Contacts of the helix formed by residues 282 - 296 (chain F) in PDB entry 3SZ9
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280F ASP 3.7 1.0 + - - -
281F ALA* 1.3 70.3 - - - +
283F MET* 1.3 59.4 + - - +
284F ASP* 3.5 8.1 + - - +
285F TRP* 3.3 35.2 + - + +
286F ALA* 2.8 31.8 + - - +
432F PHE* 6.2 0.4 - - - -
434F LYS* 4.3 24.4 - - + +
454F ASN* 5.8 1.0 + - - -
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Residues in contact with MET 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F ALA* 3.3 8.5 + - - +
282F ASP* 1.3 72.8 + - - +
284F ASP* 1.3 66.2 + - - +
286F ALA* 3.8 3.2 - - - +
287F VAL* 2.9 44.4 + - - +
314F ILE* 3.8 39.7 - - + +
317F GLU* 3.9 24.7 - - - +
318F PHE* 3.9 27.4 - - - +
321F ARG* 3.7 28.3 - - - +
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Residues in contact with ASP 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F ASP* 3.5 7.0 + - - +
283F MET* 1.3 79.7 - - - +
285F TRP* 1.3 62.7 + - - +
287F VAL* 3.8 5.5 - - - +
288F GLU* 3.2 23.7 + - - +
321F ARG* 2.8 32.5 + - - +
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Residues in contact with TRP 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494E LYS* 3.7 31.4 - - + +
282F ASP* 3.3 30.4 + - + +
283F MET 3.3 0.4 - - - -
284F ASP* 1.3 77.2 - - - +
286F ALA* 1.3 60.2 + - - +
288F GLU* 3.2 10.8 + - + +
289F GLN* 2.8 67.1 + - + +
432F PHE* 3.7 24.9 - + - -
454F ASN* 2.8 28.6 + - + -
455F CYS* 5.1 2.9 - - + -
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Residues in contact with ALA 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ILE* 3.9 32.6 - - + +
281F ALA* 4.3 2.5 - - + -
282F ASP 2.8 22.2 + - - +
283F MET* 3.9 3.8 - - - +
285F TRP* 1.3 75.5 - - - +
287F VAL* 1.3 56.7 + - - +
289F GLN* 4.0 0.3 - - - +
290F ALA* 2.8 33.4 + - - +
318F PHE* 4.0 5.4 - - + -
432F PHE* 3.9 26.4 - - + -
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Residues in contact with VAL 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F MET* 2.9 40.3 + - - +
284F ASP* 3.8 6.3 - - - +
286F ALA* 1.3 77.6 - - - +
288F GLU* 1.3 63.8 + - + +
290F ALA* 3.4 2.4 + - - +
291F HIS* 3.1 21.8 + - - +
318F PHE* 3.8 22.9 - - + +
321F ARG* 3.9 46.0 - - + +
322F SER* 4.1 8.8 + - - +
325F ARG* 4.8 8.1 - - + -
405F MET* 5.8 0.2 - - - +
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Residues in contact with GLU 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ASP 3.2 15.0 + - - +
285F TRP* 3.8 10.5 - - + +
287F VAL* 1.3 81.3 - - + +
289F GLN* 1.3 66.8 + - + +
291F HIS* 3.3 8.2 - - - +
292F PHE* 3.0 29.8 + - + +
325F ARG* 3.0 47.8 + - - +
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Residues in contact with GLN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ASN* 4.7 1.1 - - - -
285F TRP* 2.8 64.5 + - + +
286F ALA 4.0 0.2 - - - +
288F GLU* 1.3 81.0 - - - +
290F ALA* 1.3 56.4 + - - +
292F PHE* 3.7 15.1 - - - +
293F ALA* 2.7 36.1 + - - +
432F PHE* 3.5 22.2 - - + -
455F CYS* 3.5 6.4 - - - +
456F TYR* 3.3 33.7 + - + +
458F VAL* 5.7 0.2 - - - +
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ASN* 3.5 24.3 + - - +
277F ILE* 4.7 1.1 - - + -
286F ALA 2.8 22.3 + - - +
287F VAL 3.9 2.2 - - - +
