Contacts of the helix formed by residues 325 - 330 (chain E) 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 ASN 325 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263E MET* 3.4 24.0 - - + +
264E PRO* 3.2 18.9 - - + +
265E LYS* 2.8 47.4 + - - +
323E THR* 3.3 8.4 + - - +
324E VAL* 1.3 76.7 - - - +
326E SER* 1.3 67.2 + - - +
328E LYS* 3.0 30.4 + - - +
329E ARG 3.7 2.1 + - - -
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Residues in contact with SER 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E PRO* 3.8 5.8 - - - +
321E ASN* 3.3 21.3 + - - -
323E THR* 2.8 39.0 + - - -
324E VAL 3.1 1.4 - - - -
325E ASN* 1.3 76.6 - - - +
327E TYR* 1.3 61.1 + - - +
329E ARG* 3.1 24.6 + - - +
330E LEU* 3.5 10.5 + - - +
371E ASP* 2.7 29.0 + - - +
373E SER* 3.2 6.1 + - - -
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Residues in contact with TYR 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E LEU* 3.4 10.6 + - + +
321E ASN* 2.9 35.0 + - + +
323E THR 3.2 17.7 - - - -
324E VAL 3.1 7.6 + - - +
325E ASN 3.1 1.2 - - - -
326E SER* 1.3 73.8 - - - +
328E LYS* 1.3 66.2 + - + +
329E ARG 3.2 1.6 - - - -
330E LEU* 3.7 31.6 + - + +
331E VAL* 4.0 10.0 - - - +
420E PRO* 3.4 27.6 - - + +
421E THR 3.2 19.1 - - - +
422E GLN* 3.7 13.5 - - + -
423E LEU* 3.5 23.1 - - + +
426E VAL* 3.3 37.5 - - + +
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Residues in contact with LYS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS* 3.6 27.9 - - + -
324E VAL* 4.0 31.7 - - - +
325E ASN* 3.0 24.0 + - - +
327E TYR* 1.3 79.5 - - + +
329E ARG* 1.3 59.5 + - - +
331E VAL* 3.4 22.7 - - - +
463E VAL* 5.5 3.8 - - - +
468E HIS* 5.4 13.7 - - - -
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Residues in contact with ARG 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E PRO* 3.7 29.6 - - + +
265E LYS* 4.1 10.2 + - + -
272E GLY* 4.4 5.4 - - - +
273E SER 3.5 17.9 - - - +
274E GLY* 3.5 19.8 - - - -
276E HIS* 4.2 0.8 - - - -
321E ASN* 3.9 5.7 - - - +
325E ASN 3.7 1.0 + - - -
326E SER 3.1 11.3 + - - +
328E LYS* 1.3 75.5 - - - +
330E LEU* 1.3 63.7 + - - +
331E VAL* 2.7 25.4 + - - +
334E TYR* 5.4 2.1 - - + +
336E ALA* 3.6 25.2 - - + +
337E PRO* 4.3 0.8 - - - +
368E ARG 2.9 24.2 + - - -
369E SER 2.9 24.5 + - - -
370E PRO 3.6 5.5 + - - -
371E ASP* 4.1 2.8 + - - +
505E P3S 2.8 39.0 + - - +
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Residues in contact with LEU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E LEU* 4.0 21.5 - - + -
321E ASN* 3.8 18.8 - - - +
326E SER 3.5 9.6 + - - +
327E TYR* 3.7 28.1 + - + +
328E LYS 3.5 0.6 - - - -
329E ARG* 1.3 97.5 - - - +
331E VAL* 1.3 63.9 + - - +
336E ALA* 4.5 1.1 - - + -
337E PRO* 3.6 41.5 - - + +
338E ILE* 4.0 6.4 - - - +
369E SER* 4.3 4.7 - - - +
419E THR* 4.2 20.0 + - + +
420E PRO 4.6 3.8 - - - +
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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