Contacts of the helix formed by residues 322 - 332 (chain B) in PDB entry 5ZR1
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 LYS 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B PHE* 3.4 23.1 - - + +
317B TYR* 3.8 16.8 - - - +
318B GLY 3.3 14.5 + - - +
320B GLY 3.1 14.9 + - - +
321B SER* 1.3 75.2 - - - +
323B ARG* 1.3 57.4 + - - +
324B ASN 3.6 1.6 - - - -
325B PHE* 3.6 10.6 + - - +
326B LEU* 3.1 31.1 + - + +
425B HIS* 5.0 0.9 - - - -
426B ASN* 5.3 0.7 - - - -
455B SER* 4.0 20.0 - - - +
456B THR 3.3 20.0 + - - -
457B ASP* 2.4 30.9 + - - -
480B ILE* 3.7 29.8 - - + +
482B ASN* 4.7 0.9 - - - +
489B GLU* 5.3 1.0 + - - -
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B SER* 3.4 8.6 + - - +
322B LYS* 1.3 75.9 - - - +
324B ASN* 1.3 78.4 + - - +
326B LEU 3.1 9.7 + - - -
327B GLU* 3.1 50.1 + - - +
364B ASN* 3.9 7.5 - - - +
366B TYR* 3.0 26.4 + - - -
425B HIS* 3.6 26.5 + - + +
488B VAL* 4.3 22.3 - - - +
489B GLU* 3.4 26.8 + - - +
17C ASP* 5.3 0.8 + - - -
18C ALA* 3.4 34.2 - - - +
23C TYR* 4.3 7.9 + - - -
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Residues in contact with ASN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 5.2 1.3 - - - -
321B SER* 4.6 7.2 + - - -
323B ARG* 1.3 85.7 + - - +
325B PHE* 1.3 63.7 + - - +
327B GLU* 3.9 18.1 + - - +
328B GLU* 3.3 30.3 + - - +
484B GLU* 5.4 7.8 - - + +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 3.5 30.0 - + + -
297B GLN* 3.8 34.1 - - + -
301B PHE* 3.4 33.3 - + - -
304B TYR* 4.0 15.9 - + - -
316B PHE* 3.9 22.2 - + - -
321B SER 5.4 0.8 + - - -
322B LYS* 3.6 13.5 + - - +
323B ARG 3.2 0.2 - - - -
324B ASN* 1.3 79.6 - - - +
326B LEU* 1.3 66.6 + - + +
328B GLU* 3.5 1.4 + - - +
329B PHE* 3.0 29.7 + - + +
480B ILE* 3.5 31.4 - - + -
482B ASN* 4.7 8.9 - - - +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B PHE* 3.5 35.0 - - + -
322B LYS* 3.1 17.0 + - + +
323B ARG 3.1 0.8 + - - -
325B PHE* 1.3 81.1 - - + +
327B GLU* 1.3 58.6 + - - +
329B PHE* 3.9 4.4 - - + +
330B ALA* 3.1 29.5 + - - +
423B VAL* 3.7 19.2 - - + +
424B VAL 3.7 20.6 - - - +
425B HIS* 3.6 28.3 - - + +
453B VAL* 3.7 17.9 - - + +
454B ALA 4.4 2.0 - - - +
455B SER* 3.9 17.3 - - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ARG* 3.1 57.6 + - - +
324B ASN* 3.9 14.7 + - - +
326B LEU* 1.3 77.2 - - - +
328B GLU* 1.3 62.2 + - + +
330B ALA* 4.1 5.8 - - - +
331B ILE* 3.3 41.4 - - + +
332B ASP* 4.9 1.0 - - - +
362B ILE* 3.6 19.0 - - + +
423B VAL* 5.2 1.8 - - - -
425B HIS* 4.1 10.8 - - + +
23C TYR* 3.9 4.3 + - - -
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 3.2 38.1 - - + -
298B LYS* 4.1 12.0 + - - -
301B PHE* 4.9 6.7 - - + -
324B ASN* 3.3 20.8 + - - +
325B PHE 3.5 2.8 + - - +
326B LEU 3.3 0.4 - - - -
327B GLU* 1.3 79.6 - - + +
329B PHE* 1.3 64.3 + - - +
330B ALA 3.4 0.2 - - - -
332B ASP* 3.2 46.9 + - + +
333B TYR* 3.5 2.8 + - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B PHE* 3.5 62.9 - + + -
304B TYR* 3.8 21.8 - + + -
305B TRP 4.7 0.9 - - - -
308B LEU* 4.3 4.5 - - + -
314B LEU* 4.3 7.9 - - + -
316B PHE* 4.7 8.5 - + - -
325B PHE* 3.0 21.2 + + + +
326B LEU* 3.9 3.8 - - + +
328B GLU* 1.3 78.5 - - - +
330B ALA* 1.3 61.0 + - - +
333B TYR* 3.4 13.2 + + - -
334B LEU* 2.8 59.5 + - + +
453B VAL* 4.2 28.7 - - + -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B LEU 3.1 18.6 + - - +
327B GLU* 4.7 2.9 - - - -
329B PHE* 1.3 84.8 - - + +
331B ILE* 1.3 59.6 + - - +
334B LEU* 3.6 11.6 - - + +
335B SER* 3.3 26.2 + - - -
360B CYS* 4.1 10.5 - - - -
362B ILE* 5.8 0.2 - - + -
421B ILE* 4.5 8.4 - - + +
423B VAL* 3.7 30.3 - - + -
453B VAL* 5.2 2.7 - - + -
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B GLU* 3.3 35.8 + - + +
329B PHE 3.5 0.2 - - - -
330B ALA* 1.3 80.2 - - - +
332B ASP* 1.3 75.7 + - - +
335B SER* 3.9 6.1 - - - -
336B PRO* 3.3 19.8 - - - +
360B CYS* 3.9 17.3 - - + -
362B ILE* 4.7 9.2 - - + -
23C TYR* 5.5 1.6 - - - +
25C VAL* 3.9 33.0 - - + -
27C PRO* 3.8 24.7 - - + +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B GLU 5.0 0.2 - - - -
328B GLU* 3.2 38.1 + - + +
331B ILE* 1.3 89.1 - - - +
333B TYR* 1.3 60.2 + - + +
336B PRO* 3.5 17.1 - - - +
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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