Contacts of the helix formed by residues 395 - 406 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289I VAL* 3.7 8.7 - - - -
393I VAL* 3.6 8.1 - - - +
394I ALA* 1.3 79.4 - - + +
396I MET* 1.3 75.1 + - - +
397I GLN* 3.2 14.3 + - + +
398I ASP* 3.0 44.3 + - - +
399I ALA 3.3 7.6 + - - -
487K ARG 3.3 13.2 + - - -
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Residues in contact with MET 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I ILE* 4.7 7.9 - - + -
256I MET* 3.6 39.9 - - + +
289I VAL* 3.9 8.2 - - - +
395I THR* 1.3 75.6 + - - +
397I GLN* 1.3 62.5 + - - +
399I ALA* 3.3 7.8 + - - +
400I MET* 3.2 43.8 + - + +
414I ILE* 3.8 14.8 - - + -
421I ALA* 3.6 31.6 - - - +
424I TYR* 4.2 5.6 - - + -
425I PHE* 3.9 11.2 - - + +
487K ARG* 3.4 35.7 + - - +
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Residues in contact with GLN 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I THR* 3.2 13.3 + - + +
396I MET* 1.3 76.7 - - - +
398I ASP* 1.3 63.9 + - - +
400I MET* 3.3 16.2 + - - +
401I ASP* 3.0 56.5 + - - +
404I ASP* 5.8 0.8 + - - -
424I TYR* 2.9 36.2 + - - -
487K ARG* 4.4 9.1 + - - +
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Residues in contact with ASP 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I VAL* 4.0 18.0 - - + +
394I ALA* 3.6 13.3 + - - +
395I THR* 3.0 39.4 + - - +
397I GLN* 1.3 78.2 - - - +
399I ALA* 1.3 61.9 + - - +
401I ASP* 3.6 11.3 + - - +
402I LEU* 3.2 22.7 + - - +
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Residues in contact with ALA 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I ILE* 3.7 24.2 - - + -
287I VAL* 3.4 33.4 - - + +
289I VAL* 5.5 1.1 - - + -
393I VAL* 3.8 8.7 - - + +
395I THR 3.3 4.4 + - - +
396I MET* 3.7 8.7 - - - +
397I GLN 3.2 0.8 - - - -
398I ASP* 1.3 78.9 - - - +
400I MET* 1.3 58.2 + - - +
402I LEU* 3.3 7.3 + - - +
403I ILE* 3.1 31.8 + - - +
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Residues in contact with MET 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I ILE* 3.8 5.8 - - + -
396I MET* 3.2 35.9 + - + +
397I GLN* 3.9 16.8 - - - +
399I ALA* 1.3 74.9 - - - +
401I ASP* 1.3 61.3 + - - +
403I ILE* 3.4 2.3 + - - +
404I ASP* 2.8 41.1 + - - +
424I TYR* 3.4 35.7 - - + +
425I PHE* 3.7 40.2 - - + +
428I ASN* 5.3 3.4 - - - -
429I ILE* 3.6 26.0 - - + -
487K ARG* 5.1 0.7 - - - -
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Residues in contact with ASP 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I GLN* 3.0 47.4 + - - +
398I ASP* 3.8 11.7 - - - +
400I MET* 1.3 72.9 - - - +
402I LEU* 1.3 61.0 + - - +
404I ASP* 3.4 9.7 + - - +
405I ALA* 2.9 32.5 + - - +
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Residues in contact with LEU 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252I HIS* 4.5 2.7 - - + +
287I VAL* 4.2 19.5 - - + -
374I PRO* 3.8 30.7 - - + -
379I TYR* 3.3 32.1 + - + +
391I VAL* 3.6 30.7 - - + -
393I VAL* 4.5 10.5 - - + -
398I ASP 3.2 11.7 + - - +
399I ALA 3.4 8.5 - - - +
400I MET 3.2 0.2 - - - -
401I ASP* 1.3 78.0 - - - +
403I ILE* 1.3 63.9 + - - +
405I ALA* 3.2 17.6 + - + +
406I HIS* 3.3 9.4 + - - +
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Residues in contact with ILE 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252I HIS* 3.6 44.0 - - + +
254I ILE* 4.0 25.1 - - + -
287I VAL* 5.1 1.3 - - + -
399I ALA 3.1 16.0 + - - +
400I MET 3.6 5.6 - - - +
402I LEU* 1.3 76.1 - - - +
404I ASP* 1.3 61.8 + - - +
406I HIS* 3.2 17.6 + - - +
408I TYR 4.3 2.2 - - - +
412I THR* 3.8 15.3 - - - +
425I PHE* 4.2 0.4 - - + -
429I ILE* 3.7 24.7 - - + -
431I VAL* 3.7 23.6 - - + -
453I LYS* 3.3 8.8 + - - -
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Residues in contact with ASP 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I GLN* 5.8 1.0 + - - -
400I MET* 2.8 29.2 + - - +
401I ASP* 3.8 9.9 - - - +
403I ILE* 1.3 74.1 - - - +
405I ALA* 1.3 58.0 + - - +
406I HIS 3.8 0.7 - - - +
428I ASN 4.3 7.4 - - - +
429I ILE* 3.7 10.1 - - - +
430I GLN* 2.8 48.3 + - + +
453I LYS* 3.0 24.7 + - - +
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Residues in contact with ALA 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I ASP 2.9 18.6 + - - +
402I LEU* 3.5 10.8 - - + +
403I ILE 3.2 0.4 - - - -
404I ASP* 1.3 75.9 - - - +
406I HIS* 1.3 64.9 + - - +
407I GLU 3.7 0.5 + - - -
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Residues in contact with HIS 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I LYS* 3.5 26.4 + - + +
252I HIS* 4.0 14.8 - + + -
379I TYR* 3.2 53.8 + + - -
380I GLN* 3.2 24.6 + - - -
402I LEU 3.3 9.4 + - - +
403I ILE 3.2 14.0 + - - +
404I ASP 3.8 0.5 - - - +
405I ALA* 1.3 80.5 - - - +
407I GLU* 1.3 79.3 + - + +
408I TYR* 3.3 25.0 + + - +
453I LYS* 3.2 21.0 + - - +
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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