Contacts of the helix formed by residues 395 - 406 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487F ARG 3.5 14.0 + - - -
488F GLU 4.9 0.7 + - - -
289H VAL* 3.5 8.7 - - - -
393H VAL* 3.9 4.9 - - - +
394H ALA* 1.3 79.6 - - + +
396H MET* 1.3 72.4 + - - +
397H GLN* 3.7 11.0 + - + +
398H ASP* 3.0 50.6 + - - +
399H ALA 3.3 4.9 + - - -
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Residues in contact with MET 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487F ARG* 3.6 40.5 + - + +
254H ILE* 4.8 4.9 - - + -
256H MET* 3.6 36.8 - - + -
289H VAL* 3.6 10.1 - - - +
395H THR* 1.3 75.2 + - - +
397H GLN* 1.3 62.7 + - - +
399H ALA* 3.0 19.2 + - - +
400H MET* 3.0 35.7 + - + +
414H ILE* 3.8 18.4 - - + -
421H ALA* 3.5 29.2 - - - +
424H TYR* 4.3 7.0 - - + -
425H PHE* 3.9 8.7 - - + -
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Residues in contact with GLN 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487F ARG* 4.4 10.0 + - - +
395H THR* 3.3 13.2 + - + +
396H MET* 1.3 78.0 - - - +
398H ASP* 1.3 53.5 + - - +
400H MET* 3.1 18.1 + - + +
401H ASP* 2.8 70.4 + - - +
404H ASP* 5.6 1.4 + - - -
424H TYR* 2.8 34.4 + - - -
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Residues in contact with ASP 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393H VAL* 4.1 17.2 - - + +
394H ALA* 3.9 15.6 + - - +
395H THR* 3.0 33.4 + - - +
397H GLN* 1.3 78.8 - - - +
399H ALA* 1.3 58.0 + - - +
401H ASP* 3.3 12.4 + - - +
402H LEU* 2.9 30.8 + - - +
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Residues in contact with ALA 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H ILE* 3.6 26.7 - - + -
287H VAL* 3.5 32.4 - - + +
289H VAL* 5.3 0.4 - - + -
393H VAL* 3.9 9.2 - - + +
395H THR 3.3 2.4 + - - +
396H MET* 3.0 14.6 + - - +
398H ASP* 1.3 79.6 - - - +
400H MET* 1.3 54.4 + - - +
402H LEU* 3.5 5.6 + - - +
403H ILE* 3.1 30.8 + - - +
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Residues in contact with MET 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487F ARG* 5.5 0.7 - - - +
254H ILE* 3.6 20.9 - - + -
396H MET* 3.0 28.0 + - + +
397H GLN* 3.1 32.1 + - + +
399H ALA* 1.3 72.4 - - - +
401H ASP* 1.3 60.3 + - - +
402H LEU 3.1 1.6 - - - -
403H ILE* 3.4 1.3 + - - +
404H ASP* 2.8 40.2 + - - +
424H TYR* 3.3 39.3 - - + +
425H PHE* 3.7 28.7 - - + +
428H ASN* 5.6 2.2 - - - -
429H ILE* 3.8 18.6 - - + -
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Residues in contact with ASP 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H GLN* 2.8 55.4 + - - +
398H ASP* 3.7 12.6 - - - +
400H MET* 1.3 72.0 - - - +
402H LEU* 1.3 58.8 + - - +
404H ASP* 3.9 7.4 - - - +
405H ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H HIS* 4.6 1.8 - - + +
287H VAL* 4.2 18.8 - - + -
374H PRO* 3.8 30.1 - - + -
379H TYR* 3.3 33.0 + - + +
391H VAL* 3.6 34.3 - - + -
393H VAL* 4.5 9.0 - - + -
398H ASP 2.9 17.4 + - - +
399H ALA 3.5 5.6 - - - +
401H ASP* 1.3 75.1 - - - +
403H ILE* 1.3 65.0 + - - +
405H ALA* 3.5 13.3 + - + +
406H HIS* 3.5 8.3 + - - +
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Residues in contact with ILE 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H HIS* 3.6 46.4 - - + +
254H ILE* 3.9 25.6 - - + -
287H VAL* 5.1 0.9 - - + -
399H ALA 3.1 17.3 + - - +
400H MET 3.7 4.5 - - - +
402H LEU* 1.3 76.2 - - - +
404H ASP* 1.3 65.1 + - - +
406H HIS* 3.1 20.1 + - - +
408H TYR 4.5 2.9 - - - +
412H THR* 3.7 15.3 - - - +
425H PHE* 4.3 0.7 - - + -
429H ILE* 3.7 21.1 - - + -
430H GLN 5.4 0.7 - - - +
431H VAL* 3.8 22.9 - - + -
453H LYS* 3.5 6.0 + - - +
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Residues in contact with ASP 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H GLN* 5.6 1.0 + - - -
400H MET* 2.8 31.6 + - - +
401H ASP* 4.1 8.2 - - - +
403H ILE* 1.3 73.3 - - - +
405H ALA* 1.3 58.0 + - - +
406H HIS 3.7 0.7 - - - +
428H ASN 4.4 6.1 - - - +
429H ILE* 3.7 9.9 - - - +
430H GLN* 2.7 47.2 + - + +
453H LYS* 3.0 24.8 + - - +
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Residues in contact with ALA 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401H ASP 3.0 19.5 + - - +
402H LEU* 3.8 9.4 - - + +
403H ILE 3.2 0.4 - - - -
404H ASP* 1.3 73.2 - - - +
406H HIS* 1.3 65.4 + - - +
407H GLU 3.8 0.3 + - - -
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Residues in contact with HIS 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H LYS* 3.4 27.2 - - + +
252H HIS* 4.1 13.9 - + + -
379H TYR* 3.3 52.9 + + - -
380H GLN* 3.3 24.3 + - + -
402H LEU 3.5 6.2 + - - +
403H ILE 3.1 14.9 + - - +
404H ASP 3.7 0.5 - - - +
405H ALA* 1.3 81.1 - - - +
407H GLU* 1.3 74.3 + - + +
408H TYR* 3.3 26.9 + + - +
453H 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