Contacts of the helix formed by residues 282 - 296 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280J ASP 3.9 0.4 + - - -
281J ALA* 1.3 69.4 - - - +
283J MET* 1.3 56.6 + - - +
284J ASP* 3.2 10.4 + - - +
285J TRP* 3.1 36.1 + - + +
286J ALA* 2.8 36.1 + - - +
432J PHE* 6.3 0.2 - - - -
434J LYS* 4.0 28.2 + - + +
454J ASN* 5.9 0.4 + - - -
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Residues in contact with MET 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 6.3 0.2 - - - -
281J ALA* 3.1 9.2 + - - +
282J ASP* 1.3 72.9 + - - +
284J ASP* 1.3 65.8 + - - +
286J ALA* 3.3 2.9 + - - +
287J VAL* 2.9 44.3 + - - +
314J ILE* 3.8 41.5 - - + +
317J GLU* 3.8 30.7 - - + +
318J PHE* 4.0 15.5 - - + -
321J ARG* 3.6 33.4 - - - +
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Residues in contact with ASP 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282J ASP* 3.2 7.3 + - - +
283J MET* 1.3 78.7 - - - +
285J TRP* 1.3 63.2 + - - +
287J VAL* 3.9 3.8 - - - +
288J GLU* 3.2 24.3 + - - +
321J ARG* 2.7 36.4 + - - +
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Residues in contact with TRP 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494I LYS* 3.7 34.7 - - + +
282J ASP* 3.1 32.3 + - + +
284J ASP* 1.3 77.3 - - - +
286J ALA* 1.3 58.0 + - - +
288J GLU* 3.3 12.1 + - + +
289J GLN* 2.9 69.2 + - + +
432J PHE* 4.0 15.3 - + - -
454J ASN* 2.8 30.5 + - + -
455J CYS* 5.1 1.8 - - + -
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Residues in contact with ALA 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 3.9 30.9 - - + +
281J ALA* 4.4 2.7 - - + -
282J ASP 2.8 22.8 + - - +
283J MET* 3.8 4.9 - - - +
285J TRP* 1.3 72.9 - - - +
287J VAL* 1.3 57.7 + - - +
289J GLN* 4.1 0.2 - - - +
290J ALA* 2.8 33.6 + - - +
318J PHE* 4.0 5.8 - - + -
432J PHE* 4.0 25.5 - - + -
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Residues in contact with VAL 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283J MET* 2.9 28.4 + - - +
284J ASP* 3.9 5.6 - - - +
286J ALA* 1.3 76.6 - - - +
288J GLU* 1.3 66.2 + - - +
290J ALA* 3.3 1.7 + - - +
291J HIS* 3.0 22.3 + - - +
318J PHE* 3.8 29.8 - - + +
321J ARG* 3.8 48.7 - - + +
322J SER* 4.2 8.6 + - - +
325J ARG* 4.6 10.3 - - + -
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Residues in contact with GLU 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284J ASP 3.2 14.6 + - - +
285J TRP* 3.8 11.9 - - + +
287J VAL* 1.3 81.9 - - + +
289J GLN* 1.3 66.3 + - + +
291J HIS* 3.3 8.2 + - - +
292J PHE* 3.0 29.7 + - + +
325J ARG* 3.0 43.5 + - - +
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Residues in contact with GLN 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J ASN* 4.8 0.9 - - - -
285J TRP* 2.9 63.2 + - + +
286J ALA 4.1 0.2 - - - +
288J GLU* 1.3 79.1 - - - +
290J ALA* 1.3 57.0 + - - +
292J PHE* 3.3 18.0 + - - +
293J ALA* 2.7 37.0 + - - +
432J PHE* 3.4 24.9 - - + -
455J CYS* 3.5 6.9 - - - +
456J TYR* 3.5 29.0 + - + +
458J VAL* 5.8 0.2 - - - +
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Residues in contact with ALA 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ASN* 3.5 24.1 + - - +
277J ILE* 4.7 2.0 - - + -
286J ALA 2.8 20.5 + - - +
287J VAL 3.8 1.6 - - - +
289J GLN* 1.3 77.0 - - - +
