Contacts of the helix formed by residues 448 - 457 (chain A) 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 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A PRO* 4.0 17.9 + - - +
447A ILE* 1.3 69.5 - - - +
449A THR* 1.3 50.6 + - - +
451A LEU* 5.1 1.9 - - + +
452A MET* 2.8 38.5 + - - +
285B ILE* 3.5 34.6 - - + +
289B LYS* 3.2 37.1 + - - +
439B GLU* 3.3 15.5 - - - +
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ILE* 2.9 28.5 + - - +
448A ASP* 1.3 73.3 - - - +
450A PHE* 1.3 70.8 + - + +
452A MET* 3.6 6.0 - - - +
453A GLU* 2.7 40.9 + - + +
439B GLU* 4.4 2.0 - - - -
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A THR* 1.3 80.9 - - + +
451A LEU* 1.3 57.8 + - - +
453A GLU* 3.2 19.0 - - - +
454A MET* 3.1 35.6 + - + +
435B PRO* 3.4 47.8 - - + -
436B LEU* 4.1 18.6 - - + -
439B GLU* 3.0 31.1 + - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ASP* 4.3 3.1 - - + +
450A PHE* 1.3 72.3 - - - +
452A MET* 1.3 66.0 + - - +
453A GLU 2.8 6.1 + - - -
454A MET* 3.2 15.7 + - + +
455A LEU* 3.1 28.4 + - + +
263B VAL* 4.5 8.5 - - + -
267B VAL* 3.9 29.4 - - + -
285B ILE* 4.3 23.3 - - + +
288B LEU* 4.1 27.4 - - + -
289B LYS* 4.2 13.7 - - + +
436B LEU* 5.1 1.8 - - + -
439B GLU* 3.1 12.0 + - - +
440B ILE* 4.0 26.9 - - + -
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Residues in contact with MET 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ASP 2.8 28.0 + - - +
449A THR* 3.6 6.7 - - - +
451A LEU* 1.3 72.2 - - - +
453A GLU* 1.3 66.7 + - - +
455A LEU* 4.0 4.6 + - - +
456A GLU* 2.9 34.8 + - - +
281B ARG* 3.5 41.7 - - + -
282B GLU* 5.0 6.1 - - + +
285B ILE* 3.7 24.3 - - + +
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A THR* 2.7 21.4 + - + +
450A PHE* 3.2 24.9 - - - +
451A LEU 2.8 0.4 + - - -
452A MET* 1.3 77.7 - - - +
454A MET* 1.3 55.6 + - - +
455A LEU 2.5 0.7 + - - -
456A GLU* 2.4 47.8 + - + +
457A ALA* 4.3 9.9 - - + +
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Residues in contact with MET 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 3.1 24.1 + - + +
451A LEU* 3.7 13.9 - - + +
453A GLU* 1.3 82.2 - - - +
455A LEU* 1.3 61.4 + - - +
456A GLU 3.1 0.8 + - - -
457A ALA* 3.6 18.3 + - + +
263B VAL* 4.5 5.4 - - - -
264B GLN* 4.0 33.9 - - + +
267B VAL* 4.3 27.1 - - + +
271B LYS* 3.7 9.0 + - - -
436B LEU* 3.5 31.0 - - + -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.1 17.1 + - + +
452A MET 4.2 3.8 - - - +
453A GLU 2.5 6.0 + - - +
454A MET* 1.3 74.7 - - - +
456A GLU* 1.3 54.7 + - - +
267B VAL* 3.6 23.1 - - + -
271B LYS* 2.5 35.8 + - + +
276B PHE* 3.7 17.5 - - + -
277B LEU* 5.0 0.3 - - - +
281B ARG* 3.0 34.2 + - + +
284B GLN* 3.4 42.2 - - + +
285B ILE* 4.4 11.2 - - + +
288B LEU* 3.6 18.8 - - + -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A MET* 2.9 39.6 - - - +
453A GLU* 2.4 28.5 + - + +
455A LEU* 1.3 66.5 - - - +
457A ALA* 1.3 69.2 + - - +
271B LYS* 4.3 1.2 + - - -
281B ARG* 3.9 24.0 + - - +
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A GLU* 3.5 11.8 + - + +
454A MET* 3.6 18.5 + - + +
456A GLU* 1.3 84.4 - - - +
271B LYS* 4.0 15.8 + - - -
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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