Contacts of the strand formed by residues 384 - 392 (chain A) in PDB entry 3VOQ
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 LYS 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A HIS* 6.1 0.2 - - + -
383A TYR* 1.3 81.3 - - - +
385A SER* 1.3 69.7 + - - +
386A PHE* 3.4 32.8 - - + -
404A ILE 2.9 30.4 + - - +
477A GLU* 2.5 39.6 + - - +
481A LYS* 4.2 12.8 - - + +
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Residues in contact with SER 385 (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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383A TYR* 3.4 28.5 - - - -
384A LYS* 1.3 86.5 - - - +
386A PHE* 1.3 65.9 + - - +
387A LYS* 5.7 2.5 + - - +
401A GLN* 3.8 24.2 + - - +
402A LEU 3.1 7.6 - - - -
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Residues in contact with PHE 386 (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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384A LYS* 3.4 46.0 - - + -
385A SER* 1.3 78.5 - - - +
387A LYS* 1.3 64.9 + - - +
388A VAL* 3.5 8.4 + - + -
401A GLN* 3.5 2.5 - - - -
402A LEU* 2.7 45.0 + - + +
404A ILE* 4.1 19.7 - - + -
474A THR* 4.2 11.7 - - + -
477A GLU* 3.6 33.4 - - + -
478A ILE* 3.7 40.8 - - + -
481A LYS* 4.2 14.8 - - + -
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Residues in contact with LYS 387 (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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385A SER* 5.8 2.7 - - - +
386A PHE* 1.3 72.7 - - - +
388A VAL* 1.3 65.1 + - - +
400A VAL 3.6 9.4 - - - +
401A GLN* 3.1 35.2 + - + +
414A VAL* 4.1 19.5 - - + +
470A SER* 4.1 6.8 + - - -
474A THR* 5.1 2.5 - - - +
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Residues in contact with VAL 388 (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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386A PHE* 4.0 9.0 - - + -
387A LYS* 1.3 80.4 - - - +
389A SER* 1.3 60.6 + - - +
399A ASP* 3.7 5.8 - - - +
400A VAL* 3.0 38.0 + - + +
402A LEU* 4.1 17.3 - - + -
453A PHE* 5.1 1.3 - - + -
468A PHE* 3.8 31.4 - - + -
469A GLU 3.8 10.5 - - - +
470A SER* 3.9 17.0 - - - +
474A THR* 4.1 2.5 - - + -
478A ILE* 3.9 26.9 - - + -
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Residues in contact with SER 389 (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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388A VAL* 1.3 73.7 - - - +
390A MET* 1.3 59.0 + - - +
397A THR* 3.8 23.0 + - - -
398A THR 3.3 7.4 - - - -
399A ASP* 3.8 11.9 + - - -
468A PHE* 3.2 7.1 - - - +
469A GLU* 2.8 60.6 + - - +
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Residues in contact with MET 390 (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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388A VAL 3.9 2.2 + - - -
389A SER* 1.3 71.4 - - - +
391A ILE* 1.3 67.4 + - - +
392A HIS* 3.4 35.3 - - + +
397A THR* 3.1 4.6 - - - -
398A THR 2.9 30.0 + - - +
400A VAL* 3.8 20.6 - - + +
411A ILE* 4.1 22.9 - - - -
427A GLN* 5.7 0.2 - - - +
430A ILE* 4.7 10.1 - - + -
466A LEU* 3.8 27.4 - - + -
467A TYR 3.6 8.7 - - - +
468A PHE* 3.8 22.1 - - + -
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Residues in contact with ILE 391 (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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390A MET* 1.3 82.9 - - - +
392A HIS* 1.4 61.2 + - - +
393A ARG 4.2 0.9 + - - -
394A LEU* 3.9 28.4 + - + +
395A ARG 4.2 3.4 - - - +
396A PHE 3.4 8.3 - - - +
397A THR* 4.1 9.4 - - + +
452A ILE* 3.6 34.1 - - + -
467A TYR* 2.9 37.6 + - + +
468A PHE 4.1 6.7 - - - -
469A GLU* 4.2 10.3 - - + +
394B LEU* 3.6 35.4 - - + -
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Residues in contact with HIS 392 (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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390A MET* 3.4 46.7 + - + +
391A ILE* 1.4 68.8 - - - +
393A ARG* 1.3 77.7 + - - +
394A LEU 3.1 1.6 - - - -
395A ARG* 2.9 15.8 + - - +
396A PHE* 2.6 57.3 + + + -
398A THR* 2.5 33.7 + - - +
427A GLN* 3.6 31.7 + - + -
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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