Contacts of the strand formed by residues 411 - 415 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250J LYS 4.6 1.2 - - - +
251J ASN* 3.2 41.7 + - - +
252J HIS 3.9 1.2 + - - -
281J MET* 3.5 10.3 - - - -
403J ILE* 5.8 0.7 - - - +
410J ASN* 1.3 83.8 + - - +
412J THR* 1.3 65.8 + - - -
431J VAL* 3.7 5.4 - - - +
433J MET 3.3 8.5 - - - -
441J PRO* 5.0 1.1 - - - -
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Residues in contact with THR 412 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251J ASN* 4.2 1.1 + - - -
252J HIS* 3.3 15.5 + - - +
283J LEU* 5.8 0.7 - - - -
403J ILE* 3.9 17.1 - - - +
411J GLY* 1.3 77.3 - - - -
413J CYS* 1.3 66.3 + - - +
425J PHE* 3.4 29.1 - - + -
429J ILE* 4.1 1.8 - - + -
431J VAL* 3.3 32.3 - - + -
433J MET 3.1 2.6 + - - -
434J VAL* 3.7 16.4 - - + -
435J GLY 3.0 22.2 + - - -
439J PRO 5.6 0.9 - - - -
441J PRO* 3.4 12.9 - - - +
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Residues in contact with CYS 413 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252J HIS 3.2 3.7 + - - +
253J ALA* 3.2 14.7 - - + -
254J ILE 2.9 20.9 + - - -
283J LEU* 4.1 3.1 - - + -
412J THR* 1.3 79.5 + - - +
414J ILE* 1.3 78.0 + - - +
415J PHE* 3.8 22.4 - - - -
425J PHE* 3.7 10.6 - - - -
435J GLY 3.4 8.5 - - - -
437J ASN 4.2 0.7 - - - -
438J ILE 3.4 41.5 - - - +
439J PRO* 3.8 10.8 - - + +
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Residues in contact with ILE 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254J ILE* 3.4 19.1 - - + +
256J MET* 3.9 17.3 - - + -
396J MET* 3.5 32.5 - - + -
413J CYS* 1.3 77.0 - - - +
415J PHE* 1.3 68.6 + - - +
416J THR* 3.9 23.5 + - + -
421J ALA* 4.6 3.1 - - + +
422J ALA* 4.8 1.6 - - - -
425J PHE* 3.2 33.9 - - + -
435J GLY 3.2 8.8 + - - +
436J ILE* 3.8 14.4 - - + +
437J ASN* 2.9 23.9 + - - -
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Residues in contact with PHE 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253J ALA* 3.8 17.3 - - + -
254J ILE 2.7 20.6 + - - +
255J VAL* 4.1 14.6 - - + -
256J MET* 3.2 24.4 + - - +
259J ALA* 3.5 20.2 - - + +
260J ASP 5.6 0.9 - - - +
263J ASN* 4.8 2.9 - - - -
264J ALA* 3.9 33.9 - - + -
267J GLN* 3.6 26.2 - - + -
268J LEU* 4.3 15.5 - - + -
413J CYS* 3.8 23.1 - - - -
414J ILE* 1.3 71.2 - - - +
416J THR* 1.3 65.4 + - - +
437J ASN* 3.4 19.7 - - + +
439J PRO* 4.1 16.8 - - + -
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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
------------------------------------------------------------
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