Contacts of the helix formed by residues 36 - 40 (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 36 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31P LEU* 4.1 25.8 - - + -
32P GLY 4.5 1.2 + - - -
33P TYR 4.9 0.2 + - - -
34P GLY 3.7 0.4 - - - -
35P ASP* 1.4 78.6 - - - +
37P GLY* 1.4 61.0 + - - +
38P CYS* 4.0 23.3 - - - +
39P TYR* 2.8 38.6 + - + +
41P HIS* 3.4 11.1 + - - -
46P THR* 4.0 8.3 - - + +
49P LEU* 4.1 33.9 - - + -
251P LEU* 4.2 13.0 - - + -
278P PHE* 3.8 20.4 - - + -
313P PRO* 4.4 7.6 - - + -
315P LEU* 4.3 7.6 - - + -
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Residues in contact with GLY 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ASP 3.7 1.0 + - - -
36P LEU* 1.4 68.7 - - - +
38P CYS* 1.3 58.3 + - - +
40P GLY* 3.0 20.1 + - - -
41P HIS* 3.9 15.3 + - - +
44P SER* 4.4 10.2 - - - -
46P THR* 2.9 17.7 + - - +
50P ASP* 3.6 15.0 - - - -
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Residues in contact with CYS 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P LEU* 3.1 17.4 - - - -
37P GLY* 1.3 78.8 - - - +
39P TYR* 1.3 73.9 + - - +
40P GLY 3.3 1.8 - - - -
49P LEU 4.4 2.2 - - - -
50P ASP* 3.0 31.6 + - + +
53P ALA* 3.8 27.8 - - + -
58P ARG* 3.8 23.5 + - - +
315P LEU* 4.8 1.3 - - - -
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Residues in contact with TYR 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P TYR* 3.3 59.5 - + + +
34P GLY* 4.3 9.3 - - - -
36P LEU* 2.8 23.2 + - + +
38P CYS* 1.3 92.5 - - - +
40P GLY* 1.4 58.7 + - - +
41P HIS 3.5 2.9 - - - -
58P ARG* 3.4 33.8 - - + +
59P PHE 2.8 28.9 + - - -
313P PRO* 3.7 22.9 - - + -
314P ALA 2.9 25.3 + - - -
315P LEU* 4.6 3.1 - - + -
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Residues in contact with GLY 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P GLY 3.0 10.4 + - - -
38P CYS 3.3 1.6 - - - -
39P TYR* 1.4 80.2 - - - +
41P HIS* 1.4 68.0 + - - +
42P PRO* 3.2 7.6 - - - +
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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