Contacts of the strand formed by residues 411 - 415 (chain L) in PDB entry 4ZZ7
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 GLY 411 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250L LYS 4.8 0.2 - - - +
251L ASN* 2.8 48.0 + - - +
252L HIS 3.8 0.5 + - - -
281L MET* 3.7 11.0 - - - -
409L GLY 3.7 1.4 - - - -
410L ASN* 1.3 80.8 - - - +
412L THR* 1.3 61.9 + - - -
431L VAL* 4.0 3.8 - - - +
433L MET 3.4 8.5 - - - -
441L PRO* 5.1 2.5 - - - -
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Residues in contact with THR 412 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251L ASN* 5.1 1.1 - - - -
252L HIS 2.7 22.7 + - - -
283L LEU* 5.8 0.7 - - - -
403L ILE* 3.7 13.2 - - - +
411L GLY* 1.3 75.1 - - - -
413L CYS* 1.3 66.8 + - - +
425L PHE* 3.4 30.8 - - + -
429L ILE* 4.0 2.5 - - + -
431L VAL* 3.4 33.4 - - + -
433L MET 3.0 9.4 + - - +
434L VAL* 4.0 12.3 - - + -
435L GLY 3.0 20.4 + - - -
439L PRO 5.4 0.9 - - - -
441L PRO* 3.5 9.7 - - - +
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Residues in contact with CYS 413 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252L HIS 3.3 2.6 + - - -
253L ALA* 3.4 11.9 - - + -
254L ILE 3.0 22.7 + - - -
283L LEU* 4.3 2.7 - - + -
412L THR* 1.3 79.4 + - - +
414L ILE* 1.3 85.8 + - - +
415L PHE* 3.9 16.4 - - - -
425L PHE* 3.4 12.3 - - - -
435L GLY 3.4 7.6 - - - -
438L ILE 3.0 43.3 - - - +
439L PRO* 3.7 12.8 - - + -
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Residues in contact with ILE 414 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254L ILE* 3.6 15.5 - - + +
256L MET* 4.0 17.3 - - + -
396L MET* 3.7 29.6 - - + -
413L CYS* 1.3 80.1 - - - +
415L PHE* 1.3 57.6 - - - +
416L THR* 3.7 23.6 + - + -
421L ALA* 4.2 4.0 - - + +
422L ALA* 4.9 1.3 - - - -
425L PHE* 3.3 36.1 - - + -
435L GLY 3.1 1.8 + - - -
436L ILE* 3.6 27.7 - - + +
437L ASN* 2.7 33.6 + - - +
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Residues in contact with PHE 415 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L ALA* 3.9 22.0 - - + -
254L ILE 2.9 19.8 + - - +
255L VAL* 4.1 15.7 - - + -
256L MET* 3.2 16.3 + - - +
259L ALA* 3.2 27.7 - - + +
263L ASN* 5.2 2.2 - - - -
264L ALA* 4.1 32.3 - - + -
267L GLN* 3.8 23.3 - - - -
268L LEU* 4.1 17.7 - - + -
413L CYS* 3.9 13.0 - - - -
414L ILE* 1.3 69.3 - - - +
416L THR* 1.3 64.9 + - - +
437L ASN* 3.1 22.9 - - + +
439L PRO* 3.8 25.1 - - + -
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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