Contacts of the helix formed by residues 64 - 76 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I ALA 4.3 5.2 - - - -
24I LYS* 4.4 17.0 - - - +
25I ILE 5.7 0.2 - - - -
62I ALA* 6.1 0.7 - - + -
63I ILE* 1.3 103.3 - - - +
65I PHE* 1.3 65.1 - - - +
66I GLU* 3.1 25.1 + - - +
67I GLU* 2.9 33.6 + - - +
68I PHE* 3.2 2.8 + - - +
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Residues in contact with PHE 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I PHE* 5.6 0.9 - - + -
11I LYS* 3.9 34.5 - - + -
14I PHE* 3.4 39.7 - + + -
23I ALA* 4.3 12.2 + - + +
64I THR* 1.3 74.7 - - - +
66I GLU* 1.3 75.1 + - + +
67I GLU 3.2 0.4 - - - -
68I PHE* 3.8 6.3 - - - -
69I LEU* 3.0 59.8 + - + +
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Residues in contact with GLU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I THR* 3.0 24.0 + - - +
65I PHE* 1.3 97.0 + - + +
67I GLU* 1.3 60.4 + - + +
69I LEU* 5.1 1.3 - - - -
70I PRO* 3.3 20.5 - - - +
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Residues in contact with GLU 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I LYS* 4.6 20.2 + - - +
62I ALA 5.0 0.9 - - - +
63I ILE* 3.9 14.8 - - + +
64I THR* 2.9 39.3 + - - +
66I GLU* 1.3 81.3 - - + +
68I PHE* 1.3 65.2 + - - +
69I LEU 3.4 1.3 - - - -
70I PRO* 3.3 7.0 - - - +
71I MET* 3.1 35.2 + - + +
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Residues in contact with PHE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I PHE* 3.8 29.2 - + + -
25I ILE* 3.6 45.8 - - + -
30I VAL* 3.7 40.4 - - + -
33I ILE* 3.5 29.6 - - + -
34I ALA* 4.8 6.3 - - + -
37I LEU* 5.0 3.4 - - + -
63I ILE* 4.2 5.8 - - + -
64I THR 3.2 12.8 + - - +
65I PHE* 3.4 7.6 + - - +
67I GLU* 1.3 78.0 - - - +
69I LEU* 1.3 64.2 + - - +
71I MET* 3.2 11.4 + - + +
72I LEU* 3.0 28.5 + - + +
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Residues in contact with LEU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I PHE* 4.9 20.6 - - + -
14I PHE* 4.8 4.8 - - + -
65I PHE* 3.0 47.9 + - + +
66I GLU* 5.1 0.9 - - - -
68I PHE* 1.3 78.6 - - - +
70I PRO* 1.3 70.8 - - + +
72I LEU* 3.0 17.2 + - + +
73I GLN* 3.1 40.9 + - + +
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Residues in contact with PRO 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I GLU* 3.3 24.2 - - - +
67I GLU* 3.3 12.8 - - - +
69I LEU* 1.3 94.5 - - + +
71I MET* 1.3 55.7 + - + -
73I GLN* 3.2 16.3 + - + +
74I ALA* 2.9 28.8 + - - +
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Residues in contact with MET 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I VAL* 4.0 25.6 - - + -
49I ILE* 5.5 15.1 - - + +
50I LEU* 4.6 18.6 - - + -
53I PRO* 6.2 0.7 - - - -
55I LYS* 3.7 27.8 - - - +
63I ILE* 4.0 21.3 - - + -
67I GLU* 3.1 23.5 + - + +
68I PHE* 3.2 17.0 + - + +
69I LEU 3.2 0.2 + - - -
70I PRO* 1.3 75.5 - - + +
72I LEU* 1.3 57.8 + - - +
74I ALA* 3.3 8.0 + - - +
75I ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I PHE* 4.0 31.2 - - + -
14I PHE* 5.0 3.6 - - + -
34I ALA* 4.1 27.8 - - + -
37I LEU* 3.6 31.6 - - + -
39I GLN* 4.0 22.0 - - + -
68I PHE* 3.0 20.2 + - + +
69I LEU* 3.4 14.8 - - + +
71I MET* 1.3 75.6 - - - +
73I GLN* 1.3 60.0 + - + +
75I ALA* 3.3 4.6 + - + +
76I ALA* 3.0 28.3 + - + +
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Residues in contact with GLN 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I SER* 4.5 16.6 - - - +
69I LEU* 3.1 50.6 + - + +
70I PRO* 3.2 15.0 - - + +
71I MET 3.3 0.2 - - - -
72I LEU* 1.3 81.6 - - + +
74I ALA* 1.3 58.2 + - - +
76I ALA* 3.7 12.8 + - - +
77I ASN* 3.2 19.4 + - - +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I ILE* 5.6 13.5 - - + -
70I PRO 2.9 16.5 + - - +
71I MET* 3.3 8.0 + - - +
73I GLN* 1.3 77.2 - - - +
75I ALA* 1.3 60.3 + - - +
77I ASN* 3.2 18.7 + - - +
78I ASN* 3.4 13.8 + - - +
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Residues in contact with ALA 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ALA* 5.4 2.9 - - + -
39I GLN* 3.0 19.6 - - + +
41I PRO* 4.2 27.3 - - + +
45I GLU* 5.1 0.4 - - - +
49I ILE* 5.6 7.8 - - + +
71I MET 3.0 16.1 + - - +
72I LEU* 3.3 9.1 + - + +
74I ALA* 1.3 75.3 - - - +
76I ALA* 1.3 56.5 + - - +
77I ASN 3.2 1.8 - - - -
78I ASN* 3.0 34.4 + - - +
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I GLN* 3.3 20.2 - - + +
72I LEU* 3.0 17.1 + - + +
73I GLN* 3.8 12.8 - - - +
74I ALA 3.3 1.0 - - - -
75I ALA* 1.3 78.2 - - - +
77I ASN* 1.3 58.5 + - - +
79I LYS* 3.1 30.9 - - + +
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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