Contacts of the helix formed by residues 62 - 70 (chain C) in PDB entry 4KZZ
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 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.4 18.0 - - - +
61C LYS* 1.3 80.5 - - - +
63C LEU* 1.3 61.9 + - - +
64C GLU* 3.0 29.6 + - - +
65C GLU* 3.3 20.6 + - - +
66C ILE* 4.2 0.7 + - - +
82C PHE* 3.7 6.3 - - - -
83C LEU* 4.8 4.5 - - - -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER* 1.3 67.7 - - - +
64C GLU* 1.3 60.3 + - - +
65C GLU 3.0 3.1 - - - -
66C ILE* 2.8 28.4 + - + +
67C TYR* 2.5 80.5 + - + +
73C ILE* 5.4 2.2 - - + -
78C ILE* 5.0 0.4 - - + -
79C ILE* 4.5 27.6 - - + -
82C PHE* 3.7 22.0 - - + -
83C LEU* 3.3 41.7 - - + +
121C HIS* 4.3 2.0 - - + -
147C ILE* 4.6 2.9 - - + -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C SER* 3.0 19.5 - - - +
63C LEU* 1.3 90.8 + - - +
65C GLU* 1.3 60.6 + - - +
67C TYR* 3.5 18.6 - - - +
68C LEU* 2.7 36.6 + - + +
83C LEU* 4.8 1.7 - - - +
121C HIS* 3.5 24.2 + - - -
233C TYR* 5.7 1.2 + - - -
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LYS 6.0 0.2 - - - +
60C ILE* 4.0 19.3 - - + -
61C LYS* 5.0 9.6 - - - +
62C SER* 3.3 23.8 + - - +
63C LEU 3.0 0.2 - - - -
64C GLU* 1.3 81.6 - - - +
66C ILE* 1.3 62.5 + - + +
68C LEU* 3.5 2.6 + - - +
69C PHE* 2.9 50.1 + - - -
250C PRO* 4.2 19.2 - - + +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.9 37.7 - - + -
60C ILE* 4.9 6.1 - - + -
62C SER 4.8 3.6 - - - +
63C LEU* 2.8 29.2 + - + +
65C GLU* 1.3 76.6 - - - +
67C TYR* 1.3 63.5 + - + +
69C PHE 3.3 0.9 + - - -
70C SER* 2.6 31.7 + - - -
71C LEU* 3.0 49.7 + - + +
72C PRO 5.2 2.5 - - - +
73C ILE* 4.5 9.9 - - + -
78C ILE* 3.9 16.8 - - + -
82C PHE* 5.1 2.9 - - + -
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 2.5 71.9 + - + +
64C GLU* 3.5 24.9 - - - +
66C ILE* 1.3 83.4 - - + +
68C LEU* 1.3 61.6 + - - +
70C SER* 3.2 17.0 + - - +
121C HIS* 4.1 10.7 - + - -
147C ILE* 3.6 32.1 - - + +
149C PRO* 5.0 24.0 - - + -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLU* 2.7 21.2 + - + +
65C GLU* 3.9 5.2 - - - +
67C TYR* 1.3 73.0 - - - +
69C PHE* 1.3 65.3 + - + +
70C SER* 4.1 3.3 + - - -
246C PHE* 4.1 25.3 - - + +
247C THR* 3.0 38.4 - - + -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN* 4.5 5.4 - - - +
65C GLU* 2.9 40.0 + - - +
68C LEU* 1.3 79.1 - - + +
70C SER* 1.3 70.6 + - - +
71C LEU* 3.4 28.1 + - + +
247C THR* 1.9 57.2 - - + -
248C LYS 4.0 1.3 - - - -
249C SER* 2.9 33.0 - - - -
250C PRO* 3.1 25.1 - - + -
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASN* 3.1 31.6 + - - -
66C ILE* 2.6 14.7 + - - -
67C TYR* 3.2 14.9 + - - +
68C LEU 4.1 3.8 + - - -
69C PHE* 1.3 76.7 - - - +
71C LEU* 1.3 64.0 + - - +
72C PRO* 4.5 0.3 - - - +
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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