Contacts of the helix formed by residues 323 - 332 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A TYR 3.5 9.0 + - - +
319A GLU* 3.8 11.7 - - - -
322A ILE* 1.3 86.7 - - - +
324A ASP* 1.3 61.3 + - - +
325A LYS* 3.8 10.8 + - - +
326A PHE* 3.1 31.1 + - - +
327A ALA* 3.1 12.5 + - - +
356D LYS* 5.7 4.9 - - - -
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Residues in contact with ASP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLU* 3.7 28.4 + - - +
323A SER* 1.3 75.4 - - - +
325A LYS* 1.3 61.3 + - + +
327A ALA* 3.7 8.4 + - - +
328A GLN* 3.3 35.0 + - - +
339A ALA* 5.3 1.2 - - - +
343A ARG* 3.3 31.2 + - - +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A SER* 3.2 9.8 - - - +
324A ASP* 1.3 80.0 - - + +
326A PHE* 1.3 61.3 + - - +
328A GLN* 3.8 8.7 - - - +
329A HIS* 3.0 36.3 + - + +
356D LYS 5.2 6.5 - - - +
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Residues in contact with PHE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PRO* 5.6 1.8 - - + -
246A LEU* 3.5 26.2 - - + -
318A TYR* 3.5 31.0 - + + -
322A ILE* 4.6 21.1 - - + -
323A SER* 3.1 25.5 + - - +
325A LYS* 1.3 76.8 - - - +
327A ALA* 1.3 62.9 + - - +
328A GLN 3.3 0.2 - - - -
329A HIS* 3.3 3.5 + - - +
330A LEU* 3.2 68.4 + - + +
353D ILE* 3.6 19.3 - - + -
354D GLU 4.1 6.1 - - - -
355D ILE* 4.1 14.6 - - + -
356D LYS* 4.1 21.3 + - - +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ALA* 3.8 33.0 - - + +
318A TYR* 4.3 14.1 - - + +
319A GLU* 4.3 6.7 - - + +
323A SER 3.1 11.1 + - - +
324A ASP* 3.7 9.6 + - - +
325A LYS 3.6 0.2 - - - -
326A PHE* 1.3 76.4 - - - +
328A GLN* 1.3 60.5 + - - +
330A LEU* 3.8 4.1 + - - +
331A LEU* 3.4 30.8 + - - +
339A ALA* 6.0 2.9 - - + -
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASP* 3.3 21.9 + - - +
325A LYS* 3.8 10.0 - - - +
327A ALA* 1.3 79.6 - - - +
329A HIS* 1.3 62.7 + - - +
330A LEU 3.5 0.3 + - - -
331A LEU* 3.6 11.2 + - - +
333A HIS* 2.9 38.4 + - + +
334A LYS 3.8 8.5 + - - +
335A SER 2.9 28.3 + - - -
336A ASP* 3.9 7.7 + - - +
339A ALA* 3.5 31.6 - - + +
343A ARG* 5.2 1.7 + - - -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 3.8 10.6 - - + +
325A LYS* 3.0 24.7 + - + +
326A PHE* 3.3 10.3 + - - +
328A GLN* 1.3 78.7 - - - +
330A LEU* 1.3 61.9 + - - +
331A LEU 3.5 0.2 + - - -
332A GLY* 3.9 4.2 + - - -
333A HIS 5.1 0.4 - - - -
351D ASP* 3.7 26.2 + - - -
352D LYS 5.9 0.2 - - - -
353D ILE* 3.1 43.1 - - + +
356D LYS 4.1 19.4 + - - +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL 4.8 2.0 - - - +
209A THR 4.3 9.4 - - - +
210A GLY* 6.0 0.9 - - - -
211A GLN* 2.9 20.9 + - - -
240A ILE* 3.3 12.5 - - - +
242A ILE* 4.5 14.1 - - + -
243A PRO* 6.2 0.2 - - + -
246A LEU* 4.0 9.6 - - + -
318A TYR* 3.7 31.6 - - + -
326A PHE* 3.2 64.9 + - + +
327A ALA* 4.1 5.4 - - - +
328A GLN 3.4 0.4 - - - -
329A HIS* 1.3 76.2 - - - +
331A LEU* 1.3 63.2 + - + +
353D ILE* 3.7 20.0 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLY 4.0 12.3 - - - +
211A GLN* 3.8 4.9 - - - +
212A ARG* 4.4 0.2 + - - -
233A GLN* 3.2 16.3 + - - +
311A ARG* 3.0 41.6 + - + +
314A SER* 5.0 3.8 - - - +
315A ALA* 4.1 22.2 - - + -
318A TYR* 6.5 0.4 - - + -
327A ALA 3.4 22.5 + - - +
328A GLN* 4.0 2.5 - - - +
329A HIS 3.4 1.0 - - - -
330A LEU* 1.3 83.6 - - + +
332A GLY* 1.3 58.3 + - - +
333A HIS* 3.0 30.1 - - + +
339A ALA* 6.1 2.5 - - + -
342A PHE* 3.7 36.1 - - + -
12I T 4.7 0.2 - - - +
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Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLN* 5.3 0.2 - - - -
212A ARG* 5.3 0.7 - - - -
233A GLN* 3.9 13.3 - - - +
236A THR* 3.8 2.9 + - - -
238A VAL* 3.3 38.4 - - - +
240A ILE* 5.1 8.0 - - - +
328A GLN 4.2 0.4 + - - -
329A HIS 3.9 7.3 + - - -
330A LEU 3.4 4.6 + - - -
331A LEU* 1.3 77.6 - - - +
333A HIS* 1.3 58.9 + - - +
334A LYS 4.1 0.3 + - - -
13I T 3.0 17.0 + - - -
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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