Contacts of the helix formed by residues 63 - 76 (chain F) in PDB entry 4IVZ
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 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57F MET* 4.7 0.4 - - - -
62F VAL* 1.3 75.6 - - - +
64F ASP* 1.3 61.9 + - - +
65F VAL* 2.4 25.3 + - - +
66F VAL* 2.6 44.4 + - - +
67F PHE* 3.3 7.3 + - - +
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Residues in contact with ASP 64 (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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4E PHE* 3.1 34.0 - - - -
5E LEU* 4.2 14.6 - - + +
75E ILE* 3.5 8.7 - - - +
54F GLU* 5.2 2.6 - - + +
57F MET* 3.5 29.9 - - + +
62F VAL 3.6 3.2 + - - -
63F SER* 1.3 72.7 - - - +
65F VAL* 1.3 76.8 + - - +
67F PHE* 3.6 3.8 + - - +
68F PHE* 2.7 41.5 + - + -
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Residues in contact with VAL 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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72E ILE* 3.5 22.7 - - + +
75E ILE* 3.8 25.4 - - + -
76E LEU* 4.1 15.0 - - + +
63F SER* 2.4 24.1 + - - +
64F ASP* 1.3 82.7 - - - +
66F VAL* 1.3 56.0 + - + +
67F PHE 3.0 5.4 + - - -
68F PHE* 3.3 14.9 + - - +
69F GLU* 2.2 43.0 + - - +
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Residues in contact with VAL 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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16F ILE* 5.8 0.5 - - - +
62F VAL* 3.4 20.8 - - + +
63F SER* 2.6 31.8 + - - +
65F VAL* 1.3 77.2 - - + +
67F PHE* 1.3 58.4 + - - +
69F GLU* 3.0 12.8 - - - +
70F MET* 3.7 22.7 + - + +
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Residues in contact with PHE 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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9F VAL* 4.1 22.4 - - + -
12F VAL* 3.2 36.0 - - + +
13F ILE* 4.1 17.0 - - + -
16F ILE* 3.8 13.9 - - + -
53F LEU* 3.8 26.7 - - + -
56F ILE* 5.6 0.4 - - + -
57F MET* 3.4 40.4 - - + -
60F LEU* 5.2 4.3 - - + -
62F VAL* 4.4 7.9 - - + -
63F SER 3.3 5.4 + - - +
64F ASP 3.7 2.7 - - - +
65F VAL 3.0 0.8 - - - -
66F VAL* 1.3 79.6 - - - +
68F PHE* 1.3 75.4 + + - +
69F GLU 3.4 0.4 - - - -
70F MET* 3.9 3.9 + - - +
71F LEU* 3.3 26.5 + - + +
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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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5E LEU* 3.8 26.2 - - + -
68E PHE* 3.8 24.7 - + + -
71E LEU* 3.5 29.6 - - + -
72E ILE* 4.2 20.6 - - + -
75E ILE* 4.9 6.1 - - + -
53F LEU* 4.7 10.5 - - + -
57F MET* 4.9 3.4 - - + -
64F ASP* 2.7 29.8 - - + -
65F VAL* 3.3 10.1 + - - +
67F PHE* 1.3 92.6 - + - +
69F GLU* 1.3 59.3 + - - +
71F LEU* 3.0 22.9 - - + +
72F ILE* 2.8 36.3 + - + +
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Residues in contact with GLU 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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72E ILE* 3.8 23.7 - - + +
76E LEU* 5.7 0.2 - - - +
65F VAL* 2.2 45.3 - - - +
66F VAL* 3.0 18.6 - - - +
68F PHE* 1.3 75.1 - - - +
70F MET* 1.3 56.5 + - - +
72F ILE* 3.0 11.1 + - + +
73F LYS* 2.8 46.7 + - + +
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Residues in contact with MET 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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12F VAL* 3.9 32.5 - - + +
15F LYS* 3.3 46.2 + - + +
16F ILE* 3.9 22.7 - - + -
19F GLU* 4.5 6.7 - - - +
66F VAL* 3.7 20.9 + - + +
67F PHE* 4.0 6.1 - - - +
69F GLU* 1.3 78.3 - - - +
71F LEU* 1.3 61.9 + - - +
73F LYS* 3.5 19.9 - - + +
74F GLU* 3.3 27.3 + - + +
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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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68E PHE* 3.8 32.3 - - + -
5F LEU* 4.9 0.7 - - + -
8F LYS* 4.5 5.8 - - + -
9F VAL* 4.0 37.7 - - + +
12F VAL* 4.2 13.4 - - + +
67F PHE* 3.3 20.5 + - + +
68F PHE* 3.0 31.2 - - + +
70F MET* 1.3 77.2 - - - +
72F ILE* 1.3 52.4 + - - +
74F GLU* 2.8 9.8 + - + +
75F ILE* 2.8 55.1 + - + +
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Residues in contact with ILE 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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65E VAL* 3.4 32.8 - - + +
68E PHE* 3.7 31.6 - - + -
69E GLU* 4.1 17.0 - - + +
72E ILE* 3.6 29.8 - - + -
68F PHE 2.8 24.0 + - - +
69F GLU* 3.5 8.5 - - + +
71F LEU* 1.3 68.7 - - - +
73F LYS* 1.3 65.5 + - - +
75F ILE* 3.4 10.5 + - - +
76F LEU* 3.2 28.7 + - + +
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Residues in contact with LYS 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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15F LYS* 6.2 1.3 - - - +
69F GLU* 2.8 30.8 + - + +
70F MET* 3.5 25.0 - - + +
72F ILE* 1.3 74.4 - - + +
74F GLU* 1.3 64.8 + - + +
76F LEU* 3.2 22.1 + - - +
77F LYS 4.4 1.0 + - - -
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Residues in contact with GLU 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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8F LYS* 4.0 21.6 + - + +
11F PHE* 3.1 40.2 - - + -
12F VAL* 4.3 12.3 - - + -
15F LYS* 4.0 20.1 + - + +
70F MET 3.3 12.3 + - - +
71F LEU* 2.8 13.5 + - - +
73F LYS* 1.3 74.5 - - + +
75F ILE* 1.3 66.3 + - + +
76F LEU 3.0 3.3 + - - -
77F LYS* 3.3 12.5 + - - -
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Residues in contact with ILE 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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64E ASP* 4.0 19.7 - - + +
65E VAL* 4.2 25.8 - - + +
68E PHE* 4.0 6.1 - - + -
4F PHE* 3.8 23.3 - - + -
5F LEU* 4.0 23.6 - - + -
8F LYS* 4.3 20.6 - - + -
71F LEU* 2.8 40.6 + - + +
72F ILE* 3.7 9.4 - - - +
73F LYS 3.2 0.4 - - - -
74F GLU* 1.3 77.7 - - - +
76F LEU* 1.3 60.6 + - + +
77F LYS* 3.0 17.5 + - - +
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Residues in contact with LEU 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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65E VAL* 4.3 26.0 - - + -
72F ILE* 3.2 29.6 - - + +
73F LYS* 3.2 12.0 + - - +
74F GLU 3.0 2.0 - - - -
75F ILE* 1.3 79.1 - - + +
77F LYS* 1.3 85.8 + - - +
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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