Contacts of the strand formed by residues 381 - 387 (chain A) in PDB entry 1ZMC
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 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A GLU* 2.5 40.0 + - + +
374A LEU* 3.5 41.1 - - + -
375A LYS* 2.9 34.9 + - + +
379A ILE 3.4 16.8 - - - -
380A GLU* 1.3 75.8 - - - +
382A LYS* 1.3 71.7 + - - +
383A VAL* 3.7 16.3 - - + +
407A LEU* 4.2 6.3 - - + -
408A GLY 3.1 17.3 - - - +
410A LYS* 3.7 15.8 + - - +
416A LEU* 4.3 3.1 - - + -
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Residues in contact with LYS 382 (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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381A TYR* 1.3 75.3 - - - +
383A VAL* 1.3 69.4 + - - +
407A LEU* 3.5 4.2 - - - -
408A GLY* 2.8 39.2 + - - +
409A GLN 4.0 14.8 - - - +
410A LYS* 4.3 22.3 + - + +
413A ASP* 2.9 38.7 + - - +
442A CYS* 4.7 4.0 - - - -
466A ALA* 3.1 32.9 + - + +
467A SER 4.0 9.7 + - - -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 4.4 7.2 - - - +
381A TYR* 3.7 25.1 - - + +
382A LYS* 1.3 83.6 - - - +
384A GLY* 1.3 69.8 + - - +
385A LYS* 4.2 25.4 + - + -
405A LYS* 4.2 13.2 - - + -
406A ILE 3.3 8.1 - - - +
407A LEU* 3.8 8.3 - - + -
465A ALA 4.8 1.7 - - - +
466A ALA* 4.2 8.2 - - - -
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Residues in contact with GLY 384 (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 VAL* 1.3 75.8 - - - +
385A LYS* 1.3 62.6 + - - +
404A VAL 3.7 0.2 - - - +
405A LYS* 3.3 4.2 - - - -
406A ILE* 2.8 34.9 + - - +
462A ALA* 3.4 24.9 - - - +
465A ALA* 4.0 3.6 - - - -
466A ALA* 3.6 14.5 - - - +
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Residues in contact with LYS 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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221A GLU* 3.1 39.6 + - - +
371A GLU* 5.3 1.6 + - - -
383A VAL* 4.2 20.8 + - + -
384A GLY* 1.3 77.9 - - - +
386A PHE* 1.3 66.1 + - - +
387A PRO* 4.5 2.9 - - + +
403A MET* 4.3 21.1 - - - -
404A VAL 3.3 5.2 - - - +
405A LYS* 4.3 9.2 - - + +
462A ALA* 4.4 2.7 - - - -
465A ALA* 4.1 13.4 - - - +
471A SER* 4.9 1.7 + - - -
474A PHE* 4.6 9.0 - - + -
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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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385A LYS* 1.3 75.3 - - - +
387A PRO* 1.3 88.4 - - - +
390A ALA* 3.5 34.5 - - + -
391A ASN* 3.8 10.5 - - + -
403A MET* 3.2 4.1 - - - +
404A VAL* 2.7 38.1 + - - +
457A GLU 5.5 0.2 - - - -
458A ALA* 3.7 37.8 - - + +
461A GLU* 3.3 38.1 - - + -
462A ALA* 3.9 7.9 - - + +
471A SER* 3.3 23.8 - - - -
473A ASN* 3.9 6.1 - - + -
474A PHE* 3.6 16.4 - - + -
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Residues in contact with PRO 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 LYS* 4.6 0.7 - - + -
386A PHE* 1.3 101.1 - - + +
388A PHE* 1.3 64.4 + - - +
389A ALA* 3.0 13.7 - - + +
390A ALA* 3.0 20.3 + - + +
402A GLY 3.4 9.9 - - - +
403A MET* 3.7 6.1 - - + -
474A PHE* 3.6 50.9 - - + -
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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