Contacts of the strand formed by residues 57 - 59 (chain P) in PDB entry 1E33
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 LEU 57 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P ALA 5.2 0.2 - - - -
56P GLY* 1.3 71.9 - - - -
58P ARG* 1.3 58.2 + - - +
59P PHE* 4.0 20.6 - - + -
314P ALA 3.8 0.5 - - - +
315P LEU* 3.2 8.4 - - - +
316P ALA* 2.8 46.4 + - + +
322P ILE* 3.8 12.4 - - + +
323P ALA 4.5 4.7 - - - +
325P GLY* 3.8 25.1 - - - +
326P VAL 4.0 0.7 - - - +
327P THR* 3.5 31.9 - - + +
361P LEU* 4.4 11.2 - - + +
362P LEU* 4.4 29.4 - - + +
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Residues in contact with ARG 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P TYR* 5.4 0.2 + - - -
38P CYS* 3.8 29.7 + - - +
39P TYR* 3.4 52.0 - - - +
53P ALA* 4.5 12.4 - - + +
56P GLY 3.7 1.2 + - - -
57P LEU* 1.3 70.9 - - - +
59P PHE* 1.3 62.8 + - - +
60P THR* 3.9 16.4 + - - +
314P ALA 3.6 3.4 - - - -
315P LEU* 3.9 10.8 - - + -
325P GLY 3.1 12.8 + - - +
326P VAL* 3.5 35.2 - - + +
327P THR* 3.2 23.8 + - - +
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Residues in contact with PHE 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P TYR* 2.8 26.2 + - - -
57P LEU* 4.0 14.6 - - + -
58P ARG* 1.3 79.9 - - - +
60P THR* 1.4 62.7 + - - +
61P ASP 4.4 0.7 - - - +
62P PHE* 3.7 29.3 + + + +
312P GLU 4.8 2.1 - - - +
314P ALA* 2.8 32.7 + - + +
315P LEU 4.7 0.4 - - - -
316P ALA* 4.1 23.3 - - + -
327P THR* 3.5 12.8 - - - +
329P GLU 4.6 8.7 - - - -
331P ALA* 3.8 27.4 - - + -
358P LEU* 4.6 4.0 - - + -
361P LEU* 3.8 23.1 - - + -
362P LEU* 4.3 21.3 - - + -
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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
------------------------------------------------------------
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