Contacts of the helix formed by residues 324 - 329 (chain D) in PDB entry 3ZXR
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 VAL 324 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D THR* 1.3 73.2 - - - +
325D ASN* 1.3 64.0 + - - +
327D TYR* 3.2 18.6 + - - +
328D LYS* 4.0 25.9 + - - +
423D LEU* 3.7 25.4 - - + +
459D GLU* 4.2 29.4 + - + +
460D ILE* 4.3 7.4 - - - -
463D VAL* 4.1 28.7 - - + -
507D CL 4.5 4.7 - - + -
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D MET* 3.5 24.4 - - + +
264D PRO* 3.2 17.4 - - + +
265D LYS* 2.7 47.8 + - - +
323D THR* 3.2 9.0 + - - +
324D VAL* 1.3 77.5 - - - +
326D SER* 1.3 65.2 + - - +
328D LYS* 3.0 29.9 + - - +
329D ARG 3.7 2.6 + - - -
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Residues in contact with SER 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D PRO* 3.8 5.8 - - - +
321D ASN* 3.4 21.4 + - - -
323D THR* 2.8 39.6 + - - -
325D ASN* 1.3 74.7 - - - +
327D TYR* 1.3 61.2 + - - +
329D ARG* 3.1 23.7 + - - +
330D LEU* 3.6 11.3 + - - +
371D ASP* 2.7 28.3 + - - +
373D SER* 3.1 6.9 + - - -
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Residues in contact with TYR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D LEU* 3.4 11.3 + - + +
321D ASN* 2.8 34.8 + - + +
323D THR 3.2 17.0 - - - -
324D VAL 3.2 7.6 + - - +
325D ASN 3.1 1.2 - - - -
326D SER* 1.3 73.0 - - - +
328D LYS* 1.3 61.3 + - + +
329D ARG 3.2 5.5 + - - -
330D LEU* 3.6 37.1 + - + +
331D VAL* 4.0 5.2 - - - +
420D PRO* 3.5 36.8 - - + -
421D THR 3.3 19.5 - - - +
422D GLN* 3.7 13.0 - - + -
423D LEU* 3.5 23.3 - - + +
426D VAL* 3.3 26.7 - - + +
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Residues in contact with LYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LYS* 3.5 28.4 - - + +
324D VAL* 4.0 31.2 + - - +
325D ASN* 3.0 22.8 + - - +
327D TYR* 1.3 77.7 - - + +
329D ARG* 1.3 60.0 + - - +
331D VAL* 3.5 22.1 - - - +
463D VAL* 5.5 4.4 - - - +
468D HIS* 5.5 12.9 - - - -
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Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D PRO* 3.9 27.4 - - + +
265D LYS* 4.0 10.4 + - + -
272D GLY* 4.4 6.5 - - - +
273D SER 3.5 18.4 - - - +
274D GLY* 3.4 19.8 - - - -
276D HIS* 4.2 1.0 - - - -
321D ASN* 3.9 5.7 - - - +
325D ASN 3.7 1.0 + - - -
326D SER 3.1 12.6 + - - +
328D LYS* 1.3 78.4 - - - +
330D LEU* 1.3 61.4 + - - +
331D VAL* 2.8 26.8 + - - +
334D TYR* 5.4 2.6 - - + +
336D ALA* 3.7 23.8 - - + +
337D PRO* 4.4 0.6 - - - +
368D ARG 3.0 22.2 + - - -
369D SER 2.9 25.3 + - - -
370D PRO 3.6 4.8 + - - -
371D ASP* 4.2 2.6 - - - +
505D P3S 2.7 38.8 + - - +
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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