Contacts of the helix formed by residues 282 - 296 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281I ALA* 1.3 69.0 - - - +
283I MET* 1.3 57.7 + - - +
284I ASP* 3.3 13.0 + - - +
285I TRP* 3.1 34.1 + - + +
286I ALA* 2.9 31.2 + - - +
432I PHE* 5.7 0.2 - - - -
434I LYS* 3.8 29.7 + - - +
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Residues in contact with MET 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ILE* 6.2 0.2 - - - -
281I ALA 3.0 9.6 + - - +
282I ASP* 1.3 68.6 + - - +
284I ASP* 1.3 67.0 - - - +
286I ALA* 3.3 4.3 + - - +
287I VAL* 3.0 45.4 + - - +
314I ILE* 3.7 43.3 - - + +
317I GLU* 3.7 26.9 - - + +
318I PHE* 4.1 21.5 - - - -
321I ARG* 3.6 33.7 - - - +
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Residues in contact with ASP 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I ASP* 3.3 8.1 + - - +
283I MET* 1.3 79.5 - - - +
285I TRP* 1.3 63.5 + - - +
287I VAL* 3.4 4.6 + - - +
288I GLU* 3.2 22.3 + - - +
321I ARG* 2.8 29.9 + - - +
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Residues in contact with TRP 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282I ASP* 3.1 26.2 + - + +
284I ASP* 1.3 79.5 - - - +
286I ALA* 1.3 57.7 + - - +
288I GLU* 3.3 9.1 + - + +
289I GLN* 2.9 71.2 + - + +
432I PHE* 3.8 17.5 - + - -
454I ASN* 2.9 29.2 + - + -
455I CYS* 5.1 2.9 - - + -
150J PHE* 6.5 1.1 - + - -
494J LYS* 3.8 34.7 - - + +
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Residues in contact with ALA 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ILE* 3.9 35.8 - - + +
281I ALA* 4.4 4.3 - - + -
282I ASP 2.9 23.7 + - - +
283I MET* 3.8 4.3 - - - +
285I TRP* 1.3 74.2 - - - +
287I VAL* 1.3 57.7 + - - +
289I GLN* 4.1 0.2 - - - +
290I ALA* 2.9 32.9 + - - +
318I PHE* 3.8 6.1 - - + -
432I PHE* 4.0 19.5 - - + -
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Residues in contact with VAL 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 3.0 39.4 + - - +
284I ASP* 3.7 5.4 - - - +
286I ALA* 1.3 74.8 - - - +
288I GLU* 1.3 64.4 + - - +
290I ALA* 3.9 1.9 - - - +
291I HIS* 3.0 22.9 + - - +
318I PHE* 3.8 16.2 - - + -
321I ARG* 3.8 56.3 - - + +
322I SER* 4.0 11.2 + - - +
325I ARG* 4.6 9.6 - - + -
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Residues in contact with GLU 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284I ASP 3.2 15.0 + - - +
285I TRP* 3.7 10.1 - - + +
287I VAL* 1.3 81.6 - - - +
289I GLN* 1.3 67.4 + - - +
291I HIS* 3.2 9.6 + - - +
292I PHE* 2.9 29.8 + - + +
325I ARG* 3.2 44.4 + - - -
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Residues in contact with GLN 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ASN* 4.7 1.1 - - - -
285I TRP* 2.9 72.6 + - + +
286I ALA 4.1 0.7 - - - +
288I GLU* 1.3 82.7 + - - +
290I ALA* 1.3 55.5 + - - +
292I PHE* 3.3 12.7 + - - +
293I ALA* 2.7 35.7 + - - +
432I PHE* 3.4 25.8 - - + -
455I CYS* 4.0 1.9 - - - +
456I TYR* 3.9 26.4 + - + +
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Residues in contact with ALA 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ASN* 3.5 22.9 + - - +
277I ILE* 4.6 2.0 - - + -
286I ALA 2.9 20.2 + - - +
287I VAL 3.9 2.0 - - - +
289I GLN* 1.3 75.0 - - - +
