Contacts of the helix formed by residues 291 - 303 (chain F) in PDB entry 2ACL
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 SER 291 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266F ILE* 5.3 0.7 - - - +
287F LEU 2.8 22.7 + - - -
288F LEU* 3.2 10.4 + - - +
290F THR* 1.3 77.6 - - - +
292F ALA* 1.3 69.8 + - - +
293F ILE 3.2 2.7 - - - -
294F GLU* 3.0 5.6 + - - +
295F VAL* 3.0 24.0 + - - +
361F SER* 4.5 2.9 - - - -
362F ILE* 4.0 31.3 - - - +
367F ARG* 3.7 20.9 - - - +
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Residues in contact with ALA 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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263F VAL* 4.7 5.4 - - + -
266F ILE* 3.6 22.7 - - + +
288F LEU 2.8 18.1 + - - +
289F LYS* 3.8 6.7 + - - +
290F THR 3.7 0.6 - - - -
291F SER* 1.3 78.3 + - - +
293F ILE* 1.3 57.5 + - - +
295F VAL 3.4 0.2 + - - -
296F MET* 2.9 52.7 + - + +
440F ILE* 4.2 15.3 - - + -
441F TRP* 5.0 0.4 - - - +
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Residues in contact with ILE 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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103F L05 3.6 24.7 - - + -
289F LYS 4.8 1.5 + - - +
290F THR 4.2 14.4 - - - +
292F ALA* 1.3 78.4 - - - +
294F GLU* 1.3 74.4 + - + +
296F MET* 3.3 7.7 + - - +
297F LEU* 3.0 30.7 + - + +
333F PHE* 4.5 2.7 - - + -
416F SER* 3.5 27.1 - - - +
419F HIS* 3.2 50.3 - - + +
441F TRP* 3.8 19.8 - - + +
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Residues in contact with GLU 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 THR* 3.8 6.2 - - - +
291F SER 3.0 9.0 + - - +
293F ILE* 1.3 81.4 - - - +
295F VAL* 1.3 62.5 + - - +
297F LEU* 3.3 7.9 + - + +
298F LEU* 3.2 25.1 + - - +
361F SER* 3.5 15.5 + - - +
367F ARG* 2.5 45.6 + - - +
409F LEU* 5.0 4.7 - - - +
412F LEU* 3.5 46.5 - - + +
413F ARG* 3.6 17.4 + - - -
416F SER* 3.9 15.6 + - - -
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Residues in contact with VAL 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ILE* 4.1 26.0 - - + -
291F SER* 3.0 18.8 + - - +
292F ALA 3.8 5.8 - - - +
294F GLU* 1.3 72.7 - - - +
296F MET* 1.3 68.0 + - - +
298F LEU* 2.9 9.8 + - - +
299F GLU* 2.8 30.6 + - + +
358F ILE* 3.6 46.2 - - + -
361F SER* 4.4 9.0 - - - +
362F ILE* 4.0 18.2 - - + -
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Residues in contact with MET 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F L05 3.4 44.1 - - + +
259F ALA* 4.7 2.5 - - - +
262F SER* 3.3 22.7 - - - +
263F VAL* 3.8 21.3 - - + -
266F ILE* 3.9 4.0 - - + -
292F ALA* 2.9 41.7 + - + +
293F ILE 3.4 6.1 - - - +
295F VAL* 1.3 76.8 - - - +
297F LEU* 1.3 57.8 + - - +
299F GLU* 3.2 9.6 + - - +
300F THR* 2.8 33.0 + - - -
437F LEU* 5.1 0.2 - - + -
440F ILE* 4.4 0.4 - - + -
441F TRP* 3.2 39.9 - - + -
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Residues in contact with LEU 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F L05 4.0 16.6 - - + -
293F ILE* 3.0 30.2 + - + +
294F GLU* 3.4 9.6 - - + +
296F MET* 1.3 77.5 - - - +
298F LEU* 1.3 52.1 + - - +
300F THR* 2.9 8.6 + - - +
301F SER* 2.8 34.0 + - - -
333F PHE* 5.1 2.2 - - + -
337F ILE* 3.8 35.2 - - + -
340F PHE* 4.0 12.8 - - + -
412F LEU* 3.9 15.5 - - + +
