Contacts of the helix formed by residues 70 - 77 (chain L) in PDB entry 2EHO
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 70 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17L GLU* 4.8 7.6 - - - +
27L MSE 3.8 28.5 - - + -
28L SER* 3.5 10.9 + - - +
30L GLU 3.0 9.3 + - - -
32L LEU* 4.7 6.2 - - + +
68L LEU 3.6 1.6 + - - -
69L PRO* 1.3 69.4 - - - +
71L TRP* 1.3 55.8 + - - +
73L ALA* 3.9 6.5 - - - +
74L LYS* 2.7 65.5 + - + +
119L PHE* 3.9 35.2 - - + +
122L GLN* 3.9 25.4 - - + +
123L LEU* 4.9 1.1 - - + +
126L PHE* 4.9 14.8 - - + -
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Residues in contact with TRP 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J PHE* 4.0 21.1 - + - -
3J CYS* 3.9 22.4 - - - -
64J PHE* 6.1 0.4 - + - -
67J CYS* 3.6 26.3 - - + +
68J SER* 4.0 8.5 - - - -
71J ARG* 3.2 56.4 - - + +
74J ARG* 5.6 3.1 - - - +
17L GLU* 5.9 0.9 - - - +
28L SER* 3.1 35.9 + - - +
29L HIS* 4.1 7.7 - - - -
69L PRO* 2.9 20.4 + - + +
70L LEU* 1.3 80.6 - - - +
72L LEU* 1.3 104.8 + - + +
74L LYS* 3.5 8.1 - - - +
75L GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J PHE* 5.1 2.2 - - + -
64J PHE* 4.0 33.7 - - + +
67J CYS* 3.9 15.0 - - + -
68L LEU* 3.7 27.8 - - + -
69L PRO* 2.9 23.6 + - + +
71L TRP* 1.3 110.0 - - + +
73L ALA* 1.3 58.8 + - - +
75L GLY* 3.0 16.5 + - - -
76L LEU* 3.0 48.5 + - + +
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Residues in contact with ALA 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU* 4.2 23.6 - - + -
34L VAL* 5.1 3.8 - - + -
68L LEU* 4.2 14.4 - - + +
69L PRO 3.0 14.4 + - - +
70L LEU 3.9 2.9 - - - +
72L LEU* 1.3 78.1 - - - +
74L LYS* 1.3 61.6 + - - +
76L LEU 3.9 0.4 - - - -
77L PHE* 3.1 27.0 + - - +
84L LEU* 3.9 22.9 - - + +
86L VAL* 4.6 5.0 - - + +
126L PHE* 4.1 4.5 - - + -
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Residues in contact with LYS 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L GLU* 2.9 31.2 + - - -
17L GLU* 4.1 15.5 - - - +
70L LEU* 2.7 42.2 + - + +
71L TRP* 3.5 7.9 - - - +
73L ALA* 1.3 73.4 - - - +
75L GLY* 1.3 63.2 + - - +
77L PHE* 3.5 15.2 + - - +
122L GLN* 5.5 1.6 - - + +
125L HIS* 5.1 20.5 - - + +
126L PHE* 4.1 16.8 - - + -
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Residues in contact with GLY 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J LYS* 5.9 2.3 - - - +
67J CYS* 4.0 21.2 - - - -
71L TRP 2.9 15.2 + - - -
72L LEU 3.0 4.2 + - - -
74L LYS* 1.3 78.2 - - - +
76L LEU* 1.3 61.4 + - - +
77L PHE 3.6 3.8 + - - +
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Residues in contact with LEU 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J PRO 4.6 2.5 - - - +
63J LYS* 4.0 17.5 - - + +
64J PHE* 3.7 44.2 - - + +
67J CYS* 4.6 2.5 - - - -
40L MSE 4.8 6.7 - - + -
68L LEU* 4.8 1.8 - - + -
72L LEU* 3.0 41.0 + - + +
74L LYS 3.3 0.2 - - - -
75L GLY* 1.3 78.2 - - - +
77L PHE* 1.3 63.7 + - - +
78L ASP* 4.0 4.9 + - - +
83L ILE* 4.0 40.7 - - + +
84L LEU* 3.9 24.8 - - + +
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Residues in contact with PHE 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L ALA 3.1 18.9 + - - +
74L LYS 3.8 9.7 - - - +
75L GLY 3.3 5.4 - - - +
76L LEU* 1.3 79.0 - - - +
78L ASP* 1.3 97.1 + - - +
79L ASN* 4.1 8.5 - - - -
81L ARG* 3.7 34.1 - - + -
84L LEU* 4.5 12.3 - - + +
86L VAL* 3.3 32.1 - - + -
125L HIS 4.7 4.5 - - - -
126L PHE* 3.5 36.6 - + + -
127L ASP* 4.7 2.2 - - - -
1008L SO4 3.8 11.4 - - - -
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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