Contacts of the helix formed by residues 60 - 66 (chain F) in PDB entry 3IZ0
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 ARG 60 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214E GLU 5.7 3.0 + - - -
54F GLN* 3.3 8.5 - - - +
58F GLY 5.1 8.5 + - - -
59F ILE* 1.3 76.6 - - - +
61F LEU* 1.3 68.0 + - - +
62F GLU* 2.9 30.1 + - + -
63F HIS* 2.8 51.5 + - + +
64F PHE* 3.4 7.4 - - - -
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Residues in contact with LEU 61 (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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107C GLY* 2.9 39.7 - - - +
108C TYR 4.6 1.6 - - - +
109C ALA* 4.5 18.4 - - + -
50F MET* 4.0 23.3 - - + -
54F GLN* 3.0 14.9 - - - +
60F ARG* 1.3 73.6 - - - +
62F GLU* 1.3 57.3 + - - +
64F PHE* 2.9 26.6 + - - +
65F TYR* 3.3 33.5 - - + +
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Residues in contact with GLU 62 (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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60F ARG* 2.9 38.2 + - + -
61F LEU* 1.3 79.7 - - - +
63F HIS* 1.3 74.3 + - + +
64F PHE 3.1 0.4 - - - -
65F TYR* 3.1 28.7 + - - +
66F MET* 3.7 17.7 - - + +
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Residues in contact with HIS 63 (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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211E TRP 4.6 22.3 + - - -
58F GLY 5.6 0.6 + - - -
59F ILE* 4.1 26.7 - - + +
60F ARG* 2.8 63.1 + - - +
62F GLU* 1.3 89.3 + - + +
64F PHE* 1.3 59.9 + - + +
65F TYR 3.1 2.0 + - - -
66F MET* 3.0 37.6 + - + +
87F ASN* 3.8 10.2 + - - +
91F HIS* 4.8 6.6 - - + -
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Residues in contact with PHE 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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50F MET* 3.5 40.4 - - + -
53F LEU* 4.2 17.9 - - + -
54F GLN* 4.3 4.5 - - + -
59F ILE* 3.6 30.7 - - + -
60F ARG 3.4 11.7 - - - -
61F LEU* 2.9 14.0 + - - +
63F HIS* 1.3 78.8 - - + +
65F TYR* 1.3 61.3 + - + +
84F PRO* 3.0 43.0 - - + +
87F ASN* 3.2 15.7 - - + +
88F LEU* 3.9 35.4 - - + -
91F HIS* 3.9 18.8 - - - -
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Residues in contact with TYR 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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109C ALA 5.0 8.3 + - - -
50F MET* 6.2 0.2 - - - -
61F LEU* 3.3 45.2 - - + +
62F GLU* 3.1 13.6 + - - +
64F PHE* 1.3 85.5 - - + +
66F MET* 1.3 67.1 + - + +
67F MET* 3.5 2.1 + - - +
80F GLU* 3.7 45.1 - - + -
83F LEU* 3.4 19.3 - - + +
84F PRO* 3.9 19.7 - - + +
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Residues in contact with MET 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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198E MET* 4.3 0.5 - - - +
202E SER* 3.8 23.7 + - - +
62F GLU* 3.7 20.2 - - + +
63F HIS* 3.0 38.6 + - + +
64F PHE 3.6 2.0 - - - -
65F TYR* 1.3 79.8 - - + +
67F MET* 1.3 59.4 + - - +
68F PRO* 3.6 9.5 - - - +
83F LEU* 3.7 6.4 - - - +
87F ASN* 3.4 17.2 + - - +
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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