Contacts of the helix formed by residues 64 - 76 (chain L) in PDB entry 1O1F
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 THR 64 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23L ALA 4.3 4.7 - - - -
24L LYS* 4.4 17.3 - - + +
62L ALA* 5.6 0.7 - - + -
63L ILE* 1.3 102.9 - - - +
65L PHE* 1.3 64.1 + - - +
66L GLU* 3.1 24.9 + - - +
67L GLU* 2.9 33.6 + - - +
68L PHE* 3.2 3.1 + - - +
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Residues in contact with PHE 65 (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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10L PHE* 5.7 0.9 - - + -
11L LYS* 3.9 34.8 - - + -
14L PHE* 3.4 38.6 - + + -
23L ALA* 4.3 11.5 + - + +
64L THR* 1.3 74.5 - - - +
66L GLU* 1.3 76.1 + - + +
67L GLU 3.2 0.7 - - - -
68L PHE* 3.8 6.1 - - - -
69L LEU* 3.0 61.0 + - + +
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Residues in contact with GLU 66 (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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64L THR* 3.0 25.0 + - - +
65L PHE* 1.3 96.1 + - + +
67L GLU* 1.3 60.9 + - + +
69L LEU* 5.1 1.1 - - - -
70L PRO* 3.3 20.2 - - - +
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Residues in contact with GLU 67 (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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55L LYS* 4.6 20.3 + - - +
62L ALA 5.0 0.5 - - - +
63L ILE* 3.9 14.4 - - + +
64L THR* 2.9 39.6 + - - +
66L GLU* 1.3 81.9 - - + +
68L PHE* 1.3 66.7 + - - +
69L LEU 3.4 0.9 - - - -
70L PRO* 3.3 6.8 - - - +
71L MET* 3.1 35.3 + - + +
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Residues in contact with PHE 68 (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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14L PHE* 3.8 27.1 - + + -
25L ILE* 3.6 47.1 - - + -
30L VAL* 3.7 39.5 - - + -
33L ILE* 3.5 30.3 - - + -
34L ALA* 4.8 6.3 - - + -
37L LEU* 5.0 3.4 - - + -
63L ILE* 4.2 7.0 - - + -
64L THR 3.2 12.8 + - - +
65L PHE* 4.0 7.9 - - - +
67L GLU* 1.3 77.8 - - - +
69L LEU* 1.3 65.7 + - - +
71L MET* 3.2 11.1 + - + +
72L LEU* 3.0 29.2 + - + +
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Residues in contact with LEU 69 (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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10L PHE* 4.9 20.2 - - + -
14L PHE* 4.8 5.0 - - + -
65L PHE* 3.0 48.9 + - + +
66L GLU* 5.1 1.1 - - - -
68L PHE* 1.3 79.6 - - - +
70L PRO* 1.3 68.2 - - + +
72L LEU* 3.0 18.0 + - + +
73L GLN* 3.1 39.9 + - + +
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Residues in contact with PRO 70 (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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66L GLU* 3.3 24.2 - - - +
67L GLU* 3.3 12.8 - - - +
69L LEU* 1.3 93.8 - - + +
71L MET* 1.3 55.0 + - + +
73L GLN* 3.2 15.8 + - + +
74L ALA* 2.9 29.1 + - - +
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Residues in contact with MET 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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30L VAL* 3.9 25.6 - - + -
49L ILE* 5.5 16.1 - - + +
50L LEU* 4.7 18.4 - - + -
53L PRO* 6.2 0.9 - - - -
55L LYS* 3.7 27.4 - - - +
63L ILE* 4.0 20.9 - - + -
67L GLU* 3.1 24.5 + - + +
68L PHE* 3.2 17.2 + - + +
70L PRO* 1.3 75.1 - - + +
72L LEU* 1.3 57.7 + - - +
74L ALA* 3.3 6.6 + - - +
75L ALA* 3.0 28.6 + - - +
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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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10L PHE* 4.0 30.5 - - + -
14L PHE* 5.0 3.6 - - + -
34L ALA* 4.1 27.6 - - + -
37L LEU* 3.6 31.9 - - + -
39L GLN* 4.0 22.7 - - + -
68L PHE* 3.0 19.9 + - + +
69L LEU* 3.0 15.5 + - + +
71L MET* 1.3 75.8 - - - +
73L GLN* 1.3 59.1 + - + +
75L ALA* 3.3 4.6 + - + +
76L ALA* 3.0 28.5 + - + +
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Residues in contact with GLN 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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3L SER* 4.5 17.0 - - - +
69L LEU* 3.1 50.3 + - + +
70L PRO* 3.2 14.8 - - + +
71L MET 3.3 0.2 - - - -
72L LEU* 1.3 79.7 - - + +
74L ALA* 1.3 57.1 + - - +
75L ALA 3.7 0.2 + - - -
76L ALA* 3.7 12.7 + - - +
77L ASN* 3.2 19.8 + - - +
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Residues in contact with ALA 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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49L ILE* 5.6 13.6 - - + +
70L PRO 2.9 15.4 + - - +
71L MET* 3.3 8.5 + - - +
73L GLN* 1.3 76.7 - - - +
75L ALA* 1.3 60.4 + - - +
76L ALA 3.3 0.2 - - - -
77L ASN* 3.2 19.2 + - - +
78L ASN* 3.4 13.0 + - - +
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Residues in contact with ALA 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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34L ALA* 5.4 2.7 - - + -
39L GLN* 3.0 19.2 - - + +
41L PRO* 4.2 27.0 - - + +
45L GLU* 5.0 0.6 - - - +
49L ILE* 5.6 7.8 - - + +
71L MET 3.0 15.5 + - - +
72L LEU* 3.3 9.2 + - + +
74L ALA* 1.3 74.2 - - - +
76L ALA* 1.3 58.5 + - - +
77L ASN 3.2 2.2 - - - -
78L ASN* 3.0 34.0 + - - +
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Residues in contact with ALA 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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39L GLN* 3.3 20.4 - - + +
72L LEU* 3.0 17.2 + - + +
73L GLN* 3.8 12.3 - - - +
74L ALA 3.3 1.0 - - - -
75L ALA* 1.3 78.5 - - - +
77L ASN* 1.3 59.2 + - - +
78L ASN 3.2 0.2 - - - -
79L LYS* 3.1 30.7 - - + +
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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