Contacts of the helix formed by residues 327 - 340 (chain Z) in PDB entry 3ZPV
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 SER 327 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797Y TRP* 4.1 1.8 - - - -
798Y CYS* 3.7 10.5 - - - +
800Y ASP* 4.5 7.6 - - - -
803Y VAL* 4.2 23.5 - - - +
325Z VAL* 4.3 1.4 + - - +
326Z PHE* 1.3 76.1 - - - +
328Z THR* 1.3 64.4 + - - +
329Z GLN* 3.5 8.8 + - - +
330Z LEU* 3.1 26.1 + - - +
331Z ALA* 2.9 21.7 + - - +
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Residues in contact with THR 328 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779Y VAL* 3.3 30.3 + - - +
780Y GLY* 3.4 25.6 - - - +
781Y LEU* 3.5 17.8 - - + +
797Y TRP* 3.1 27.6 + - - +
798Y CYS 4.2 2.0 + - - -
800Y ASP* 4.7 12.1 + - - -
327Z SER* 1.3 74.1 - - - +
329Z GLN* 1.3 59.0 + - - +
331Z ALA* 3.7 1.0 - - - +
332Z ASN* 2.9 33.8 + - - +
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Residues in contact with GLN 329 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344T GLN* 5.2 9.7 - - - +
760W ASN* 5.4 8.1 + - - +
800Y ASP* 5.5 1.5 + - - +
327Z SER* 3.2 8.2 + - - +
328Z THR* 1.3 81.2 - - - +
330Z LEU* 1.3 63.4 + - - +
332Z ASN* 3.3 6.4 + - - +
333Z LYS* 3.0 60.5 + - - +
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Residues in contact with LEU 330 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325Z VAL 4.0 10.5 - - - +
326Z PHE* 4.0 10.3 - - + -
327Z SER* 3.1 20.7 + - - +
329Z GLN* 1.3 86.1 + - - +
331Z ALA* 1.3 56.6 + - - +
333Z LYS* 3.5 5.5 + - + +
334Z GLY* 2.9 26.9 + - - -
349Z TYR* 3.9 28.4 - - + +
350Z HIS* 3.8 32.3 - - + +
353Z GLN* 4.6 10.3 - - - +
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Residues in contact with ALA 331 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781Y LEU* 4.0 8.1 - - + -
785Y ALA* 3.5 6.0 - - + +
789Y LEU* 3.8 33.7 - - + -
797Y TRP* 5.2 0.2 - - + -
326Z PHE* 3.9 18.5 - - + -
327Z SER 2.9 17.6 + - - +
328Z THR 3.7 3.6 - - - +
330Z LEU* 1.3 76.6 - - - +
332Z ASN* 1.3 58.3 + - - +
334Z GLY* 3.9 0.5 - - - -
335Z ALA* 3.0 30.7 + - - +
346Z ILE* 4.7 4.8 - - + +
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Residues in contact with ASN 332 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780Y GLY 2.9 26.3 + - - -
781Y LEU* 3.8 1.7 - - - +
782Y THR* 2.9 46.0 + - + +
785Y ALA* 3.1 10.5 - - - +
328Z THR* 2.9 25.2 + - - +
329Z GLN* 3.6 5.9 - - - +
331Z ALA* 1.3 75.4 - - - +
333Z LYS* 1.3 61.0 + - + +
335Z ALA* 3.4 3.1 + - - +
336Z GLU* 3.2 26.1 + - - +
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Residues in contact with LYS 333 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317T GLY* 4.5 19.5 - - - +
756W GLU* 5.1 5.6 - - - +
758W ASN* 4.3 17.6 - - - +
329Z GLN* 3.0 51.7 + - - +
330Z LEU* 4.0 6.1 - - + +
332Z ASN* 1.3 72.3 - - + +
334Z GLY* 1.3 65.2 + - - +
336Z GLU* 3.2 10.4 + - + +
337Z SER* 3.0 22.7 + - - -
349Z TYR* 3.3 24.6 - - + +
