Contacts of the helix formed by residues 73 - 78 (chain C) in PDB entry 1U75
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 PHE 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C THR* 3.1 21.8 + - + +
71C TYR 3.8 1.0 - - - +
72C ARG* 1.3 129.7 - - + +
74C LYS* 1.3 66.4 + - - +
75C LYS* 3.2 4.0 + - + +
76C GLU* 3.2 3.6 + - - -
77C PHE* 3.1 24.0 + - - +
133C THR 3.4 11.2 - - - -
134C PRO* 3.7 7.9 - - + -
135C GLU* 3.7 48.7 - - + +
138C THR* 3.6 26.9 - - + +
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ARG 4.1 0.4 + - - -
73C PHE* 1.3 69.5 - - - +
75C LYS* 1.3 66.1 + - - +
77C PHE* 3.2 28.8 + - - +
78C ASN* 3.3 24.0 + - + +
135C GLU* 4.6 12.3 + - - +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C PHE* 3.3 2.4 - - + +
74C LYS* 1.3 82.2 - - - +
76C GLU* 1.3 56.8 + - - +
77C PHE 3.8 0.2 + - - -
78C ASN* 4.5 1.0 - - - +
79C ASP 4.1 4.7 + - - -
135C GLU* 5.6 3.2 + - + +
136C ASP* 5.9 3.0 + - - +
138C THR* 3.5 38.5 + - + +
139C PRO 3.4 20.9 - - - +
140C ASP* 3.3 29.2 + - - +
141C ASN* 3.0 26.1 + - - +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C HIS 4.7 0.7 - - - +
53C ILE* 4.7 9.3 - - - +
56C THR* 4.1 20.4 + - + +
70C THR* 2.7 47.4 + - - +
71C TYR* 3.7 24.2 + - - +
73C PHE 3.2 4.0 + - - -
75C LYS* 1.3 77.1 - - - +
77C PHE* 1.3 60.0 + - - +
79C ASP* 3.4 10.7 - - + +
82C ASN* 2.5 39.5 + - - +
138C THR* 3.8 10.7 - - + +
139C PRO* 3.4 24.2 - - - +
141C ASN* 4.1 2.7 - - - +
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.1 50.6 + + - -
72C ARG* 3.3 20.2 - - - -
73C PHE 3.1 19.5 + - - +
74C LYS* 3.2 9.6 - - - +
76C GLU* 1.3 76.9 - - - +
78C ASN* 1.3 76.5 + - - +
79C ASP 3.0 9.6 + - - +
82C ASN* 3.5 20.4 - - - +
86C GLN* 4.4 13.0 - - + +
89C PHE* 3.8 37.2 - + + -
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Residues in contact with ASN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 3.3 24.6 + - + +
75C LYS 4.5 3.6 - - - +
77C PHE* 1.3 97.0 - - - +
79C ASP* 1.3 61.5 + - - +
80C PRO* 3.5 9.0 - - - +
86C GLN* 5.5 4.3 - - - -
141C ASN* 4.7 2.5 + - - -
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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