Contacts of the helix formed by residues 66 - 77 (chain F) in PDB entry 1YFJ
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 SER 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64F ASN 4.4 0.2 + - - -
65F VAL* 1.3 76.0 - - - +
67F TRP* 1.3 57.9 + - - +
68F ASP* 3.9 12.6 - - - -
69F ASP* 2.7 38.1 + - - +
70F VAL* 3.0 6.9 + - - +
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Residues in contact with TRP 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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65F VAL 4.2 0.4 + - - -
66F SER* 1.3 72.3 - - - +
68F ASP* 1.3 56.9 + - - +
70F VAL* 2.9 12.7 + - - +
71F LEU* 2.8 26.7 + - - +
137F GLU* 5.7 8.1 - - + -
140F PHE* 5.0 16.4 - - + -
141F ASN* 6.1 0.4 - - - +
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Residues in contact with ASP 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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66F SER* 3.0 9.1 - - - -
67F TRP* 1.3 80.0 - - - +
69F ASP* 1.3 60.4 + - - +
71F LEU* 3.1 22.4 + - - +
72F LYS* 3.5 8.1 + - - +
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Residues in contact with ASP 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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65F VAL* 4.8 5.6 - - + -
66F SER* 2.7 29.6 + - - +
68F ASP* 1.3 80.3 - - - +
70F VAL* 1.3 57.0 + - - +
72F LYS* 4.0 7.6 - - - +
73F VAL* 4.0 13.9 + - - +
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Residues in contact with VAL 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 SER 3.0 6.2 + - - +
67F TRP* 2.9 17.1 + - - +
69F ASP* 1.3 76.9 - - - +
71F LEU* 1.3 62.1 + - - +
72F LYS 3.2 2.0 - - - -
73F VAL* 3.5 8.8 + - - +
74F ILE* 3.1 22.0 + - - +
105F VAL* 6.2 3.1 - - + -
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Residues in contact with LEU 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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67F TRP 2.8 11.1 + - - +
68F ASP* 3.1 15.0 + - - +
70F VAL* 1.3 78.7 - - - +
72F LYS* 1.3 60.6 + - - +
74F ILE* 3.4 8.7 - - - +
75F LYS* 3.1 22.5 + - - +
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Residues in contact with LYS 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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68F ASP 3.5 7.7 + - - +
69F ASP* 4.0 11.0 - - - +
70F VAL 3.2 0.2 - - - -
71F LEU* 1.3 75.1 - - - +
73F VAL* 1.3 57.0 + - - +
74F ILE 3.0 1.1 - - - -
75F LYS* 2.8 7.4 + - - +
76F GLN* 2.5 39.9 + - + +
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Residues in contact with VAL 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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69F ASP 4.0 8.1 + - - +
70F VAL* 3.5 11.5 + - - +
72F LYS* 1.3 77.8 - - - +
74F ILE* 1.3 62.4 + - - +
76F GLN* 4.0 7.9 - - - -
77F TYR* 3.3 25.5 + - - +
79F LEU* 5.2 0.9 - - - +
101F LEU* 5.4 4.9 - - + +
102F LEU* 6.4 0.7 - - - -
105F VAL* 4.8 17.9 - - + -
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Residues in contact with ILE 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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70F VAL 3.1 13.5 + - - +
71F LEU* 3.4 14.1 - - - +
72F LYS 3.0 0.2 - - - -
73F VAL* 1.3 79.1 - - - +
75F LYS* 1.3 60.4 + - - +
78F LYS* 4.2 0.2 - - - -
79F LEU* 3.3 37.0 + - + +
109F HIS* 6.0 4.3 - - + +
132F ILE* 6.2 3.8 - - + -
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Residues in contact with LYS 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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71F LEU 3.1 9.8 + - - +
72F LYS* 2.8 8.1 + - - +
74F ILE* 1.3 78.5 - - - +
76F GLN* 1.3 67.0 + - - +
78F LYS* 2.9 16.2 + - - +
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Residues in contact with GLN 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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72F LYS* 2.5 25.2 + - + +
73F VAL* 3.8 8.1 - - - +
75F LYS* 1.3 73.0 - - - +
77F TYR* 1.3 59.9 + - - +
78F LYS* 3.0 8.3 + - - +
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Residues in contact with TYR 77 (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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73F VAL 3.3 13.9 + - - +
76F GLN* 1.3 75.1 - - - +
78F LYS* 1.3 69.3 + - - +
79F LEU* 3.2 9.2 - - + +
86F GLU* 2.8 28.1 - - + +
90F LEU* 4.9 18.2 - - + -
93F ASP* 5.8 2.0 - - - +
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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