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Residues in contact with GLY 334 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326Z PHE* 5.5 0.2 - - - -
330Z LEU 2.9 15.1 + - - -
331Z ALA* 3.9 1.3 - - - -
333Z LYS* 1.3 75.8 - - - +
335Z ALA* 1.3 60.7 + - - +
337Z SER* 3.1 5.5 - - - -
338Z VAL* 3.1 24.6 + - - +
346Z ILE* 3.6 14.8 - - - +
349Z TYR* 3.5 30.0 - - - +
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Residues in contact with ALA 335 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782Y THR* 4.8 1.3 - - - +
784Y ALA* 4.0 7.4 - - + -
785Y ALA* 3.7 28.3 - - + +
788Y MET* 3.6 23.3 - - - +
331Z ALA 3.0 18.5 + - - +
332Z ASN* 3.8 4.3 - - - +
333Z LYS 3.3 0.2 - - - -
334Z GLY* 1.3 72.1 - - - +
336Z GLU* 1.3 65.9 + - - +
338Z VAL* 3.3 2.3 + - - +
339Z LEU* 3.0 30.2 + - - +
346Z ILE* 3.8 2.1 - - + +
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Residues in contact with GLU 336 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A HIS* 3.7 48.4 + - + +
317T GLY* 5.1 15.0 - - - -
318T ALA* 5.3 3.6 + - - +
747W ILE* 5.9 3.6 - - - +
332Z ASN 3.2 18.1 + - - +
333Z LYS* 3.3 13.2 - - - +
335Z ALA* 1.3 75.4 - - - +
337Z SER* 1.3 52.1 + - - +
339Z LEU* 3.3 2.4 + - - +
340Z SER* 2.8 39.0 + - - +
342Z GLN* 4.8 0.2 - - - -
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Residues in contact with SER 337 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333Z LYS 3.0 9.4 + - - -
334Z GLY 3.1 11.7 - - - -
336Z GLU* 1.3 74.9 - - - +
338Z VAL* 1.3 59.1 + - - +
340Z SER* 3.5 0.5 - - - -
341Z GLY 3.5 1.7 + - - -
342Z GLN* 3.1 47.7 + - - +
343Z PHE* 3.3 26.8 + - - -
349Z TYR* 3.2 28.4 - - - -
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Residues in contact with VAL 338 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788Y MET* 3.8 22.0 - - + -
334Z GLY 3.1 13.0 + - - +
335Z ALA 3.8 6.1 - - - +
336Z GLU 3.2 0.4 - - - -
337Z SER* 1.3 74.4 - - - +
339Z LEU* 1.3 63.9 + - + +
341Z GLY* 3.1 18.2 + - - -
343Z PHE* 3.4 16.2 - - + +
344Z GLN* 3.7 17.0 - - - +
345Z THR* 3.5 34.5 - - - +
346Z ILE* 3.7 8.1 - - + +
349Z TYR* 5.7 0.2 - - + -
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Residues in contact with LEU 339 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A MET 3.9 9.0 - - - +
753A CYS* 3.2 25.6 - - - +
754A HIS* 3.3 39.3 - - + +
755A LYS* 4.4 2.6 + - - -
784Y ALA* 3.9 24.0 - - + -
788Y MET* 3.9 16.4 - - + -
335Z ALA 3.0 20.2 + - - +
336Z GLU 3.8 0.4 - - - +
338Z VAL* 1.3 78.3 - - + +
340Z SER* 1.3 59.3 + - - +
341Z GLY 3.3 0.7 + - - -
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Residues in contact with SER 340 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A CYS 3.4 6.9 + - - -
754A HIS* 4.1 15.9 + - - +
755A LYS* 2.0 46.6 - - - +
336Z GLU* 2.8 21.0 + - - +
337Z SER 3.5 3.4 - - - -
339Z LEU* 1.3 69.5 - - - +
341Z GLY* 1.3 55.9 + - - +
342Z GLN* 3.3 33.8 + - - +
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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