Contacts of the helix formed by residues 69 - 75 (chain N) in PDB entry 2DYS
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 MET 69 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23N GLY 3.7 11.0 - - - +
26N ALA* 4.3 0.2 - - + -
27N GLY* 3.5 33.0 - - - +
64N VAL 2.9 9.6 + - - +
65N MET* 3.3 28.9 - - - +
68N PHE* 1.3 79.1 - - - +
70N VAL* 1.3 92.8 + - + +
72N PRO* 3.5 0.7 - - - +
73N ILE* 3.1 43.9 + - + +
386N VAL* 3.8 20.0 - - + -
389N ILE* 3.9 7.0 - - + -
604N HEA 3.8 28.7 - - + -
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Residues in contact with VAL 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N MET 2.9 24.3 + - - +
69N MET* 1.3 92.2 - - + +
71N MET* 1.3 64.6 + - - +
73N ILE* 3.9 0.5 - - - +
74N MET* 3.0 52.4 + - + +
246N LEU* 3.6 30.5 - - + +
385N ALA* 4.5 9.9 - - + -
386N VAL* 5.3 0.2 - - + -
389N ILE* 4.2 7.2 - - + -
604N HEA 3.4 24.2 - - + -
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Residues in contact with MET 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N ILE 3.3 15.7 + - - +
67N PHE* 4.1 22.9 - - - +
70N VAL* 1.3 76.3 - - - +
72N PRO* 1.3 69.5 - - + +
74N MET* 5.1 0.9 - - - -
75N ILE* 2.9 44.6 + - + +
76N GLY 3.3 1.0 + - - -
157N SER* 3.7 16.2 - - - +
195N LEU* 3.6 31.2 - - + -
199N LEU* 5.6 1.1 - - + -
242N GLU* 3.3 22.9 - - - +
245N ILE* 3.7 13.7 - - + -
246N LEU* 3.6 15.9 - - + -
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Residues in contact with PRO 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR* 3.6 32.1 - - + +
22N PHE* 4.1 8.3 - - + -
23N GLY* 4.5 0.4 - - - -
67N PHE 3.3 24.7 - - - +
68N PHE* 3.1 32.8 - - - +
69N MET 3.5 2.9 - - - +
71N MET* 1.3 89.2 - - + +
73N ILE* 1.3 48.8 + - - +
76N GLY* 3.0 6.2 + - - +
77N GLY* 2.6 33.4 + - - -
105N LEU* 3.7 19.5 - - + -
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Residues in contact with ILE 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR 4.7 1.8 - - - +
20N LEU* 4.0 16.6 - - + +
23N GLY* 3.6 32.5 - - - +
24N ALA 4.2 2.5 - - - +
69N MET* 3.1 38.5 + - - +
70N VAL 3.9 1.8 - - - +
72N PRO* 1.3 76.5 - - - +
74N MET* 1.3 59.3 + - - +
77N GLY* 3.1 6.6 + - - +
78N PHE* 2.8 50.8 + - + -
389N ILE* 4.1 21.1 - - + -
604N HEA 3.9 24.0 - - + -
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Residues in contact with MET 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N VAL* 3.0 22.6 + - + +
71N MET* 5.1 0.2 - - - -
73N ILE* 1.3 77.8 - - - +
75N ILE* 1.3 64.0 + - + +
78N PHE* 3.5 11.4 - - - +
79N GLY* 3.1 20.3 + - - -
184N PHE* 4.2 7.3 - - - -
188N VAL* 5.3 0.5 - - - +
245N ILE 5.3 0.2 - - - +
246N LEU* 3.4 28.9 - - - +
247N ILE* 5.2 0.2 - - - -
249N PRO* 4.0 26.4 - - + +
250N GLY* 3.9 21.3 - - - -
253N MET* 3.9 13.0 - - + -
385N ALA* 3.5 34.3 - - + +
388N ALA* 4.3 2.0 - - + -
389N ILE* 3.8 20.9 - - + -
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Residues in contact with ILE 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71N MET* 2.9 43.2 + - + +
74N MET* 1.3 80.6 - - + +
76N GLY* 1.3 66.7 + - - +
79N GLY* 3.1 21.2 - - - -
160N GLY* 6.1 2.0 - - - -
164N PHE* 3.2 35.1 - - + -
188N VAL* 5.3 8.1 - - + -
191N THR* 3.8 25.6 - - + -
195N LEU* 4.1 13.0 - - + -
245N ILE* 4.3 6.7 - - + +
249N PRO* 4.2 15.5 - - + -
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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