Contacts of the helix formed by residues 363 - 376 (chain E) 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 ASP 363 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315E HIS* 3.8 5.4 - - - -
361E GLN 3.3 2.6 + - - +
362E MET* 1.3 76.4 - - - +
364E LYS* 1.3 60.3 + - - +
365E THR* 2.6 15.2 + - - -
366E GLU* 2.6 55.3 + - - +
367E LEU* 2.8 27.4 + - - +
403E TYR* 3.0 21.2 + - - -
407E LYS* 5.6 1.1 - - - +
408E TYR* 2.8 26.8 + - - +
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Residues in contact with LYS 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LEU* 3.8 16.7 - - + +
239E GLU* 4.0 14.2 - - + +
240E LEU* 3.3 34.8 - - + +
315E HIS* 4.4 18.4 - - + -
363E ASP* 1.3 72.1 - - - +
365E THR* 1.3 65.7 + - - +
367E LEU* 3.9 9.6 - - + +
368E GLY* 3.0 19.6 + - - -
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Residues in contact with THR 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E VAL* 4.0 32.3 - - + +
235E ILE* 4.6 1.8 - - + +
236E LEU* 3.2 31.0 - - + +
363E ASP* 2.6 13.1 + - - -
364E LYS* 1.3 75.7 - - - +
366E GLU* 1.3 56.2 + - - -
368E GLY* 3.4 1.6 + - - -
369E CYS* 3.0 30.6 + - - -
403E TYR* 3.5 44.0 + - + -
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Residues in contact with GLU 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E MET* 3.4 11.3 - - + -
363E ASP* 2.6 47.4 + - - +
365E THR* 1.3 71.4 - - - +
367E LEU* 1.3 66.6 + - - +
369E CYS* 2.9 13.3 + - - +
370E LEU* 3.0 18.3 + - - +
400E LEU* 4.2 10.9 - - + +
403E TYR* 4.0 11.2 - - + -
404E CYS* 4.0 2.6 - - - -
408E TYR* 3.5 7.6 - - - -
414E ARG* 2.5 50.9 + - - +
418E LEU* 3.7 28.8 - - + +
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Residues in contact with LEU 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E GLU* 3.1 24.9 - - + +
311E ALA* 3.8 23.3 - - + +
312E SER* 4.1 15.3 - - - +
315E HIS* 3.9 29.8 - - + -
357E MET* 3.7 30.1 - - + -
362E MET* 4.1 7.3 - - - -
363E ASP 2.8 17.8 + - - +
364E LYS* 3.9 8.7 - - + +
365E THR 3.5 0.2 - - - -
366E GLU* 1.3 71.8 - - - +
368E GLY* 1.3 63.0 + - - +
370E LEU* 3.3 8.4 + - + +
371E ARG* 3.0 29.1 + - + +
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Residues in contact with GLY 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ILE* 3.5 16.0 - - - +
239E GLU* 3.4 32.0 - - - +
282E TRP* 4.8 1.0 - - - -
364E LYS 3.0 11.4 + - - -
365E THR 3.7 2.0 - - - -
366E GLU 3.1 0.2 - - - -
367E LEU* 1.3 77.2 - - - +
369E CYS* 1.3 61.9 + - - +
371E ARG* 3.0 5.5 + - - +
372E ALA* 2.9 21.3 + - - +
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Residues in contact with CYS 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E VAL* 4.5 17.0 - - - -
235E ILE* 3.8 21.5 - - - +
365E THR* 3.0 18.6 + - - +
366E GLU 2.9 8.3 + - - +
368E GLY* 1.3 75.3 - - - +
370E LEU* 1.3 62.6 + - - +
372E ALA* 3.0 7.8 + - - +
373E ILE* 3.0 27.0 + - - +
396E VAL* 3.5 9.2 - - + +
399E SER* 5.4 0.9 - - - -
400E LEU* 3.7 44.4 - - + -
403E TYR* 6.0 0.4 - - - -
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Residues in contact with LEU 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E ALA* 6.4 1.3 - - + -
357E MET* 5.3 2.9 - - + -
362E MET* 3.9 32.5 - - + -
366E GLU 3.0 14.8 + - - +
367E LEU* 3.6 9.9 - - + +
369E CYS* 1.3 73.9 - - - +
