Contacts of the helix formed by residues 323 - 331 (chain D) in PDB entry 1Z1G
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 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356C LYS 5.0 2.9 + - - -
318D TYR 3.4 10.5 + - - +
319D GLU* 3.7 12.4 - - - -
322D ILE* 1.3 92.3 - - - +
324D ASP* 1.3 64.4 + - - +
325D LYS* 3.2 23.8 - - - +
326D PHE* 3.1 26.9 + - - +
327D ALA 3.2 10.6 + - - -
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Residues in contact with ASP 324 (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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319D GLU* 3.8 38.4 + - - +
323D SER* 1.3 77.4 - - - +
325D LYS* 1.3 59.5 + - + +
327D ALA* 3.7 5.0 + - - +
328D GLN* 2.8 39.2 + - + +
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Residues in contact with LYS 325 (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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356C LYS 5.2 2.7 - - - +
323D SER* 3.2 19.7 - - - +
324D ASP* 1.3 81.0 - - + +
326D PHE* 1.3 62.7 + - - +
328D GLN* 3.6 9.3 - - - +
329D HIS* 3.3 25.8 + - - +
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Residues in contact with PHE 326 (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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353C ILE* 4.3 10.8 - - + -
354C GLU 3.9 14.1 - - - -
355C ILE 4.4 8.5 - - - -
356C LYS* 3.4 36.1 + - - +
246D LEU* 3.5 31.4 - - + -
318D TYR* 3.4 44.0 - + + -
322D ILE* 4.8 16.8 - - + -
323D SER* 3.1 26.8 + - - +
325D LYS* 1.3 77.2 - - - +
327D ALA* 1.3 66.8 + - - +
329D HIS* 3.0 15.9 + - + +
330D LEU* 3.0 21.9 + - + +
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Residues in contact with ALA 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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315D ALA* 3.9 31.6 - - + +
318D TYR* 4.3 13.5 - - + -
319D GLU* 4.3 6.5 - - + +
323D SER 3.2 8.6 + - - +
324D ASP* 3.7 8.5 + - - +
326D PHE* 1.3 78.5 - - - +
328D GLN* 1.3 59.9 + - + +
330D LEU* 3.6 5.1 + - - -
331D LEU* 2.9 37.7 + - - +
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Residues in contact with GLN 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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324D ASP* 2.8 29.2 + - - +
325D LYS* 3.6 11.2 - - - +
326D PHE 3.2 0.4 - - - -
327D ALA* 1.3 75.4 - - + +
329D HIS* 1.3 61.3 + - - +
330D LEU 3.4 0.3 + - - -
331D LEU* 3.9 1.5 + - - -
333D HIS* 2.7 56.8 + - + +
334D LYS 5.9 1.1 - - - +
335D SER 3.0 27.2 + - - +
336D ASP* 3.7 31.0 + - - +
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Residues in contact with HIS 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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351C ASP* 3.9 28.8 + - - -
352C LYS 5.3 1.8 - - - -
353C ILE* 4.0 25.0 - - + +
354C GLU* 5.5 0.9 - - + -
356C LYS* 3.5 26.6 + - - -
240D ILE* 3.8 18.4 - - + +
325D LYS 3.3 12.4 + - - +
326D PHE* 3.0 12.0 + - - +
328D GLN* 1.3 78.3 - - - +
330D LEU* 1.3 62.9 + - - +
332D GLY* 3.7 7.1 + - - -
333D HIS 4.5 4.2 - - - +
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Residues in contact with LEU 330 (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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353C ILE* 4.0 24.9 - - + -
208D VAL 4.3 2.5 - - - +
209D THR 3.9 16.8 - - - +
211D GLN* 3.0 17.2 + - - -
240D ILE* 3.3 11.1 - - - +
242D ILE* 3.9 28.3 - - + -
243D PRO* 5.4 0.2 - - + -
246D LEU* 4.1 15.7 - - + -
314D SER* 5.1 2.0 - - - +
318D TYR* 3.5 37.7 - - + -
326D PHE* 3.0 19.0 + - + +
327D ALA* 3.8 5.8 - - - +
328D GLN 3.3 0.2 - - - -
329D HIS* 1.3 76.9 - - - +
331D LEU* 1.3 63.7 + - + +
332D GLY 2.9 10.4 + - - -
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Residues in contact with LEU 331 (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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210D GLY* 4.0 15.7 - - - +
211D GLN* 3.9 8.3 - - - +
212D ARG* 3.9 7.6 + - - -
233D GLN* 4.0 1.8 + - - -
311D ARG* 2.6 46.2 + - - +
314D SER* 4.8 1.3 - - - +
315D ALA* 3.9 33.2 - - + +
327D ALA* 2.9 23.1 + - - +
328D GLN* 3.9 0.8 + - - -
329D HIS 3.7 0.4 - - - -
330D LEU* 1.3 80.0 - - + +
332D GLY* 1.3 59.3 + - - +
333D HIS* 3.0 34.0 + - + +
12L G 5.0 9.4 - - - +
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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