Contacts of the helix formed by residues 418 - 429 (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 ASP 418 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417I ARG* 2.8 41.9 + - - +
418I ASP* 5.1 0.2 - - - +
258J ASP* 3.0 14.5 + - - +
416J THR* 3.2 12.2 + - - +
417J ARG* 1.3 78.8 - - - +
419J GLY* 1.3 62.9 + - - +
420J GLU* 3.4 11.2 + - - +
421J ALA* 3.1 26.3 + - + +
422J ALA* 3.3 21.1 + - - +
481K TRP* 3.7 2.1 - - - -
484L ALA 3.6 9.4 - - - +
486L VAL* 3.7 20.0 - - + +
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Residues in contact with GLY 419 (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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417I ARG 3.1 13.0 + - - -
419I GLY* 4.2 0.9 - - - +
417J ARG 3.7 2.0 + - - -
418J ASP* 1.3 70.7 - - - +
420J GLU* 1.3 65.9 + - - +
422J ALA* 3.2 2.9 + - - +
423J ARG* 3.0 19.1 + - - +
481K TRP* 4.1 12.3 - - - -
481L TRP* 3.7 40.2 + - - -
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Residues in contact with GLU 420 (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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418J ASP* 3.4 10.5 + - - +
419J GLY* 1.3 77.1 - - - +
421J ALA* 1.3 66.3 + - - +
423J ARG* 3.4 2.5 + - - +
424J TYR* 3.1 21.4 + - - +
481L TRP* 3.4 40.2 - - + +
483L SER 3.3 25.8 - - - +
484L ALA* 3.4 19.4 + - - +
487L ARG* 2.7 45.8 + - - +
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Residues in contact with ALA 421 (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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256J MET* 4.7 4.7 - - + -
396J MET* 3.6 26.4 - - + +
414J ILE* 4.8 1.3 - - + -
416J THR* 4.3 12.6 - - + +
418J ASP* 3.1 24.2 + - + +
420J GLU* 1.3 87.0 + - - +
422J ALA* 1.3 63.0 + - - +
424J TYR* 3.8 0.8 - - - +
425J PHE* 2.9 26.4 + - - +
487L ARG* 4.4 12.3 - - + +
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Residues in contact with ALA 422 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414J ILE* 4.8 1.3 - - - -
416J THR* 4.3 6.9 - - + +
418J ASP 3.3 15.2 + - - +
419J GLY 3.2 6.1 + - - +
421J ALA* 1.3 80.6 - - - +
423J ARG* 1.3 56.1 + - - +
425J PHE* 3.5 4.5 - - - +
426J SER* 3.0 30.4 + - - -
436J ILE* 3.6 29.4 - - + +
479K GLN* 5.2 2.7 - - - +
481K TRP* 3.6 23.3 - - + -
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Residues in contact with ARG 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419J GLY 3.0 15.6 + - - +
420J GLU 4.1 1.8 - - - +
422J ALA* 1.3 75.5 - - - +
424J TYR* 1.3 63.3 + - - +
426J SER* 3.6 8.5 - - - +
427J ASP* 2.9 70.0 + - + +
428J ASN* 5.6 1.0 + - - -
58K ASN* 6.3 0.4 - - - -
124L ARG* 4.7 1.4 - - - +
125L ASN* 3.5 20.9 + - - +
129L GLY* 3.8 26.2 + - - -
131L ASP* 2.8 46.6 + - - +
479L GLN* 5.0 8.3 - - - +
480L ARG* 6.4 0.4 - - - +
481L TRP* 4.0 22.7 - - + +
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Residues in contact with TYR 424 (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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396J MET* 4.5 1.3 - - + -
397J GLN* 2.8 32.9 + - - -
400J MET* 3.4 24.1 - - + +
420J GLU* 3.1 18.6 + - - +
421J ALA* 3.8 3.1 - - - +
423J ARG* 1.3 80.2 - - - +
425J PHE* 1.3 64.3 + - - +
427J ASP* 4.7 1.3 - - - -
428J ASN* 2.9 53.7 + - + +
487L ARG* 3.4 52.7 + - - +
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Residues in contact with PHE 425 (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* 3.7 21.3 - - + -
396J MET* 3.7 8.5 - - + -
400J MET* 3.7 23.8 - - + -
403J ILE* 4.5 0.7 - - + -
412J THR* 3.4 30.7 - - + -
413J CYS 3.7 16.4 - - - -
414J ILE* 3.2 33.9 - - + -
421J ALA 2.9 18.3 + - - +
422J ALA 3.5 3.6 - - - +
424J TYR* 1.3 74.7 - - - +
426J SER* 1.3 68.6 + - - +
427J ASP 3.0 0.7 + - - -
429J ILE* 2.9 50.7 + - + +
434J VAL* 3.7 23.3 - - + -
436J ILE* 4.5 1.3 - - + -
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Residues in contact with SER 426 (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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422J ALA 3.0 18.4 + - - -
423J ARG* 3.2 16.6 + - - +
425J PHE* 1.3 74.2 - - - +
427J ASP* 1.3 54.1 + - - +
429J ILE* 4.1 0.5 - - - +
434J VAL* 3.8 26.5 - - - -
436J ILE* 4.2 4.0 - - - -
133K TRP* 4.8 6.6 - - - -
135K GLU* 5.1 4.5 + - - +
137K GLN* 4.2 0.2 + - - -
475K LYS* 2.8 40.5 + - - +
477K VAL* 4.0 24.2 - - - +
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Residues in contact with ASP 427 (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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423J ARG* 2.9 54.4 + - + +
424J TYR* 4.7 0.2 - - - -
426J SER* 1.3 80.2 + - - +
428J ASN* 1.3 65.8 + - - +
57K ARG* 2.6 38.3 + - - -
58K ASN* 4.3 3.3 - - - +
135K GLU* 3.9 6.5 - - - +
137K GLN* 3.2 20.3 + - - +
475K LYS* 3.4 5.2 + - - -
124L ARG* 2.8 37.6 + - - +
125L ASN* 5.2 0.2 + - - -
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Residues in contact with ASN 428 (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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400J MET* 5.4 3.6 - - - -
404J ASP* 4.7 3.3 - - - +
423J ARG* 5.6 0.5 + - - -
424J TYR* 2.9 54.3 + - + +
425J PHE 3.2 2.0 + - - -
427J ASP* 1.3 85.3 + - - +
429J ILE* 1.3 60.4 + - - +
430J GLN* 2.7 31.6 + - - +
57K ARG* 3.3 23.8 - - - +
58K ASN* 4.6 11.3 - - - +
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Residues in contact with ILE 429 (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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400J MET* 3.8 23.9 - - + +
403J ILE* 4.0 21.3 - - + -
404J ASP* 3.8 14.8 - - - +
412J THR* 4.1 4.7 - - + -
425J PHE* 2.9 52.3 + - + +
428J ASN* 1.3 75.8 - - - +
430J GLN* 1.3 59.4 + - - +
431J VAL* 3.2 19.8 + - + +
434J VAL* 3.4 32.3 - - + -
452J TRP* 3.9 1.6 - - - -
475K LYS* 2.6 32.1 + - - +
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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