Contacts of the helix formed by residues 395 - 405 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487I ARG 3.8 14.6 + - - -
488I GLU* 4.7 7.1 - - - +
289K VAL* 3.5 9.0 - - - -
393K VAL* 3.5 6.2 - - - +
394K ALA* 1.3 79.7 - - + +
396K MET* 1.3 71.5 + - - +
397K GLN* 4.0 9.8 + - + +
398K ASP* 3.1 46.7 + - - +
399K ALA 3.3 8.0 + - - -
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Residues in contact with MET 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487I ARG* 3.5 40.7 + - + +
254K ILE* 4.7 5.4 - - + -
256K MET* 3.6 38.8 - - + -
289K VAL* 3.6 10.9 - - - +
395K THR* 1.3 77.9 + - - +
397K GLN* 1.3 56.6 + - - +
399K ALA* 2.9 24.3 + - - +
400K MET* 3.0 34.8 + - + +
414K ILE* 3.6 17.9 - - + -
421K ALA* 3.4 30.7 - - - +
425K PHE* 3.9 11.2 - - + +
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Residues in contact with GLN 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487I ARG* 5.2 3.7 + - - +
395K THR* 3.3 11.6 + - + +
396K MET* 1.3 79.1 - - - +
398K ASP* 1.3 57.8 + - - +
400K MET* 3.7 19.3 - - + +
401K ASP* 2.9 65.9 + - - +
404K ASP* 5.7 1.2 + - - -
424K TYR* 2.9 38.1 + - - -
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Residues in contact with ASP 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393K VAL* 3.9 17.8 - - + +
394K ALA* 3.7 13.2 + - - +
395K THR* 3.1 39.7 + - - +
397K GLN* 1.3 78.5 - - - +
399K ALA* 1.3 58.1 + - - +
401K ASP* 3.6 10.4 + - - +
402K LEU* 3.1 27.4 + - - +
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Residues in contact with ALA 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254K ILE* 3.7 25.6 - - + -
287K VAL* 3.4 32.4 - - + +
289K VAL* 5.3 0.7 - - + -
393K VAL* 3.9 8.2 - - + +
395K THR 3.3 2.4 + - - +
396K MET* 2.9 14.7 + - - +
398K ASP* 1.3 77.1 - - - +
400K MET* 1.3 62.7 + - - +
402K LEU* 3.3 5.4 + - - +
403K ILE* 3.1 26.7 + - - +
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Residues in contact with MET 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487I ARG* 4.7 1.1 - - - -
254K ILE* 3.9 5.8 - - + -
396K MET* 3.0 28.7 + - + +
397K GLN* 3.3 34.5 + - + +
399K ALA* 1.3 76.3 - - - +
401K ASP* 1.3 58.4 + - - +
403K ILE* 3.2 2.8 + - - +
404K ASP* 2.8 38.8 + - - +
424K TYR* 3.5 42.0 - - + +
425K PHE* 3.9 39.3 - - + +
428K ASN* 5.2 5.6 - - - -
429K ILE* 4.0 16.2 - - + -
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Residues in contact with ASP 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397K GLN* 2.9 54.1 + - - +
398K ASP* 3.8 11.0 - - - +
400K MET* 1.3 75.9 - - - +
402K LEU* 1.3 58.6 + - - +
404K ASP* 3.9 8.0 - - - +
405K ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K HIS* 4.7 1.8 - - + +
287K VAL* 4.2 18.6 - - + -
374K PRO* 3.8 29.6 - - + -
379K TYR* 3.1 34.1 + - + +
391K VAL* 3.5 34.5 - - + -
393K VAL* 4.6 9.2 - - + -
398K ASP 3.1 18.6 + - - +
399K ALA 3.5 5.4 - - - +
400K MET 3.2 0.2 - - - -
401K ASP* 1.3 77.2 - - - +
403K ILE* 1.3 61.6 + - - +
405K ALA* 3.5 12.3 + - + +
406K HIS* 3.6 8.5 + - - +
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Residues in contact with ILE 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K HIS* 3.5 45.3 - - + +
254K ILE* 3.9 27.6 - - + -
287K VAL* 5.1 1.6 - - + -
399K ALA 3.1 16.3 + - - +
400K MET 3.6 5.6 - - - +
402K LEU* 1.3 72.8 - - - +
404K ASP* 1.3 68.1 + - - +
406K HIS* 3.2 16.4 + - - +
408K TYR 4.4 2.5 - - - +
412K THR* 3.9 15.5 - - - +
425K PHE* 4.3 0.7 - - + -
429K ILE* 3.7 22.0 - - + -
431K VAL* 3.8 21.5 - - + -
453K LYS* 3.4 9.4 + - - +
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Residues in contact with ASP 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397K GLN* 5.7 0.9 + - - -
400K MET* 2.8 27.5 + - - +
401K ASP* 4.0 8.3 - - - +
403K ILE* 1.3 72.7 - - - +
405K ALA* 1.3 59.7 + - - +
406K HIS 3.6 1.2 - - - +
428K ASN 4.3 5.7 - - - +
429K ILE* 3.5 10.7 - - - +
430K GLN* 2.9 47.6 + - + +
453K LYS* 3.0 24.9 + - - +
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Residues in contact with ALA 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K ASP 2.9 18.9 + - - +
402K LEU* 3.7 11.2 - - + +
403K ILE 3.2 0.4 - - - -
404K ASP* 1.3 75.8 - - - +
406K HIS* 1.3 62.0 + - - +
407K GLU 3.8 0.7 + - - -
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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