291I HIS* 1.3 63.9 + - - +
293I ALA* 3.5 2.1 + - - +
294I LEU* 3.3 21.5 + - - +
305I GLY 5.1 1.6 - - - +
308I THR* 4.1 11.9 + - + +
318I PHE* 3.6 24.5 - - + -
322I SER* 5.4 0.9 - - - +
405I MET* 4.7 8.4 - - - +
432I PHE* 5.2 0.2 - - - -
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Residues in contact with HIS 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I VAL 3.0 14.6 + - - +
288I GLU* 3.3 11.9 - - - +
289I GLN 3.1 0.2 - - - -
290I ALA* 1.3 74.9 - - - +
292I PHE* 1.3 62.7 + - - +
294I LEU 3.4 0.9 + - - -
295I PHE* 2.9 70.9 + + - +
322I SER* 5.1 3.2 + - - -
325I ARG* 3.5 64.1 + - + +
326I ALA* 4.1 4.8 + - - +
329I ARG* 2.9 39.2 + - - -
405I MET* 5.2 5.1 - - - +
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Residues in contact with PHE 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I GLU* 2.9 18.4 + - + +
289I GLN* 3.6 16.6 - - - +
291I HIS* 1.3 82.9 - - + +
293I ALA* 1.3 66.4 + - - +
295I PHE* 5.3 0.2 - - - -
296I PHE* 3.0 73.2 + + + +
329I ARG* 5.9 0.7 - - - +
456I TYR* 4.0 12.6 - - + -
457I ASP* 3.5 35.7 - - + -
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Residues in contact with ALA 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ASN* 3.8 11.9 - - - +
289I GLN 2.7 21.7 + - - +
290I ALA 3.6 6.1 - - - +
291I HIS 3.3 0.2 - - - -
292I PHE* 1.3 75.4 - - - +
294I LEU* 1.3 58.8 + - - +
296I PHE* 5.0 1.0 + - - +
301I CYS* 5.9 0.3 - - - +
304I ALA* 3.5 7.3 - - - -
305I GLY* 2.9 23.7 + - - +
456I TYR* 3.4 47.0 - - + -
457I ASP* 4.3 4.3 - - - +
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Residues in contact with LEU 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I ALA 3.3 12.1 + - - +
291I HIS 4.2 1.1 - - - +
292I PHE 3.1 0.2 - - - -
293I ALA* 1.3 82.0 - - - +
295I PHE* 1.3 83.6 + - + +
296I PHE 3.4 1.8 + - - +
299I GLY* 3.2 20.3 - - - -
304I ALA* 4.2 11.5 - - + +
305I GLY 3.7 10.5 - - - +
306I SER* 3.6 36.8 - - - +
308I THR* 5.7 0.2 - - - +
399I GLU* 5.7 0.7 - - - +
402I GLY 3.7 10.5 - - - +
404I VAL 3.7 40.8 - - - +
405I MET* 4.0 15.9 - - + +
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Residues in contact with PHE 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I HIS* 2.9 58.6 + + - +
292I PHE* 5.3 0.2 - - - -
294I LEU* 1.3 73.0 - - + +
296I PHE* 1.3 67.8 + - - +
297I ASN 3.2 0.3 + - - -
298I GLN* 3.0 16.5 + - - -
299I GLY 3.2 4.5 + - - +
326I ALA* 4.2 19.5 - - + -
329I ARG* 3.2 37.5 + - - +
341I GLN* 5.2 0.2 - - - +
383I PRO* 3.8 14.1 - - + -
384I THR 3.9 15.9 - - - -
385I VAL* 4.5 0.4 - - + -
403I PRO* 3.4 44.4 - - + -
405I MET* 4.2 27.4 - - + -
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Residues in contact with PHE 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ILE* 3.9 28.7 - - + -
120I VAL* 4.2 24.5 - - + -
121I ASP* 5.2 0.4 - - - -
124I MET* 5.7 1.8 - - + -
170I PHE* 3.7 33.9 - + - -
292I PHE* 3.0 58.3 + + + +
293I ALA 5.2 0.9 - - - +
294I LEU 3.4 2.5 - - - +
295I PHE* 1.3 72.8 - - - +
297I ASN* 1.3 79.3 + - + +
299I GLY* 3.0 14.0 + - - -
300I GLN 3.9 1.4 + - - -
301I CYS* 4.7 11.1 - - + +
329I ARG* 4.6 4.5 - - - +
457I ASP* 3.8 23.1 - - + +
459I PHE* 6.4 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