Contacts of the helix formed by residues 54 - 60 (chain I) in PDB entry 1UW9
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 54 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A TYR* 5.8 2.0 - - - -
229A GLN* 4.9 3.7 + - - +
52I VAL* 5.9 0.3 - - - +
53I SER* 1.3 82.2 - - - +
55I GLU* 1.3 66.6 + - - +
56I SER 3.3 2.2 - - - -
57I ALA* 3.0 20.9 + - + +
67I TYR* 5.7 2.2 - - - -
68I TYR* 4.0 7.6 - - - +
69I ASP* 3.5 3.4 - - - +
55T GLU 5.3 2.0 + - - -
56T SER* 5.4 3.8 + - - +
58T ILE* 3.7 25.3 - - + +
59T ARG* 2.8 50.5 + - + +
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Residues in contact with GLU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LYS* 4.5 5.0 + - - -
53I SER* 2.4 33.6 + - - -
54I ASN* 1.3 77.4 - - - +
56I SER* 1.3 63.1 + - - +
57I ALA 3.3 0.9 + - - -
58I ILE* 3.3 24.3 + - - +
69I ASP* 3.2 8.1 + - - +
70I ASN* 4.6 3.6 + - - +
1141I EDO 2.9 36.6 + - - +
54P ASN* 5.5 1.0 + - - -
58T ILE* 4.0 8.1 - - - +
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Residues in contact with SER 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLU* 1.3 72.3 - - - +
57I ALA* 1.3 55.8 + - - +
58I ILE* 3.0 7.0 - - - -
59I ARG* 2.9 32.4 + - - +
60I PHE* 3.8 7.4 - - - -
67I TYR* 3.4 24.5 + - - -
69I ASP* 2.7 26.8 + - - -
1141I EDO 3.8 6.6 + - - -
226K TYR* 3.5 29.2 - - - +
54P ASN* 5.6 4.4 + - - +
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ASN* 3.0 19.3 + - + +
56I SER* 1.3 74.7 - - - +
58I ILE* 1.3 63.3 + - - +
59I ARG 3.0 0.4 - - - -
60I PHE* 3.0 44.5 + - + +
64I SER* 4.3 12.3 - - - -
67I TYR* 4.8 4.1 - - + -
58T ILE* 3.8 30.6 - - + +
59T ARG* 4.8 4.3 - - + +
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I GLU 3.3 19.9 + - - +
56I SER 3.0 0.6 + - - +
57I ALA* 1.3 78.2 - - - +
59I ARG* 1.3 65.2 + - + +
60I PHE 3.5 3.3 + - - +
54P ASN* 3.9 37.0 - - + +
55P GLU* 4.1 8.7 - - - +
57P ALA* 3.8 17.2 - - + +
58P ILE* 3.8 44.4 - - + +
58T ILE* 3.8 20.4 - - + +
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Residues in contact with ARG 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I SER* 2.9 15.1 + - - +
58I ILE* 1.3 82.5 - - + +
60I PHE* 1.3 60.3 + - - +
226K TYR* 3.0 44.7 + - + +
258K LYS 5.2 0.5 - - - +
259K GLU 4.0 1.0 - - - +
260K LEU 4.3 2.9 - - - +
261K GLY* 3.0 25.7 + - - -
54P ASN* 2.8 52.6 + - + +
57P ALA* 4.7 5.0 - - + +
62P SER* 5.8 2.4 - - - -
64P SER* 2.8 60.1 + - - +
66P LEU 4.0 1.2 - - - +
67P TYR 2.9 23.0 + - - -
68P TYR* 3.6 22.6 + - - -
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Residues in contact with PHE 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I SER 3.8 12.1 - - - -
57I ALA* 3.0 33.2 + - + +
58I ILE 3.3 3.5 - - - +
59I ARG* 1.3 80.9 - - - +
61I GLY* 1.3 72.8 + - - +
63I VAL* 3.9 7.6 - - + -
64I SER* 4.0 19.3 - - - -
67I TYR* 3.6 57.4 - + + -
222K THR* 4.1 2.2 - - + -
226K TYR* 4.0 9.4 - + - -
259K GLU 3.2 4.0 - - - +
260K LEU* 3.3 45.5 - - + -
61P GLY 5.0 5.1 - - - +
62P SER* 5.3 3.1 - - - -
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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