Contacts of the helix formed by residues 318 - 331 (chain A) in PDB entry 1Z59
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 GLY 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A VAL* 3.5 9.3 - - - -
317A ILE* 1.3 78.4 - - - +
319A GLU* 1.3 66.7 + - - -
320A ASP* 3.2 10.1 - - - -
321A LEU 3.2 2.8 + - - -
322A ILE* 3.0 24.5 + - - +
339A THR* 3.7 5.8 - - - -
353A GLU* 2.9 15.8 + - - -
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Residues in contact with GLU 319 (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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318A GLY* 1.3 72.6 - - - +
320A ASP* 1.3 57.9 + - - +
322A ILE* 3.4 2.1 + - - +
323A GLU* 3.0 35.4 + - - +
337A SER* 3.1 34.2 + - - +
338A ILE* 3.6 20.6 - - - +
339A THR* 2.9 43.5 + - - +
450A LYS* 4.6 5.4 + - - -
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Residues in contact with ASP 320 (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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221A LYS* 4.2 25.0 + - - +
317A ILE 4.5 0.5 - - - +
318A GLY* 3.8 11.6 - - - -
319A GLU* 1.3 80.1 + - - +
321A LEU* 1.3 74.2 + - - +
323A GLU* 4.0 4.6 - - - +
324A LEU* 3.1 27.5 + - - +
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Residues in contact with LEU 321 (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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196A ILE 4.3 2.3 - - - +
197A ILE* 5.9 0.2 - - - -
199A PRO* 4.0 16.2 - - + +
200A TYR* 3.7 16.6 - - + -
219A THR* 4.1 25.8 - - + +
221A LYS* 3.7 28.3 - - + +
223A PRO* 3.7 27.6 - - + -
317A ILE* 3.7 23.8 - - + +
318A GLY 3.2 1.0 + - - -
320A ASP* 1.3 94.0 + - - +
322A ILE* 1.3 67.0 + - - +
324A LEU* 3.7 7.6 - - + +
325A GLY* 2.9 22.3 + - - -
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Residues in contact with ILE 322 (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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196A ILE* 5.0 4.3 - - - +
197A ILE* 5.3 3.4 - - + -
317A ILE* 3.6 16.8 - - + +
318A GLY 3.0 23.0 + - - +
319A GLU* 3.7 4.5 - - - +
321A LEU* 1.3 75.7 - - - +
323A GLU* 1.3 58.6 + - - +
325A GLY* 3.8 0.9 - - - -
326A LEU* 3.0 52.1 + - + +
337A SER* 3.8 23.3 - - - -
338A ILE 4.9 1.1 - - - +
353A GLU* 3.8 38.4 - - + +
354A ALA 4.7 1.6 - - - +
355A GLY* 4.4 1.1 - - - -
412A MSE 3.9 36.1 - - + -
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Residues in contact with GLU 323 (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* 3.0 18.9 + - - +
320A ASP* 4.0 4.3 - - - +
322A ILE* 1.3 75.9 - - - +
324A LEU* 1.3 63.2 + - - +
326A LEU* 3.4 6.4 + - + +
327A LYS* 3.0 46.7 + - + +
335A ALA* 4.2 9.6 - - + +
336A ALA* 3.9 22.3 - - - +
337A SER* 2.7 41.4 + - - +
450A LYS* 5.2 2.6 + - - -
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Residues in contact with LEU 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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199A PRO* 3.9 17.3 - - + -
218A LEU* 4.5 10.8 - - + +
219A THR* 3.7 35.0 - - + -
320A ASP 3.1 19.6 + - - +
321A LEU* 3.7 9.4 - - + +
323A GLU* 1.3 76.9 - - - +
325A GLY* 1.3 56.9 + - - +
327A LYS* 3.4 6.6 + - + +
328A LYS* 3.0 64.0 + - + +
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Residues in contact with GLY 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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196A ILE* 3.3 29.8 - - - -
199A PRO* 4.7 7.4 - - - +
218A LEU* 5.4 0.7 - - - -
321A LEU 2.9 11.8 + - - -
322A ILE 3.8 0.4 - - - -
324A LEU* 1.3 75.3 - - - +
326A LEU* 1.3 64.1 + - - +
328A LYS* 5.0 0.7 - - - -
329A ILE* 3.1 38.8 + - - +
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Residues in contact with LEU 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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196A ILE* 4.3 13.4 - - + +
322A ILE* 3.0 40.0 + - + +
323A GLU* 3.9 5.8 - - - +
325A GLY* 1.3 73.5 - - - +
327A LYS* 1.3 62.2 + - - +
330A PHE* 3.1 55.5 + - + +
332A PRO* 3.7 3.8 - - - +
335A ALA* 4.6 5.4 - - + -
336A ALA 4.7 2.5 - - - +
355A GLY* 4.3 4.3 - - - -
356A VAL* 4.2 31.4 - - - +
357A ALA* 4.3 11.2 - - + -
371A LEU* 4.6 5.2 - - + -
410A VAL* 4.2 14.1 - - + -
412A MSE 4.5 8.5 - - + +
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Residues in contact with LYS 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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323A GLU* 3.0 38.7 + - + +
324A LEU* 3.8 7.2 - - + +
326A LEU* 1.3 76.6 - - - +
328A LYS* 1.3 62.3 + - + +
331A ASN* 3.0 29.8 + - - +
332A PRO* 3.6 13.4 - - + +
334A PHE* 6.1 0.4 - - - +
335A ALA* 4.0 26.5 - - + +
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Residues in contact with LYS 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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218A LEU* 3.8 42.4 - - + +
324A LEU* 3.0 40.7 + - + +
327A LYS* 1.3 80.2 - - + +
329A ILE* 1.3 66.4 + - + +
331A ASN* 4.5 3.3 + - - +
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Residues in contact with ILE 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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192A LYS* 3.9 31.1 - - + +
195A TYR* 3.8 36.1 - - + +
196A ILE* 3.9 30.5 - - + -
218A LEU* 4.5 5.2 - - + -
325A GLY* 3.1 24.9 + - - +
328A LYS* 1.3 90.9 - - + +
330A PHE* 1.3 73.2 + - + +
331A ASN* 5.5 0.2 - - - -
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Residues in contact with PHE 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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192A LYS* 4.4 16.6 - - - -
196A ILE* 4.0 28.9 - - + -
326A LEU* 3.1 37.6 + - + +
329A ILE* 1.3 89.8 - - + +
331A ASN* 1.3 70.9 + - - +
332A PRO* 3.2 4.6 - - + -
357A ALA* 5.0 1.3 - - + -
361A SER* 3.5 15.2 - - - -
362A ILE* 3.9 27.9 + - + +
363A PRO* 6.0 2.7 - - + -
369A ILE* 5.2 9.6 - - + -
371A LEU* 4.2 9.4 - - + -
410A VAL* 4.0 40.8 - - + -
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Residues in contact with ASN 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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327A LYS 3.0 12.3 + - - +
328A LYS 5.3 2.7 - - - +
329A ILE 3.7 1.6 - - - +
330A PHE* 1.3 75.7 - - - +
332A PRO* 1.3 76.6 - - - +
360A GLY* 3.7 1.9 - - - -
361A SER* 3.1 41.2 + - - +
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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