Contacts of the helix formed by residues 395 - 406 (chain A) 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 THR 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A VAL* 3.6 9.6 - - - -
393A VAL* 3.6 6.1 - - - +
394A ALA* 1.3 78.9 - - + +
396A MET* 1.3 74.8 + - - +
397A GLN* 3.7 10.9 + - + +
398A ASP* 3.0 45.4 + - - +
399A ALA 3.2 9.2 + - - -
487C ARG 4.4 9.0 + - - -
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Residues in contact with MET 396 (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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254A ILE* 4.8 4.9 - - + -
256A MET* 3.6 39.7 - - + -
289A VAL* 3.7 8.9 - - - +
395A THR* 1.3 78.1 + - - +
397A GLN* 1.3 56.6 + - - +
399A ALA* 3.1 10.4 + - - +
400A MET* 2.9 49.6 + - + +
414A ILE* 3.7 17.9 - - + -
421A ALA* 3.5 29.2 - - + +
424A TYR* 4.4 1.1 - - + -
425A PHE* 3.8 10.8 - - + +
487C ARG* 3.4 39.5 + - + +
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Residues in contact with GLN 397 (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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395A THR* 3.3 12.1 + - + +
396A MET* 1.3 81.4 - - - +
398A ASP* 1.3 58.3 + - - +
400A MET* 3.4 17.4 + - - +
401A ASP* 2.9 62.9 + - - +
404A ASP* 5.8 0.8 + - - -
424A TYR* 2.9 36.8 + - - -
487C ARG* 5.4 5.0 + - - +
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Residues in contact with ASP 398 (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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393A VAL* 4.0 17.5 - - + +
394A ALA* 3.7 17.7 + - - +
395A THR* 3.0 31.5 + - - +
397A GLN* 1.3 79.8 - - - +
399A ALA* 1.3 57.9 + - - +
401A ASP* 3.4 11.2 + - - +
402A LEU* 3.0 30.1 + - - +
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Residues in contact with ALA 399 (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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254A ILE* 3.8 27.6 - - + -
287A VAL* 3.4 32.0 - - + +
289A VAL* 5.2 0.7 - - + -
393A VAL* 3.8 10.2 - - + +
395A THR 3.2 4.2 + - - +
396A MET* 3.1 10.2 + - - +
398A ASP* 1.3 79.1 - - - +
400A MET* 1.3 61.2 + - - +
402A LEU* 3.3 6.9 + - - +
403A ILE* 3.1 26.3 + - - +
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Residues in contact with MET 400 (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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254A ILE* 3.9 6.7 - - + -
396A MET* 2.9 35.3 + - + +
397A GLN* 3.7 23.1 - - - +
398A ASP 3.3 0.2 - - - -
399A ALA* 1.3 74.6 - - - +
401A ASP* 1.3 64.7 + - - +
403A ILE* 3.4 2.3 + - - +
404A ASP* 3.1 33.5 + - - +
424A TYR* 3.4 35.7 - - + +
425A PHE* 3.8 44.6 - - + +
428A ASN* 5.2 6.3 - - - -
429A ILE* 4.0 16.2 - - + +
487C ARG* 5.3 1.1 - - + -
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Residues in contact with ASP 401 (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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397A GLN* 2.9 48.0 + - - +
398A ASP* 3.7 12.5 - - - +
400A MET* 1.3 73.8 - - - +
402A LEU* 1.3 59.7 + - - +
404A ASP* 3.4 7.6 + - - +
405A ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 402 (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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252A HIS* 4.4 2.7 - - + +
287A VAL* 4.3 25.8 - - + -
374A PRO* 3.6 32.5 - - + -
379A TYR* 3.2 32.0 + - + +
391A VAL* 4.0 30.1 - - + -
393A VAL* 4.6 5.2 - - + -
398A ASP 3.0 17.3 + - - +
399A ALA 3.4 3.4 - - - +
401A ASP* 1.3 77.1 - - - +
403A ILE* 1.3 61.9 + - - +
405A ALA* 3.4 9.0 + - + +
406A HIS* 3.4 13.7 + - - +
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Residues in contact with ILE 403 (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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250A LYS 5.9 0.9 - - - +
252A HIS* 3.5 47.1 - - + +
254A ILE* 3.9 27.8 - - + -
287A VAL* 5.0 1.6 - - + -
399A ALA 3.1 16.5 + - - +
400A MET 3.8 5.4 - - - +
401A ASP 3.2 0.2 - - - -
402A LEU* 1.3 76.1 - - - +
404A ASP* 1.3 64.0 + - - +
406A HIS* 3.0 21.6 + - - +
408A TYR 4.3 2.4 - - - +
412A THR* 3.9 15.9 - - - +
425A PHE* 4.3 0.2 - - + -
429A ILE* 3.8 21.1 - - + -
431A VAL* 3.9 21.8 - - + -
453A LYS* 3.4 6.2 + - - -
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Residues in contact with ASP 404 (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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397A GLN* 5.8 0.7 + - - -
400A MET* 3.1 25.1 + - - +
401A ASP* 3.8 9.0 - - - +
403A ILE* 1.3 75.1 - - - +
405A ALA* 1.3 59.1 + - - +
406A HIS 3.7 0.7 - - - +
428A ASN 4.5 5.5 - - - +
429A ILE* 3.8 7.5 - - - +
430A GLN* 2.9 48.1 + - + +
453A LYS* 3.0 25.3 + - - +
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Residues in contact with ALA 405 (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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401A ASP 2.9 17.9 + - - +
402A LEU* 3.5 11.7 - - + +
403A ILE 3.2 0.2 - - - -
404A ASP* 1.3 76.4 - - - +
406A HIS* 1.3 64.9 + - - +
407A GLU* 3.7 0.7 + - - -
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Residues in contact with HIS 406 (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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250A LYS* 3.4 28.1 - - + +
252A HIS* 4.1 11.2 - + + -
379A TYR* 3.2 44.4 + + - +
380A GLN* 3.2 31.1 + - + -
402A LEU 3.4 6.4 + - - +
403A ILE* 3.0 16.3 + - + +
404A ASP 3.7 1.0 - - - +
405A ALA* 1.3 82.6 - - - +
407A GLU* 1.3 81.6 + - + +
408A TYR* 3.3 26.5 + + - +
453A LYS* 3.1 18.9 + - - +
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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