + +
391B TYR* 1.3 75.8 - - - +
393B LYS* 1.3 68.5 + - - +
394B THR* 5.0 14.3 - - - +
397B GLU* 4.4 4.1 + - - +
468B LEU* 4.3 18.6 - - + +
469B VAL 3.5 8.1 - - - +
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Residues in contact with LYS 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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391B TYR* 3.1 46.1 - - + +
392B LYS* 1.3 80.8 - - - +
394B THR* 1.3 66.3 + - - +
397B GLU* 3.5 15.9 - - + +
398B PHE* 4.0 24.2 - - + +
401B GLU* 3.1 29.1 + - - +
468B LEU* 3.2 5.6 - - - +
469B VAL* 2.7 49.0 + - + +
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Residues in contact with THR 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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320B ASN* 3.8 24.5 - - - +
392B LYS* 5.0 9.1 - - - +
393B LYS* 1.3 75.6 - - - +
395B PHE* 1.3 66.9 + - - +
396B LEU* 3.5 8.7 + - - +
397B GLU* 3.0 41.0 + - - +
398B PHE* 2.9 21.4 + - - +
465B SER* 5.4 4.3 - - - +
467B TYR 3.7 8.7 - - - -
468B LEU* 4.0 3.4 - - + +
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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