Contacts of the helix formed by residues 46 - 52 (chain D) in PDB entry 1UU1
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 ASN 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 6.1 3.4 - - - +
44D ARG 3.2 4.2 + - - +
45D LEU* 1.3 77.2 - - - +
47D SER* 1.3 67.6 + - - +
48D ASP* 2.7 41.5 + - - +
49D ALA* 2.8 31.1 + - + +
50D LEU* 3.5 3.3 + - - +
235D TYR* 3.1 18.4 + - - +
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Residues in contact with SER 47 (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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32C PRO* 3.9 9.4 - - - +
33C PHE 3.4 33.5 + - - -
35C GLU* 2.9 35.5 + - - -
38C VAL* 4.1 10.3 - - - -
45D LEU* 3.8 6.7 + - - +
46D ASN* 1.3 72.2 + - - +
48D ASP* 1.3 65.4 + - - +
50D LEU* 3.2 29.1 + - - +
51D ARG 4.0 0.3 + - - -
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Residues in contact with ASP 48 (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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30C PRO 4.8 0.7 - - - +
32C PRO* 3.4 27.2 - - + +
320C LYS* 6.1 1.0 - - - -
46D ASN* 2.7 20.8 + - - +
47D SER* 1.3 79.4 + - - +
49D ALA* 1.3 59.1 + - - -
51D ARG* 2.8 56.4 + - - +
52D ILE* 4.3 1.6 + - - +
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Residues in contact with ALA 49 (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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208C ALA* 3.3 15.5 - - - +
46D ASN* 2.8 27.1 + - + +
48D ASP* 1.3 72.1 - - - +
50D LEU* 1.3 63.5 + - - +
51D ARG 3.3 0.2 - - - -
52D ILE* 3.4 23.0 + - + +
54D TYR* 4.9 8.0 - - + +
235D TYR* 3.7 32.0 - - + +
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Residues in contact with LEU 50 (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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33C PHE* 3.8 19.1 - - + -
38C VAL* 4.2 3.1 - - + -
205C SER 3.1 17.3 - - - +
206C LEU* 3.4 4.1 - - + -
207C ALA 3.2 2.4 + - - -
208C ALA* 3.0 27.6 + - + +
209C GLN* 3.8 28.4 + - + +
240C PHE* 3.6 31.6 - - + -
45D LEU* 4.0 12.6 - - + -
46D ASN 3.5 7.2 + - - +
47D SER* 3.3 15.0 - - - +
48D ASP 3.1 0.8 - - - -
49D ALA* 1.3 79.3 - - - +
51D ARG* 1.3 57.2 + - - +
235D TYR* 3.8 23.6 - - + -
236D VAL* 3.9 9.2 - - + -
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Residues in contact with ARG 51 (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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19C ARG* 4.1 10.3 - - - +
23C TYR* 5.2 6.3 + - - +
28C GLU* 3.8 14.1 + - - +
29C ASN 2.7 29.3 + - - +
30C PRO* 3.3 18.6 + - - +
31C PHE 3.3 29.2 - - - +
32C PRO* 3.9 2.0 - - + -
201C SER 4.2 2.1 - - - +
205C SER* 3.3 21.7 + - - +
207C ALA* 3.3 15.6 + - - +
320C LYS* 6.2 1.7 - - - +
47D SER 4.0 1.2 + - - -
48D ASP* 2.8 52.5 + - - +
50D LEU* 1.3 78.4 - - - +
52D ILE* 1.3 78.4 + - + +
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Residues in contact with ILE 52 (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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19C ARG* 3.3 35.7 - - - +
28C GLU* 2.9 19.5 - - + +
207C ALA* 3.6 5.4 - - - -
208C ALA* 3.1 27.4 + - - +
48D ASP 4.4 0.7 - - - +
49D ALA* 3.4 22.4 - - + +
50D LEU 3.2 0.6 - - - -
51D ARG* 1.3 109.6 - - + +
53D TYR* 1.3 78.5 + - - +
54D TYR* 4.0 18.2 - - + +
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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