Contacts of the helix formed by residues 435 - 441 (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 HIS 435 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A TRP* 5.1 3.6 - + - -
432A CYS 4.2 5.6 + - - +
433A LEU* 3.1 50.8 - - + +
434A GLU 3.2 16.2 - - - +
435A HIS* 4.2 3.3 - + + +
433E LEU 3.6 2.4 + - - -
434E GLU* 1.3 74.8 - - - +
436E LEU* 1.3 67.2 + - - +
437E PHE* 2.9 27.9 + + + +
438E PHE* 3.0 54.7 + + - +
439E PHE* 3.0 8.2 + - - -
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Residues in contact with LEU 436 (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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265A VAL* 4.4 15.8 - - + +
269A CYS* 4.0 1.9 - - - -
342A VAL* 4.2 9.4 - - + -
432A CYS 4.5 2.9 + - - +
434A GLU 3.7 6.1 + - - +
436A LEU* 4.6 19.3 - - + +
439A PHE* 3.5 48.2 - - + -
502A REA 3.9 31.9 - - + -
434E GLU 3.9 0.8 + - - -
435E HIS* 1.3 71.9 - - - +
437E PHE* 1.3 57.3 + - - +
439E PHE* 3.6 20.4 - - + -
440E LYS* 2.9 37.6 + - + +
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Residues in contact with PHE 437 (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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269A CYS* 3.3 42.4 - - - -
272A ALA* 4.0 14.8 - - + -
273A ASP* 4.8 9.9 - - - -
276A LEU* 4.9 2.5 - - + -
305A TRP* 3.8 29.6 - + + -
432A CYS 4.8 3.4 + - - +
502A REA 4.6 19.7 - - + +
435E HIS* 2.9 20.8 + + + +
436E LEU* 1.3 76.1 - - - +
438E PHE* 1.3 70.0 + + - +
441E LEU* 2.8 57.3 + - + +
424F PHE* 3.6 30.1 - + - -
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Residues in contact with PHE 438 (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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305A TRP* 5.4 2.2 - + - -
431E LYS* 3.7 4.9 + - - -
434E GLU* 3.2 33.2 - - + +
435E HIS* 3.0 44.9 + + - +
437E PHE* 1.3 88.6 - + - +
439E PHE* 1.3 61.1 + - - +
441E LEU* 4.2 17.1 - - + +
420F SER 5.8 0.4 - - - -
421F GLU* 4.9 20.0 - - + -
424F PHE* 3.4 61.0 - + + -
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Residues in contact with PHE 439 (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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436A LEU* 3.4 35.7 - - + -
341E GLY 4.9 1.8 - - - -
342E VAL* 4.4 13.0 - - + -
345E ILE* 4.5 15.7 - - + -
431E LYS* 3.4 56.4 + - + -
432E CYS* 4.6 7.6 - - - -
434E GLU* 4.1 12.6 - - + +
435E HIS 3.0 17.2 + - - +
436E LEU* 3.5 14.4 - - + +
437E PHE 3.0 0.2 - - - -
438E PHE* 1.3 79.5 - - - +
440E LYS* 1.3 76.3 + - + +
441E LEU 3.2 10.9 + - - +
504E REA 4.5 13.7 - - + -
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Residues in contact with LYS 440 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ASP* 2.9 32.3 + - - -
265A VAL* 3.3 40.2 - - + -
266A THR* 2.9 31.9 + - - +
269A CYS* 4.0 3.6 - - - -
340E ALA 5.0 1.6 - - - -
341E GLY* 3.2 37.8 + - - +
342E VAL* 5.9 0.2 - - - -
436E LEU* 2.9 15.3 + - + +
439E PHE* 1.3 90.3 - - + +
441E LEU* 1.3 62.2 + - - +
442E ILE* 3.8 5.6 + - - +
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Residues in contact with LEU 441 (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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269A CYS* 3.8 31.4 - - - +
270A GLN 4.7 0.7 - - - +
273A ASP* 4.3 18.2 - - + +
437E PHE* 2.8 47.0 + - + +
438E PHE* 4.2 21.5 - - + +
439E PHE 3.2 6.7 - - - +
440E LYS* 1.3 79.5 - - - +
442E ILE* 1.3 85.4 + - - +
443E GLY* 4.9 1.3 - - - +
424F PHE* 5.6 2.5 - - + -
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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