Contacts of the helix formed by residues 64 - 76 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F ALA 4.3 4.3 - - - -
24F LYS* 4.4 17.7 - - + -
25F ILE 5.7 0.2 - - - -
62F ALA* 6.1 0.4 - - + -
63F ILE* 1.3 103.6 - - - +
65F PHE* 1.3 64.1 + - - +
66F GLU* 3.1 25.3 + - - +
67F GLU* 2.9 33.6 + - - +
68F PHE* 3.2 3.7 + - - +
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PHE* 5.2 0.9 - - + -
11F LYS* 3.9 35.7 - - + -
14F PHE* 3.4 40.2 - + + -
23F ALA* 4.3 11.2 + - + +
64F THR* 1.3 74.7 - - - +
66F GLU* 1.3 76.3 + - + +
67F GLU 3.2 0.9 - - - -
68F PHE* 3.8 6.5 - - - -
69F LEU* 3.0 60.2 + - + +
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F THR* 3.0 24.4 + - - +
65F PHE* 1.3 96.6 + - + +
67F GLU* 1.3 60.0 + - + +
69F LEU* 5.1 1.3 - - - -
70F PRO* 3.3 19.9 - - - +
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LYS* 4.6 19.9 + - - +
62F ALA 5.0 0.3 - - - +
63F ILE* 3.9 15.9 - - + +
64F THR* 2.9 39.1 + - - +
66F GLU* 1.3 80.4 - - + +
68F PHE* 1.3 66.3 + - - +
69F LEU 3.4 1.6 - - - -
70F PRO* 3.3 6.7 - - - +
71F MET* 3.1 35.9 + - + +
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F PHE* 3.8 26.7 - + + -
25F ILE* 3.6 47.1 - - + -
30F VAL* 3.7 40.2 - - + -
33F ILE* 3.5 29.8 - - + -
34F ALA* 4.8 6.3 - - + -
37F LEU* 5.0 3.6 - - + -
63F ILE* 4.2 7.0 - - + -
64F THR 3.2 12.6 + - - +
65F PHE* 3.4 7.8 + - - +
67F GLU* 1.3 78.3 - - - +
69F LEU* 1.3 65.2 + - - +
71F MET* 3.2 11.0 + - + +
72F LEU* 3.0 29.0 + - + +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PHE* 4.9 21.1 - - + -
14F PHE* 4.8 4.8 - - + -
65F PHE* 3.0 48.8 + - + +
66F GLU* 5.1 1.1 - - - -
68F PHE* 1.3 78.4 - - - +
70F PRO* 1.3 69.9 - - + +
72F LEU* 3.0 17.8 + - + +
73F GLN* 3.1 40.3 + - + +
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Residues in contact with PRO 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F GLU* 3.3 25.1 - - - +
67F GLU* 3.3 12.8 - - - +
69F LEU* 1.3 93.8 - - + +
71F MET* 1.3 56.1 + - + -
73F GLN* 3.2 15.9 + - + +
74F ALA* 2.9 28.4 + - - +
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL* 3.9 25.8 - - + -
49F ILE* 5.5 15.6 - - + +
50F LEU* 4.6 18.2 - - + -
53F PRO* 6.2 0.7 - - - -
55F LYS* 3.7 27.8 - - - +
63F ILE* 4.0 21.5 - - + -
67F GLU* 3.1 23.7 + - + +
68F PHE* 3.2 16.6 + - + +
70F PRO* 1.3 75.8 - - + +
72F LEU* 1.3 57.2 + - - +
74F ALA* 3.3 7.1 + - - +
75F ALA* 3.0 28.5 + - - +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PHE* 4.0 31.0 - - + -
14F PHE* 5.0 3.4 - - + -
34F ALA* 4.1 27.4 - - + -
37F LEU* 3.6 31.9 - - + -
39F GLN* 4.0 22.0 - - + -
68F PHE* 3.0 20.0 + - + +
69F LEU* 3.4 15.0 - - + +
71F MET* 1.3 76.0 - - - +
73F GLN* 1.3 60.5 + - + +
75F ALA* 3.3 4.3 + - + +
76F ALA* 3.0 28.3 + - + +
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Residues in contact with GLN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F SER* 4.5 16.6 - - - +
69F LEU* 3.1 51.0 + - + +
70F PRO* 3.2 15.2 - - + +
71F MET 3.3 0.2 - - - -
72F LEU* 1.3 81.1 - - + +
74F ALA* 1.3 56.8 - - - +
76F ALA* 3.7 13.3 + - - +
77F ASN* 3.2 19.4 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 5.6 13.2 - - + +
70F PRO 2.9 15.8 + - - +
71F MET* 3.7 7.9 - - - +
73F GLN* 1.3 76.1 - - - +
75F ALA* 1.3 61.7 + - - +
76F ALA 3.3 0.2 - - - -
77F ASN* 3.2 18.6 + - - +
78F ASN* 3.4 13.9 + - - +
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ALA* 5.4 2.7 - - + -
39F GLN* 3.0 18.6 - - + +
41F PRO* 4.2 27.6 - - + +
45F GLU* 5.0 1.1 - - - +
49F ILE* 5.6 7.6 - - + +
71F MET 3.0 16.1 + - - +
72F LEU* 3.3 9.2 + - + +
74F ALA* 1.3 75.1 - - - +
76F ALA* 1.3 56.5 + - - +
77F ASN 3.2 2.0 - - - -
78F ASN* 3.0 33.7 + - - +
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLN* 3.3 20.4 - - + +
72F LEU* 3.0 16.5 + - + +
73F GLN* 3.8 12.1 - - - +
74F ALA 3.3 1.2 - - - -
75F ALA* 1.3 77.5 - - - +
77F ASN* 1.3 59.3 + - - +
78F ASN 3.2 0.2 - - - -
79F 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