289F GLN* 1.3 73.4 - - - +
291F HIS* 1.3 62.8 + - - +
293F ALA* 3.6 1.7 - - - +
294F LEU* 3.2 23.7 + - - +
305F GLY 4.9 1.4 - - - +
308F THR* 4.1 9.8 + - + -
318F PHE* 3.5 25.6 - - + -
405F MET* 3.8 11.3 - - + +
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Residues in contact with HIS 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F VAL 3.1 13.9 + - - +
288F GLU* 3.3 13.0 - - - +
290F ALA* 1.3 74.2 - - - +
292F PHE* 1.3 65.6 + - + +
294F LEU 3.1 1.7 + - - -
295F PHE* 2.8 65.1 + + - +
322F SER* 5.0 3.3 + - - -
325F ARG* 3.4 66.3 + - + +
326F ALA* 4.0 5.0 + - - -
329F ARG* 2.9 39.1 + - - -
405F MET* 4.5 5.9 - - - +
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Residues in contact with PHE 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 6.5 0.7 - - + -
288F GLU* 3.0 15.9 + - + +
289F GLN* 3.8 17.9 - - - +
291F HIS* 1.3 85.1 - - + +
293F ALA* 1.3 64.7 + - - +
295F PHE* 5.2 0.4 - - - -
296F PHE* 3.0 71.3 + + + +
329F ARG* 5.8 0.9 - - - +
456F TYR* 4.4 9.2 - - + -
457F ASP* 3.6 36.8 - - + -
8001F I3E 5.1 2.9 - - + -
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Residues in contact with ALA 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ASN* 4.0 10.8 - - - +
289F GLN 2.7 23.5 + - - +
290F ALA 3.6 5.8 - - - +
291F HIS 3.2 0.2 - - - -
292F PHE* 1.3 73.8 - - - +
294F LEU* 1.3 57.1 + - - +
296F PHE* 4.9 0.6 - - - +
301F CYS* 6.2 0.3 - - - -
304F ALA* 3.4 8.7 - - - +
305F GLY* 2.8 25.3 + - - +
456F TYR* 3.3 46.1 - - + -
457F ASP* 4.3 5.9 - - - +
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Residues in contact with LEU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F ALA 3.2 12.7 + - - +
291F HIS 3.1 4.0 + - - +
292F PHE 3.1 0.2 - - - -
293F ALA* 1.3 79.4 - - - +
295F PHE* 1.3 85.1 + - + +
296F PHE 3.5 1.7 + - - +
299F GLY* 3.4 18.9 - - - -
304F ALA* 4.2 10.9 - - + +
305F GLY 3.7 10.5 - - - +
306F SER* 3.7 33.0 - - - -
402F GLY 4.1 4.7 - - - +
403F PRO 4.0 0.4 - - - -
404F VAL 3.6 46.4 - - - +
405F MET* 3.8 17.3 - - + +
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Residues in contact with PHE 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F HIS* 2.8 54.6 + + - +
294F LEU* 1.3 84.0 - - + +
296F PHE* 1.3 68.1 + - - +
297F ASN 3.3 0.3 + - - -
298F GLN* 3.1 15.1 + - - -
299F GLY 3.2 4.1 + - - +
326F ALA* 4.5 10.1 - - + -
329F ARG* 3.3 41.3 + - - +
341F GLN* 4.1 0.9 - - - -
383F PRO* 3.7 18.6 - - + -
384F THR 4.0 17.7 - - - -
385F VAL* 4.6 0.4 - - + -
403F PRO* 3.4 42.0 - - + -
405F MET* 4.2 20.4 - - + -
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Residues in contact with PHE 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F LYS* 6.0 0.2 - - - -
116F ILE* 3.8 34.8 - - + -
120F VAL* 4.2 16.6 - - + -
121F ASP* 5.2 0.7 - - - -
170F PHE* 3.8 25.6 - + - -
292F PHE* 3.0 50.0 + + + +
293F ALA 5.4 0.2 - - - -
294F LEU 3.5 2.7 - - - +
295F PHE* 1.3 75.2 - - - +
297F ASN* 1.3 76.0 + - + +
299F GLY* 3.0 13.5 + - - -
301F CYS* 3.6 28.3 - - - -
329F ARG* 4.5 5.6 - - - +
457F ASP* 4.0 16.4 - - - +
8001F I3E 3.5 27.8 - - + -
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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