Contacts of the helix formed by residues 66 - 71 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E THR* 1.3 72.9 - - - +
67E ILE* 1.3 58.3 + - + +
69E ALA* 3.0 5.9 + - + +
70E LEU* 2.8 26.2 + - - +
84E TRP* 3.7 27.8 - - + -
87E PHE* 3.8 29.5 - - + -
89E GLU* 3.3 6.9 + - - +
109E ARG* 3.8 15.0 - - + +
112E VAL* 3.8 16.2 - - + -
113E ALA* 3.7 31.6 - - - +
118E LEU* 4.2 10.1 - - + -
267E ILE* 3.5 32.1 - - + -
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Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 3.3 2.7 - - + +
66E LEU* 1.3 74.1 - - + +
68E ASP* 1.3 57.7 + - - +
70E LEU* 3.1 13.3 + - + +
71E LEU* 2.8 38.3 + - + +
100E TYR* 3.6 26.5 - - + +
102E VAL* 4.2 6.1 - - + -
105E TYR* 3.6 42.2 - - + +
108E LEU* 3.6 30.3 - - + -
109E ARG* 3.7 31.6 - - + +
112E VAL* 5.1 2.7 - - + -
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 3.1 30.7 + - - +
67E ILE* 1.3 76.1 - - - +
69E ALA* 1.3 54.5 + - - +
71E LEU* 4.6 4.3 - - - -
72E GLY* 2.7 29.8 + - - -
73E ASP* 3.2 28.0 + - + +
76E CYS* 4.0 11.7 - - - +
94E PHE 3.7 5.9 - - - +
95E SER* 3.5 33.1 + - - -
100E TYR* 3.2 27.5 + - - -
148E PHE* 5.0 1.9 - - - -
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E CYS* 4.9 1.1 - - + -
65E THR 3.0 12.6 + - - +
66E LEU* 3.2 13.0 - - - +
68E ASP* 1.3 76.4 - - - +
70E LEU* 1.3 64.0 + - - +
72E GLY* 3.6 8.0 + - - -
76E CYS* 4.1 15.7 - - + +
79E PHE* 3.9 26.6 - - + +
80E GLN* 5.6 3.5 + - - +
87E PHE* 4.7 6.3 - - + -
118E LEU* 3.8 25.4 - - + +
150E ARG* 5.6 3.6 + - - -
258E PHE* 5.8 0.2 - - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU 2.8 12.5 + - - +
67E ILE* 3.3 14.8 - - + +
69E ALA* 1.3 79.3 - - - +
71E LEU* 1.3 67.1 + - + +
72E GLY* 4.1 0.5 - - - -
108E LEU* 3.9 35.4 - - + -
112E VAL* 4.0 19.3 - - + -
118E LEU* 3.9 23.3 - - + +
150E ARG* 4.0 7.4 + - - +
177E LEU* 4.7 2.7 - - + -
179E ILE* 3.9 17.7 - - + -
258E PHE* 3.4 57.2 - - + -
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ILE* 2.8 27.5 + - + +
68E ASP* 4.2 2.7 - - - +
70E LEU* 1.3 76.4 - - + +
72E GLY* 1.3 59.4 + - - +
100E TYR* 4.0 27.6 - - + -
148E PHE* 3.1 42.8 - - + +
150E ARG* 3.2 22.3 + - + +
151E LEU* 3.8 10.3 - - + +
179E ILE* 3.6 31.2 - - + -
232E ILE* 3.8 36.6 - - + -
258E PHE* 6.2 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