Contacts of the helix formed by residues 62 - 72 (chain C) in PDB entry 2UZC
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 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C LYS* 4.1 16.4 - - + +
23C ASP* 3.4 28.7 - - + +
60C GLY 3.7 0.4 + - - -
61C MET* 1.3 79.4 - - - +
63C HIS* 1.3 64.9 + - - +
64C LEU* 3.6 6.3 + - - +
65C GLU* 2.8 45.7 + - - +
66C ALA* 3.0 19.5 + - - +
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Residues in contact with HIS 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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18C LEU* 3.1 43.7 + - + +
19C GLN* 3.9 3.3 - - - -
20C GLY 2.8 33.5 + - - +
21C GLY* 4.2 1.3 - - - -
23C ASP* 2.9 17.1 + - - +
24C PHE* 3.9 13.8 - + + -
28C LEU* 4.5 4.3 - - + +
61C MET 3.9 0.2 + - - -
62C THR* 1.3 70.5 - - - +
64C LEU* 1.3 61.5 + - + +
66C ALA* 3.2 7.3 + - - +
67C GLN* 2.9 45.2 + - + +
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Residues in contact with LEU 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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23C ASP* 5.0 1.4 + - - +
62C THR* 3.3 7.1 + - - +
63C HIS* 1.3 82.4 - - + +
65C GLU* 1.3 52.0 + - - +
67C GLN* 3.2 22.3 + - - +
68C ASN* 2.8 64.6 + - - +
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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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22C LYS* 5.8 0.2 - - - +
60C GLY 4.1 2.9 - - - +
61C MET* 3.4 19.6 - - + +
62C THR* 2.8 49.9 + - - +
64C LEU* 1.3 76.2 - - + +
66C ALA* 1.3 58.1 + - - +
68C ASN* 3.3 10.7 + - - +
69C LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 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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18C LEU* 4.5 3.6 - - + -
28C LEU* 3.6 38.6 - - + -
53C ILE* 4.0 8.0 - - + +
61C MET* 3.8 16.5 - - + -
62C THR 3.0 12.7 + - - +
63C HIS 3.6 7.4 - - - +
65C GLU* 1.3 75.7 - - - +
67C GLN* 1.3 64.3 + - - +
69C LYS* 3.2 2.6 + - - +
70C ILE* 3.0 29.7 + - - +
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Residues in contact with GLN 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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18C LEU* 5.0 5.3 - - + +
63C HIS* 2.9 35.9 + - + +
64C LEU* 3.5 23.8 - - - +
66C ALA* 1.3 76.2 - - - +
68C ASN* 1.3 60.5 + - - +
70C ILE* 3.3 9.3 + - + +
71C LYS* 2.8 63.7 + - + +
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Residues in contact with ASN 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 LEU* 2.8 50.6 + - - +
65C GLU* 3.5 9.8 - - - +
67C GLN* 1.3 77.5 + - - +
69C LYS* 1.3 57.2 + - - +
71C LYS* 3.5 9.1 + - - +
72C GLY* 2.9 27.2 + - - -
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Residues in contact with LYS 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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53C ILE* 3.6 42.7 - - + +
54C ASP* 4.2 18.3 + - - +
56C ILE* 3.9 21.4 - - + +
61C MET* 4.5 14.1 - - + -
65C GLU 2.9 17.2 + - - +
66C ALA* 3.5 9.0 - - - +
68C ASN* 1.3 75.5 - - - +
70C ILE* 1.3 62.3 + - - +
72C GLY* 3.3 3.7 + - - -
73C CYS* 3.3 18.7 + - - +
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Residues in contact with ILE 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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14C TRP* 3.7 33.6 + - + +
16C PHE* 3.9 20.0 - - + -
18C LEU* 3.6 28.9 - - + -
50C VAL* 6.0 0.2 - - + -
53C ILE* 3.9 28.5 - - + -
66C ALA 3.0 17.9 + - - +
67C GLN* 3.7 5.2 - - - +
69C LYS* 1.3 73.0 - - - +
71C LYS* 1.3 69.2 + - + +
73C CYS* 3.2 19.8 + - - +
77C LEU* 4.1 17.0 - - + -
79C MET* 4.7 3.8 - - - -
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Residues in contact with LYS 71 (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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67C GLN* 2.8 55.0 + - + +
68C ASN* 4.0 8.7 - - - +
70C ILE* 1.3 74.5 - - + +
72C GLY* 1.3 57.1 + - - +
73C CYS 3.3 4.4 + - - +
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Residues in contact with GLY 72 (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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68C ASN 2.9 17.4 + - - -
69C LYS* 3.3 5.1 + - - -
70C ILE 3.1 0.4 - - - -
71C LYS* 1.3 74.9 - - - +
73C CYS* 1.3 66.8 + - - +
74C THR* 3.3 7.4 + - - -
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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