Contacts of the helix formed by residues 327 - 340 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797W TRP* 3.9 1.8 - - - -
798W CYS* 3.6 12.2 - - - +
800W ASP* 4.4 8.7 - - - -
803W VAL* 4.2 21.7 - - - +
325X VAL* 4.2 1.4 + - - +
326X PHE* 1.3 74.9 - - - +
328X THR* 1.3 64.2 + - - +
329X GLN* 3.5 9.2 + - - +
330X LEU* 3.2 26.4 + - - +
331X ALA* 2.9 21.5 + - - +
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Residues in contact with THR 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779W VAL* 3.1 32.6 + - - +
780W GLY* 3.4 25.8 - - - +
781W LEU* 3.5 17.9 - - + +
797W TRP* 3.1 27.9 + - - +
798W CYS 4.1 2.0 + - - -
800W ASP* 4.7 11.0 + - - -
327X SER* 1.3 73.9 - - - +
329X GLN* 1.3 58.9 + - - +
331X ALA 3.3 0.2 + - - -
332X ASN* 2.9 32.6 + - - +
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Residues in contact with GLN 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800W ASP* 5.5 1.9 + - - +
327X SER* 3.2 8.4 + - - +
328X THR* 1.3 81.2 - - - +
330X LEU* 1.3 63.4 + - - +
332X ASN* 3.3 7.2 + - - +
333X LYS* 3.0 60.5 + - - +
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Residues in contact with LEU 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325X VAL 4.0 11.0 - - - +
326X PHE* 4.1 10.9 - - + -
327X SER* 3.2 21.2 + - - +
329X GLN* 1.3 85.1 + - - +
331X ALA* 1.3 57.9 + - - +
333X LYS* 3.5 5.8 + - + +
334X GLY* 2.9 26.5 + - - -
349X TYR* 3.9 28.7 - - + +
350X HIS* 3.8 31.9 - - + +
353X GLN* 4.6 13.5 - - + +
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Residues in contact with ALA 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781W LEU* 3.9 7.6 - - + -
785W ALA* 3.4 11.6 - - + +
789W LEU* 3.7 34.8 - - + -
326X PHE* 3.9 17.6 - - + -
327X SER 2.9 18.6 + - - +
328X THR 3.7 3.1 - - - +
330X LEU* 1.3 77.3 - - - +
332X ASN* 1.3 58.5 + - - +
334X GLY* 3.9 0.7 - - - -
335X ALA* 3.0 24.3 + - - +
346X ILE* 4.7 5.2 - - + +
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Residues in contact with ASN 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780W GLY 2.6 27.9 + - - -
781W LEU* 3.6 2.6 - - - +
782W THR* 2.7 46.3 + - + +
785W ALA* 3.0 10.1 - - - +
328X THR* 2.9 25.1 + - - +
329X GLN* 3.6 7.2 - - - +
331X ALA* 1.3 73.4 - - - +
333X LYS* 1.3 64.8 + - + +
335X ALA* 3.4 3.5 + - - +
336X GLU* 3.2 26.5 + - - +
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Residues in contact with LYS 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329X GLN* 3.0 49.6 + - - +
330X LEU* 3.9 6.1 - - + +
332X ASN* 1.3 72.5 - - + +
334X GLY* 1.3 65.8 + - - +
336X GLU* 3.2 10.8 + - + +
337X SER* 3.0 23.2 + - - -
349X TYR* 3.4 24.4 - - + +
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Residues in contact with GLY 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326X PHE* 5.5 0.4 - - - -
330X LEU 2.9 14.3 + - - -
331X ALA 3.9 1.3 - - - -
333X LYS* 1.3 77.2 - - - +
335X ALA* 1.3 61.2 + - - +
337X SER* 3.1 6.2 - - - -
338X VAL* 3.1 24.8 + - - +
346X ILE* 3.7 14.3 - - - +
349X TYR* 3.5 29.9 - - - +
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Residues in contact with ALA 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782W THR* 4.7 1.6 - - - +
784W ALA* 3.9 7.9 - - + -
785W ALA* 3.5 29.8 - - + +
788W MET* 3.6 22.3 - - - +
331X ALA 3.0 18.5 + - - +
332X ASN 3.8 4.5 - - - +
333X LYS 3.2 0.2 - - - -
334X GLY* 1.3 71.9 - - - +
336X GLU* 1.3 65.2 + - - +
338X VAL* 3.3 2.8 + - - +
339X LEU* 3.1 30.3 + - - +
346X ILE* 3.8 1.9 - - + +
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Residues in contact with GLU 336 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782W THR* 6.5 1.1 - - + -
332X ASN 3.2 17.0 + - - +
333X LYS* 3.3 13.5 - - - +
335X ALA* 1.3 76.3 - - - +
337X SER* 1.3 51.1 + - - +
339X LEU* 3.3 9.8 + - + +
340X SER* 2.8 37.4 + - - -
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Residues in contact with SER 337 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333X LYS 3.0 9.4 + - - -
334X GLY 3.1 11.4 - - - -
336X GLU* 1.3 75.7 - - - +
338X VAL* 1.3 58.8 + - - -
340X SER* 2.9 19.4 + - - -
342X GLN* 3.1 28.9 + - - +
343X PHE* 3.3 27.4 + - - -
349X TYR* 3.2 29.1 - - - -
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Residues in contact with VAL 338 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788W MET* 3.8 26.5 - - + -
791W LYS* 5.9 2.7 - - - +
334X GLY 3.1 13.3 + - - +
335X ALA 3.8 6.5 - - - +
336X GLU 3.2 0.2 - - - -
337X SER* 1.3 74.3 - - - +
339X LEU* 1.3 62.7 + - + +
341X GLY* 3.1 17.5 + - - -
343X PHE* 3.4 16.4 - - + +
344X GLN 3.7 16.4 - - - +
345X THR* 3.5 35.9 - - - +
346X ILE 3.7 2.9 - - - +
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Residues in contact with LEU 339 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784W ALA* 3.8 25.6 - - + -
788W MET* 3.9 16.4 - - + -
335X ALA 3.1 22.2 + - - +
336X GLU* 3.8 7.4 - - + +
338X VAL* 1.3 78.0 - - + +
340X SER* 1.4 60.5 + - - +
341X GLY 3.3 0.7 + - - -
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Residues in contact with SER 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336X GLU 2.8 15.2 + - - -
337X SER* 2.9 26.9 + - - -
339X LEU* 1.4 70.3 - - - +
341X GLY* 1.3 56.3 + - - +
342X GLN* 2.9 34.0 + - - +
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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