Contacts of the helix formed by residues 282 - 296 (chain H) in PDB entry 1ZUM
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 ASP 282 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H ASP 3.8 1.2 + - - -
281H ALA* 1.3 68.0 - - - +
283H MET* 1.3 58.9 + - - +
284H ASP* 3.3 10.9 + - - +
285H TRP* 3.0 36.1 + - + +
286H ALA* 2.8 30.4 + - - +
432H PHE* 5.6 0.6 - - - -
434H LYS* 4.0 27.9 + - + +
454H ASN* 5.9 0.2 + - - -
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Residues in contact with MET 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE* 6.1 0.4 - - - -
281H ALA 3.0 9.8 + - - +
282H ASP* 1.3 70.9 + - - +
284H ASP* 1.3 65.5 + - - +
286H ALA* 3.2 4.1 + - - +
287H VAL* 2.9 43.2 + - - +
314H ILE* 3.6 45.8 - - + +
317H GLU* 3.6 27.8 - - + +
318H PHE* 3.9 15.3 - - + -
321H ARG* 3.5 35.0 - - - +
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Residues in contact with ASP 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H ASP* 3.3 8.0 + - - +
283H MET* 1.3 77.7 - - - +
285H TRP* 1.3 62.8 + - - +
287H VAL* 3.9 3.7 - - - +
288H GLU* 3.3 23.9 + - - +
321H ARG* 2.8 36.1 + - - +
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Residues in contact with TRP 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150G PHE* 6.5 0.2 - + - -
494G LYS* 3.9 34.5 - - + +
282H ASP* 3.0 31.4 + - + +
284H ASP* 1.3 76.2 - - - +
286H ALA* 1.3 57.9 + - - +
288H GLU* 3.9 7.3 - - + +
289H GLN* 3.0 68.5 + - + +
432H PHE* 3.6 24.9 - + - -
454H ASN* 2.7 36.1 + - + -
455H CYS* 4.9 3.8 - - + -
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Residues in contact with ALA 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE* 3.8 32.8 - - + +
281H ALA* 4.4 4.3 - - + -
282H ASP 2.8 22.9 + - - +
283H MET* 3.8 4.9 - - - +
285H TRP* 1.3 72.2 - - - +
287H VAL* 1.3 59.7 + - - +
289H GLN* 4.2 0.3 - - - +
290H ALA* 2.9 32.1 + - - +
318H PHE* 3.7 6.4 - - + -
432H PHE* 3.9 22.6 - - + -
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Residues in contact with VAL 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET* 2.9 31.6 + - - +
284H ASP* 3.9 5.2 - - - +
286H ALA* 1.3 78.1 - - - +
288H GLU* 1.3 63.0 + - - +
290H ALA* 3.4 1.7 + - - +
291H HIS* 3.0 22.7 + - - +
318H PHE* 3.7 27.1 - - + -
321H ARG* 3.8 50.0 - - + +
322H SER* 4.0 10.4 + - - +
325H ARG* 4.7 9.2 - - + -
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Residues in contact with GLU 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ASP 3.3 14.9 + - - +
285H TRP* 3.9 9.2 - - + +
287H VAL* 1.3 80.5 - - - +
289H GLN* 1.3 65.0 + - - +
291H HIS* 3.3 8.3 + - - +
292H PHE* 2.9 30.8 + - + +
325H ARG* 2.9 44.3 + - - -
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Residues in contact with GLN 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 4.7 0.7 - - - -
285H TRP* 3.0 66.5 + - + +
286H ALA 4.2 0.4 - - - +
288H GLU* 1.3 81.3 + - - +
290H ALA* 1.3 56.6 + - - +
292H PHE* 3.6 14.4 - - - +
293H ALA* 2.7 36.1 + - - +
432H PHE* 3.4 26.0 - - + -
455H CYS* 3.9 2.9 - - - +
456H TYR* 3.6 30.8 + - + +
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 3.5 22.0 + - - +
277H ILE* 4.7 1.6 - - + -
286H ALA 2.9 20.4 + - - +
287H VAL 3.7 1.8 - - - +