371E ARG* 1.3 58.6 + - + +
373E ILE* 2.9 31.4 + - + +
374E VAL* 2.9 18.7 + - - +
400E LEU* 3.9 20.2 - - + -
418E LEU* 3.7 39.3 - - + +
419E LEU* 4.3 4.0 - - - +
421E ARG* 4.8 5.6 - - + -
422E LEU* 4.4 17.5 - - + +
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Residues in contact with ARG 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E GLU* 2.7 20.7 + - - +
242E VAL* 4.1 12.9 - - - +
279E LEU* 5.2 3.8 - - - +
282E TRP* 2.8 54.3 - - + +
308E LEU* 2.9 48.9 + - + +
309E LEU* 4.7 6.7 - - - +
311E ALA* 4.3 13.9 - - + -
312E SER* 2.8 31.0 + - - -
367E LEU* 3.0 26.3 + - + +
368E GLY 3.0 8.4 + - - +
370E LEU* 1.3 77.1 - - + +
372E ALA* 1.3 51.5 + - - +
374E VAL* 2.9 7.6 + - + +
375E LEU* 2.7 33.4 + - - +
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Residues in contact with ALA 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ILE* 4.3 10.1 - - + -
282E TRP* 4.3 4.9 - - - -
286E ILE* 4.2 24.5 - - + -
368E GLY 2.9 11.4 + - - +
369E CYS 3.0 8.9 + - - +
371E ARG* 1.3 76.2 - - - +
373E ILE* 1.3 57.5 + - - +
375E LEU* 3.8 7.0 - - - -
376E PHE* 2.9 38.0 + - + +
396E VAL* 4.0 21.1 - - + -
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Residues in contact with ILE 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E CYS 3.0 17.2 + - - +
370E LEU* 2.9 23.0 + - + +
372E ALA* 1.3 78.1 - - - +
374E VAL* 1.3 62.2 + - - +
376E PHE 3.3 6.2 + - - -
393E ARG* 3.2 41.0 + - + +
396E VAL* 3.6 20.0 - - + -
397E TYR* 4.0 19.1 - - + +
400E LEU* 4.3 8.3 - - + -
419E LEU* 3.6 27.4 - - + -
422E LEU* 3.6 22.4 - - + -
407F MET* 4.1 13.0 - - - -
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Residues in contact with VAL 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E LEU 5.5 0.5 - - - +
304E GLY* 4.3 11.3 - - - +
307E GLU* 3.7 36.3 - - + +
308E LEU* 3.9 20.2 - - + +
311E ALA* 6.1 1.1 - - + -
370E LEU 2.9 17.6 + - - +
371E ARG* 2.9 11.2 + - + +
373E ILE* 1.3 79.7 - - - +
375E LEU* 1.3 61.6 + - - +
376E PHE 3.4 0.2 + - - -
377E ASN* 3.5 17.9 + - - +
393E ARG* 4.7 3.8 - - - +
422E LEU* 4.1 20.6 - - + -
425E LEU* 4.2 15.3 - - + -
426E ARG* 5.7 0.9 - - - +
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Residues in contact with LEU 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E TRP* 3.2 32.5 - - + -
283E ALA* 3.8 10.5 - - + -
286E ILE* 4.4 13.5 - - + -
289E PHE* 3.7 39.7 - - + -
300E LEU* 3.6 30.8 - - + +
301E LEU* 4.0 24.0 - - + +
304E GLY* 5.7 0.7 - - - -
308E LEU* 4.4 9.6 - - + -
371E ARG 2.7 18.8 + - - +
372E ALA* 4.0 4.0 - - - +
374E VAL* 1.3 76.2 - - - +
376E PHE* 1.3 59.9 + - + +
377E ASN* 3.0 6.6 + - - +
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Residues in contact with PHE 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E MET* 4.6 2.2 - - - -
286E ILE* 3.7 26.0 - - + -
287E PRO 3.6 17.0 - - - -
289E PHE* 4.0 17.7 - + + -
292E LEU* 3.9 17.9 - - + -
300E LEU* 4.6 4.7 - - + -
372E ALA* 2.9 25.3 + - - +
373E ILE 3.3 5.1 + - - +
374E VAL 3.3 0.4 - - - -
375E LEU* 1.3 80.0 - - + +
377E ASN* 1.3 57.2 + - - +
378E PRO* 3.3 3.8 - - - +
389E VAL* 3.5 12.0 - - + +
392E LEU* 3.3 46.9 - - + -
393E ARG* 2.8 40.1 + - + +
396E VAL* 3.9 21.1 - - + -
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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