Contacts of the helix formed by residues 395 - 406 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B VAL* 3.5 9.6 - - - -
393B VAL* 3.6 5.4 - - - +
394B ALA* 1.3 81.1 - - + +
396B MET* 1.3 68.5 + - - +
397B GLN* 4.0 9.8 + - + +
398B ASP* 3.0 47.0 + - - +
399B ALA 3.2 8.7 + - - -
487D ARG 3.6 14.9 + - - -
488D GLU* 5.0 3.3 - - - -
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Residues in contact with MET 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 4.7 6.3 - - + -
256B MET* 3.7 40.6 - - + +
289B VAL* 3.5 10.5 - - - +
395B THR* 1.3 75.3 + - - +
397B GLN* 1.3 58.3 + - - +
399B ALA* 3.0 10.6 + - - +
400B MET* 2.8 44.8 + - + +
414B ILE* 3.4 16.6 - - + -
421B ALA* 3.3 31.4 - - - +
425B PHE* 3.8 13.7 - - + +
487D ARG* 3.7 39.4 + - - +
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B THR* 3.3 11.6 + - + +
396B MET* 1.3 80.0 - - - +
398B ASP* 1.3 59.6 + - - +
400B MET* 3.2 17.8 + - + +
401B ASP* 2.8 65.9 + - - +
404B ASP* 5.7 1.2 + - - -
424B TYR* 2.8 36.6 + - - -
487D ARG* 4.9 4.9 + - - +
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B VAL* 4.0 17.7 - - + +
394B ALA* 3.7 17.5 + - - +
395B THR* 3.0 32.9 + - - +
397B GLN* 1.3 78.3 - - - +
399B ALA* 1.3 57.1 + - - +
401B ASP* 3.3 11.2 + - - +
402B LEU* 2.9 31.1 + - - +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 3.6 27.4 - - + -
287B VAL* 3.7 30.4 - - + +
289B VAL* 5.4 0.9 - - + -
393B VAL* 3.9 9.2 - - + +
395B THR 3.2 2.8 + - - +
396B MET* 3.0 15.0 + - - +
398B ASP* 1.3 78.0 - - - +
400B MET* 1.3 63.3 + - - +
402B LEU* 3.2 7.1 + - - +
403B ILE* 3.0 25.8 + - - +
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Residues in contact with MET 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.9 7.6 - - + -
396B MET* 2.8 26.2 + - + +
397B GLN* 3.6 33.9 - - - +
399B ALA* 1.3 72.4 - - - +
401B ASP* 1.3 57.2 + - - +
403B ILE* 3.3 3.1 + - - +
404B ASP* 2.9 37.6 + - - +
424B TYR* 3.3 43.1 - - + +
425B PHE* 3.8 39.0 - - + +
428B ASN* 5.2 2.5 - - - -
429B ILE* 3.9 19.7 - - + -
487D ARG* 4.9 0.9 - - - -
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Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B GLN* 2.8 56.6 + - - +
398B ASP* 3.6 11.0 - - - +
400B MET* 1.3 72.8 - - - +
402B LEU* 1.3 62.1 + - - +
404B ASP* 3.4 8.1 + - - +
405B ALA* 3.0 26.4 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B HIS* 4.6 0.9 - - + +
287B VAL* 4.2 25.6 - - + -
374B PRO* 3.6 31.2 - - + -
379B TYR* 3.1 34.7 + - + +
391B VAL* 3.9 26.9 - - + -
393B VAL* 4.6 6.3 - - + -
398B ASP 2.9 13.3 + - - +
399B ALA 3.3 7.2 - - - +
401B ASP* 1.3 76.1 - - - +
403B ILE* 1.3 66.6 + - - +
405B ALA* 3.4 12.9 + - + +
406B HIS* 3.5 7.3 + - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B HIS* 3.6 46.4 - - + +
254B ILE* 3.9 28.9 - - + -
287B VAL* 5.2 2.5 - - + -
399B ALA 3.0 19.5 + - - +
400B MET 3.6 6.1 - - - +
402B LEU* 1.3 75.0 - - - +
404B ASP* 1.3 62.1 + - - +
406B HIS* 3.1 22.0 + - - +
408B TYR 4.6 2.0 - - - +
412B THR* 3.8 15.9 - - - +
425B PHE* 4.3 0.4 - - + -
429B ILE* 3.7 21.3 - - + -
431B VAL* 3.9 21.1 - - + -
453B LYS* 3.6 6.3 + - - +
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Residues in contact with ASP 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B GLN* 5.7 1.0 + - - -
400B MET* 2.9 28.5 + - - +
401B ASP* 3.8 8.4 - - - +
403B ILE* 1.3 72.7 - - - +
405B ALA* 1.3 58.5 + - - +
406B HIS 3.7 0.7 - - - +
428B ASN 4.5 5.2 - - - +
429B ILE* 3.8 10.4 - - - +
430B GLN* 2.8 47.4 + - + +
453B LYS* 2.8 26.0 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ASP 3.0 17.8 + - - +
402B LEU* 3.6 10.3 - - + +
403B ILE 3.2 0.2 - - - -
404B ASP* 1.3 74.2 - - - +
406B HIS* 1.3 66.0 + - - +
407B GLU* 3.7 0.7 + - - -
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Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LYS* 3.4 25.5 + - + +
252B HIS* 4.1 14.4 - + + -
379B TYR* 3.3 43.0 + + - -
380B GLN* 3.1 31.8 + - + -
402B LEU 3.5 5.8 + - - +
403B ILE* 3.1 16.2 + - + +
404B ASP 3.7 0.7 - - - +
405B ALA* 1.3 81.2 - - - +
407B GLU* 1.3 76.6 + - + +
408B TYR* 3.4 29.2 + + - +
453B LYS* 3.0 23.2 + - - +
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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