289H GLN* 1.3 73.3 - - - +
291H HIS* 1.3 68.6 + - - +
293H ALA* 3.4 2.3 + - - +
294H LEU* 3.2 21.1 + - - +
305H GLY 5.1 0.5 - - - +
308H THR* 4.2 13.5 + - + +
318H PHE* 3.5 23.8 - - + -
322H SER* 5.4 1.3 - - - +
405H MET* 4.7 8.2 - - - +
432H PHE* 5.2 0.2 - - - -
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Residues in contact with HIS 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 3.0 13.9 + - + +
288H GLU* 3.4 11.4 - - - +
290H ALA* 1.3 79.0 - - - +
292H PHE* 1.3 61.7 + - - +
295H PHE* 2.9 71.5 + + - +
322H SER* 5.1 1.7 + - - -
325H ARG* 3.2 65.2 - - + +
326H ALA* 4.0 6.1 + - - +
329H ARG* 3.1 40.0 + - - -
405H MET* 5.2 4.4 - - - +
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Residues in contact with PHE 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H GLU* 2.9 21.0 + - + +
289H GLN* 3.6 19.7 - - - +
291H HIS* 1.3 80.2 - - + +
293H ALA* 1.3 67.0 + - - +
295H PHE* 5.3 0.4 - - - -
296H PHE* 3.0 74.0 + + + +
329H ARG* 6.1 0.4 - - - +
456H TYR* 4.0 11.7 - - + -
457H ASP* 3.6 33.2 - - + -
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Residues in contact with ALA 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 3.9 9.6 - - - +
289H GLN 2.7 23.2 + - - +
290H ALA 3.5 6.7 - - - +
292H PHE* 1.3 74.8 - - - +
294H LEU* 1.3 58.5 + - - +
296H PHE* 4.9 1.2 + - - +
301H CYS* 5.9 0.3 - - - +
304H ALA* 3.5 8.0 - - - -
305H GLY* 2.9 23.2 + - - +
456H TYR* 3.4 47.6 - - + -
457H ASP* 4.4 4.5 - - - +
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Residues in contact with LEU 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290H ALA 3.2 9.0 + - - +
291H HIS 3.2 3.0 + - - +
292H PHE 3.2 0.4 - - - -
293H ALA* 1.3 81.1 - - - +
295H PHE* 1.3 80.6 + - + +
296H PHE 3.3 3.8 + - - +
299H GLY* 3.2 22.3 - - - -
304H ALA* 4.3 8.4 - - + +
305H GLY 3.4 13.0 - - - +
306H SER* 3.4 34.3 - - - -
308H THR* 5.6 0.2 - - - +
402H GLY 4.0 5.8 - - - +
403H PRO 4.0 0.7 - - - -
404H VAL 3.2 48.7 - - - +
405H MET* 3.5 22.9 - - + +
406H GLN 4.5 0.2 - - - +
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Residues in contact with PHE 295 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H HIS* 2.9 57.0 + + + +
292H PHE* 5.3 0.4 - - - -
294H LEU* 1.3 81.1 - - + +
296H PHE* 1.3 66.4 + - - +
297H ASN 3.3 0.3 + - - -
298H GLN* 3.1 16.1 + - - -
299H GLY 3.3 4.6 + - - +
326H ALA* 4.3 18.8 - - + -
329H ARG* 3.3 39.9 + - - +
341H GLN* 4.3 0.6 - - - +
383H PRO* 3.8 13.7 - - + -
384H THR 3.8 15.7 - - - -
385H VAL* 4.4 0.4 - - + -
403H PRO* 3.3 43.1 - - + -
405H MET* 4.1 20.6 - - + -
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Residues in contact with PHE 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H ILE* 4.0 27.6 - - + -
120H VAL* 4.2 24.9 - - + -
121H ASP* 5.3 0.7 - - - -
124H MET* 5.8 1.8 - - + -
170H PHE* 3.8 32.3 - + - -
292H PHE* 3.0 55.9 + + + +
293H ALA 5.2 1.1 - - - +
294H LEU 3.3 2.3 - - - +
295H PHE* 1.3 74.3 - - - +
297H ASN* 1.3 80.1 + - + +
299H GLY* 3.0 13.9 + - - -
300H GLN 3.7 1.0 + - - -
301H CYS* 4.5 11.0 - - + +
329H ARG* 4.5 4.7 - - - +
457H ASP* 3.9 22.7 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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