291J HIS* 1.3 60.4 + - - +
293J ALA* 3.5 2.0 - - - +
294J LEU* 3.3 22.2 + - - +
305J GLY 5.1 1.4 - - - +
308J THR* 4.2 11.9 + - + +
318J PHE* 3.6 24.9 - - + -
322J SER* 5.6 0.4 - - - +
405J MET* 4.7 9.0 - - - +
432J PHE* 5.0 0.4 - - - -
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Residues in contact with HIS 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287J VAL* 3.0 13.7 + - + +
288J GLU* 3.4 11.4 - - - +
289J GLN 3.2 0.2 - - - -
290J ALA* 1.3 74.7 - - - +
292J PHE* 1.3 62.6 + - - +
294J LEU 3.4 0.5 + - - -
295J PHE* 2.9 72.1 + + - +
322J SER* 5.0 3.4 + - - -
325J ARG* 3.3 61.9 - - + +
326J ALA* 3.9 8.4 + - - +
329J ARG* 3.0 41.2 + - - -
405J MET* 5.1 5.5 - - - +
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Residues in contact with PHE 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J GLU* 3.0 17.0 + - + +
289J GLN* 3.6 23.3 - - - +
291J HIS* 1.3 80.7 - - - +
293J ALA* 1.3 67.8 + - - +
295J PHE* 5.2 0.2 - - - -
296J PHE* 2.9 76.8 + + + +
329J ARG* 5.7 1.3 - - - +
456J TYR* 3.8 14.1 - - + -
457J ASP* 3.6 31.6 - - + -
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Residues in contact with ALA 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ASN* 4.0 6.1 - - - +
289J GLN 2.7 22.0 + - - +
290J ALA* 3.5 12.1 - - - +
292J PHE* 1.3 74.6 - - - +
294J LEU* 1.3 57.5 + - - +
296J PHE* 5.0 1.2 + - - +
301J CYS* 6.0 0.5 - - - +
304J ALA* 3.5 7.6 - - - +
305J GLY* 2.9 24.2 + - - +
456J TYR* 3.4 46.3 - - + -
457J ASP* 4.3 4.7 - - - +
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Residues in contact with LEU 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J ALA 3.3 11.0 + - - +
291J HIS 4.3 0.7 - - - +
292J PHE 3.1 0.4 - - - -
293J ALA* 1.3 80.0 - - - +
295J PHE* 1.3 84.3 + - + +
296J PHE 3.3 3.2 + - - +
299J GLY* 3.1 24.3 - - - -
304J ALA* 4.3 8.8 - - + +
305J GLY 3.5 13.5 - - - +
306J SER* 3.4 35.0 - - - -
308J THR* 5.6 0.2 - - - +
402J GLY 4.2 4.7 - - - +
403J PRO 4.2 0.4 - - - -
404J VAL 3.2 43.3 - - - +
405J MET* 3.6 21.5 - - + +
406J GLN 4.6 0.2 - - - +
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Residues in contact with PHE 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J HIS* 2.9 58.6 + + - +
294J LEU* 1.3 85.3 - - + +
296J PHE* 1.3 68.9 + - - +
297J ASN 3.3 0.3 + - - -
298J GLN* 3.1 14.6 + - - -
299J GLY* 3.1 4.1 + - - +
326J ALA* 4.3 5.4 - - + -
329J ARG* 3.4 32.9 + - - +
341J GLN* 4.3 6.2 - - - +
383J PRO* 3.9 20.9 - - + -
384J THR 3.9 14.8 - - - -
385J VAL* 4.3 7.2 - - + -
403J PRO* 3.4 40.8 - - + -
405J MET* 4.1 19.5 - - + -
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Residues in contact with PHE 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J LYS* 6.1 0.2 - - - -
116J ILE* 4.0 28.0 - - + -
120J VAL* 4.4 22.9 - - + -
121J ASP* 5.4 0.4 - - - -
124J MET* 5.8 1.6 - - + -
170J PHE* 3.9 32.8 - + - -
292J PHE* 2.9 54.9 + + + +
293J ALA 5.1 1.3 - - - +
294J LEU 3.3 3.1 - - - +
295J PHE* 1.3 74.1 - - - +
297J ASN* 1.3 74.1 + - + +
299J GLY* 2.9 21.0 + - - -
300J GLN 3.7 1.4 + - - -
301J CYS* 4.7 10.4 - - + +
329J ARG* 4.4 4.7 - - - +
457J ASP* 3.7 25.4 - - + +
459J PHE* 6.3 1.1 - + - -
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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