Contacts of the helix formed by residues 66 - 71 (chain C) in PDB entry 5HMG
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 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C THR* 1.3 72.2 - - - +
67C ILE* 1.3 59.4 + - + +
69C ALA* 3.0 5.7 + - - +
70C LEU* 2.9 25.3 + - - +
84C TRP* 3.7 27.8 - - + -
87C PHE* 3.8 30.5 - - + -
89C GLU* 3.3 7.1 + - - +
109C ARG* 3.8 13.9 - - + +
112C VAL* 3.8 17.0 - - + -
113C ALA* 3.7 30.7 - - - +
118C LEU* 4.2 9.6 - - + -
267C ILE* 3.5 32.1 - - + -
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Residues in contact with ILE 67 (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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65C THR* 3.3 2.8 - - + +
66C LEU* 1.3 73.7 - - + +
68C ASP* 1.4 57.5 + - - +
70C LEU* 3.1 14.1 + - + +
71C LEU* 2.8 37.6 + - + +
89C GLU* 4.9 0.2 + - - -
100C TYR* 3.6 26.9 - - + +
102C VAL* 4.1 5.8 - - + -
105C TYR* 3.6 42.0 - - + +
108C LEU* 3.5 31.6 - - + +
109C ARG* 3.7 31.6 - - + +
112C VAL* 5.2 2.2 - - + -
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Residues in contact with ASP 68 (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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65C THR* 3.1 30.5 + - - +
67C ILE* 1.4 73.8 - - - +
69C ALA* 1.3 57.6 + - - +
71C LEU* 4.4 4.5 - - - +
72C GLY* 2.7 29.8 + - - -
73C ASP* 3.2 27.3 + - + +
76C CYS* 4.1 11.8 - - - +
94C PHE 3.7 5.5 - - - +
95C SER* 3.4 34.2 + - - -
100C TYR* 3.1 28.5 + - - -
148C PHE* 5.0 1.7 - - - -
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Residues in contact with ALA 69 (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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64C CYS* 4.9 1.3 - - + -
65C THR 3.0 12.2 + - - +
66C LEU* 3.0 13.0 + - - +
68C ASP* 1.3 75.9 - - - +
70C LEU* 1.3 63.4 + - - +
72C GLY* 3.6 8.1 + - - -
76C CYS* 4.1 15.9 - - + +
79C PHE* 3.9 26.8 - - + +
80C GLN* 5.6 3.8 + - - +
87C PHE* 4.7 6.5 - - + -
118C LEU* 3.8 26.1 - - + +
150C ARG* 5.6 3.3 + - - -
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Residues in contact with LEU 70 (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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66C LEU 2.9 12.1 + - - +
67C ILE* 3.1 14.8 + - + +
69C ALA* 1.3 79.9 - - - +
71C LEU* 1.3 70.1 + - + +
72C GLY* 3.3 0.5 + - - -
108C LEU* 3.9 34.5 - - + -
112C VAL* 4.0 20.9 - - + -
118C LEU* 3.8 21.5 - - + +
150C ARG* 4.0 7.6 - - - +
177C LEU* 4.7 1.8 - - + -
179C ILE* 4.0 14.6 - - + -
258C PHE* 3.4 57.8 - - + -
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Residues in contact with LEU 71 (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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67C ILE* 2.8 28.0 + - + +
68C ASP* 4.2 2.5 - - - +
70C LEU* 1.3 76.2 - - + +
72C GLY* 1.3 59.6 + - - +
100C TYR* 3.9 27.8 - - + -
148C PHE* 3.2 37.7 - - + +
150C ARG* 3.1 28.1 + - - +
151C LEU* 3.9 10.9 - - + +
179C ILE* 3.6 31.0 - - + -
232C ILE* 3.8 36.1 - - + -
258C PHE* 5.6 0.2 - - - -
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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