Contacts of the helix formed by residues 50 - 55 (chain D) in PDB entry 1L0N
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 50 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ARG* 4.2 18.7 - - + +
72C ASP* 3.2 24.2 + - - -
45D TYR 4.4 3.8 - - - -
46D VAL* 3.8 10.2 - - + -
47D ALA* 2.8 45.4 + - + +
48D TYR 3.1 0.8 - - - -
49D ARG* 1.3 92.8 + - - +
51D LEU* 1.3 61.9 + - - +
52D VAL* 3.1 2.1 + - - -
53D GLY 4.8 0.3 + - - -
54D VAL* 3.8 9.5 - - - +
90D TYR* 4.0 13.9 - + - -
192D TRP* 3.2 34.8 - + + -
196D PRO* 6.0 6.1 - - + -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.9 21.1 - - + -
46D VAL* 5.0 0.9 - - + -
47D ALA 4.1 4.7 - - - +
48D TYR* 3.0 25.7 + - + +
50D HIS* 1.3 77.7 - - - +
52D VAL* 1.3 65.9 + - - +
55D CYS* 3.4 24.0 + - - -
56D TYR* 3.1 24.2 + - + +
61D ALA* 4.9 5.6 - - + -
64D LEU* 4.7 6.3 - - + -
91D PHE* 3.5 31.9 - - + -
189D PHE* 4.0 18.8 - - + -
192D TRP* 3.7 26.5 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ARG* 2.9 37.8 + - + +
50D HIS 3.1 1.4 - - - -
51D LEU* 1.3 79.3 - - - +
53D GLY* 1.3 73.8 + - - +
54D VAL 2.6 4.0 + - - -
55D CYS 3.4 1.6 + - - -
56D TYR 2.8 20.8 - - - +
57D THR* 4.4 0.4 - - - -
58D GLU* 4.0 37.7 - - + +
61D ALA* 3.8 20.9 - - + -
87D LEU* 4.4 6.7 - - + -
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Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG 4.7 0.8 + - - -
50D HIS 4.8 1.0 + - - -
52D VAL* 1.3 82.7 - - - +
54D VAL* 1.3 64.2 + - - +
56D TYR 4.6 0.6 - - - +
51J LEU* 3.4 23.6 - - - +
54J HIS* 4.4 6.4 + - - -
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D HIS* 3.3 37.8 + - + +
26D ILE* 4.4 6.1 - - + -
50D HIS 3.8 9.6 - - - +
51D LEU 4.3 0.7 - - - +
52D VAL 2.6 4.9 + - - -
53D GLY* 1.3 78.7 - - - +
55D CYS* 1.3 74.6 + - + +
192D TRP* 3.4 46.9 - - + +
51J LEU* 3.5 16.2 - - - +
54J HIS* 4.4 3.3 + - - -
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Residues in contact with CYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D HIS* 3.9 12.1 - - - +
26D ILE* 4.4 8.1 - - + -
27D ARG* 3.6 34.4 - - + +
30D PHE* 5.2 2.2 - - - -
51D LEU* 3.4 29.9 + - - -
54D VAL* 1.3 86.9 - - + +
56D TYR* 1.3 86.4 + - + +
54J HIS* 3.2 19.8 + - - -
58J LYS* 2.9 15.0 + - - -
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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