415F LEU* 3.5 44.6 - - + +
416F SER 5.1 0.4 - - - +
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Residues in contact with LEU 298 (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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294F GLU 3.2 15.1 + - - +
295F VAL* 2.9 11.3 + - - +
297F LEU* 1.3 78.2 - - - +
299F GLU* 1.3 57.6 + - - +
301F SER* 2.5 20.6 + - - -
302F ARG 2.9 13.7 + - - -
340F PHE* 4.3 8.7 - - + -
344F MET* 3.6 28.3 - - + -
354F PHE* 3.5 16.2 - - + -
357F LEU* 3.8 23.3 - - + -
358F ILE* 3.8 36.6 - - + -
361F SER* 4.7 6.3 - - - -
408F LYS* 5.7 0.9 - - + -
412F LEU* 4.2 21.1 - - + -
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Residues in contact with GLU 299 (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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103F L05 4.9 14.1 - - - +
219F GLN* 5.5 2.0 + - - +
262F SER* 5.3 3.8 - - - +
265F GLU* 4.8 13.5 - - - +
266F ILE* 5.6 3.3 - - - +
295F VAL* 2.8 18.3 + - + +
296F MET* 3.3 13.2 - - - +
298F LEU* 1.3 77.0 - - - +
300F THR* 1.3 64.1 + - - +
302F ARG* 3.1 41.9 + - - +
303F ARG* 2.9 59.0 + - - +
313F PHE* 5.7 0.2 - - - -
354F PHE* 5.6 0.3 - - - -
358F ILE* 4.2 15.8 - - - +
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Residues in contact with THR 300 (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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103F L05 3.8 19.2 + - + -
296F MET 2.8 15.2 + - - -
297F LEU* 2.9 15.0 + - + +
299F GLU* 1.3 77.8 - - - +
301F SER* 1.3 61.3 + - - +
303F ARG* 3.1 14.9 + - - +
304F TYR* 3.4 9.7 + - - +
311F ILE* 3.3 44.6 - - + +
313F PHE* 3.9 17.0 - - + -
337F ILE* 4.2 11.2 - - + -
341F SER* 4.0 11.2 - - - +
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Residues in contact with SER 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F LEU 2.8 13.1 + - - -
298F LEU* 2.5 29.3 + - - -
300F THR* 1.3 75.7 - - - +
302F ARG* 1.3 60.2 + - - +
304F TYR* 3.4 14.6 + - - +
340F PHE* 4.2 4.5 - - - -
341F SER* 3.9 26.0 + - - +
344F MET* 3.4 36.5 - - - +
345F ASN* 4.8 7.6 + - - +
354F PHE* 3.7 8.2 - - - -
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Residues in contact with ARG 302 (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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219F GLN* 2.5 50.7 + - - +
223F ASN* 5.8 5.1 - - - +
298F LEU 2.9 12.4 + - - +
299F GLU* 3.1 33.4 + - - +
300F THR 3.2 0.4 - - - -
301F SER* 1.3 78.4 + - - +
303F ARG* 1.3 73.7 + - + +
304F TYR 3.3 5.1 + - - +
351F ASP* 5.5 5.2 - - - +
354F PHE* 3.3 53.8 - - + +
358F ILE* 4.0 5.5 - - - +
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Residues in contact with ARG 303 (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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103F L05 5.5 5.8 - - - -
223F ASN* 3.5 25.1 + - - -
265F GLU* 4.3 9.7 + - - -
299F GLU* 2.9 59.5 + - - +
300F THR 3.1 7.6 + - - +
302F ARG* 1.3 92.4 - - + +
304F TYR* 1.3 55.8 + - - +
305F ASN* 3.3 12.6 + - - +
311F ILE* 3.8 4.1 - - + -
312F THR* 2.9 54.0 + - - +
313F PHE* 4.2 13.1 - - - +
314F LEU 4.6 8.7 - - - +
315F LYS* 5.2 13.1 - - - +
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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