Contacts of the helix formed by residues 62 - 72 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY* 4.6 0.4 - - - -
22A LYS* 4.1 11.0 - - + +
23A ASP* 3.5 21.8 - - + +
60A GLY 3.5 1.5 + - - +
61A MET* 1.3 78.1 - - - +
63A HIS* 1.3 64.9 + - - +
64A LEU* 3.7 6.6 + - - +
65A GLU* 2.9 44.7 + - - +
66A ALA* 3.0 19.6 + - - +
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.1 43.3 + - + +
19A GLN* 3.7 6.3 - - - -
20A GLY 2.7 30.0 + - - +
21A GLY* 4.2 0.2 - - - -
23A ASP* 3.0 22.5 + - - +
24A PHE* 4.1 11.0 - + + -
28A LEU* 4.3 7.4 - - + +
61A MET 3.9 0.4 + - - -
62A THR* 1.3 71.7 - - - +
64A LEU* 1.3 57.8 + - - +
66A ALA* 3.3 3.5 + - - +
67A GLN* 3.0 63.4 + - + +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 5.2 0.6 + - - -
62A THR* 3.3 6.3 + - - +
63A HIS* 1.3 76.3 - - - +
65A GLU* 1.3 60.2 + - + +
67A GLN* 3.8 17.5 - - + +
68A ASN* 2.8 54.1 + - - +
71A LYS* 5.8 2.2 - - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLY 4.6 1.0 - - - +
61A MET* 3.5 21.8 - - + +
62A THR* 2.9 48.2 + - - +
64A LEU* 1.3 77.3 - - + +
66A ALA* 1.3 57.8 + - - +
68A ASN* 3.4 7.1 + - - +
69A LYS* 2.9 29.1 + - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 7.0 - - + -
28A LEU* 3.4 38.4 - - + -
53A ILE* 4.0 10.5 - - + -
61A MET* 3.8 13.6 - - - -
62A THR 3.0 11.3 + - - +
63A HIS 3.7 6.7 - - - +
65A GLU* 1.3 74.9 - - - +
67A GLN* 1.3 57.7 + - - +
69A LYS* 3.2 3.7 + - - +
70A ILE* 2.9 36.0 + - - +
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 5.9 3.0 - - - +
18A LEU* 4.8 12.8 + - + +
63A HIS* 3.0 48.1 + - + +
64A LEU* 3.7 23.0 - - + +
66A ALA* 1.3 73.7 - - - +
68A ASN* 1.3 58.8 + - - +
70A ILE* 3.2 9.8 + - - +
71A LYS* 2.8 56.2 + - - +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 2.8 51.1 + - - +
65A GLU* 3.7 7.1 - - - +
67A GLN* 1.3 71.1 - - - +
69A LYS* 1.3 65.6 + - - +
71A LYS* 3.3 13.9 + - - +
72A GLY* 2.9 21.3 + - - -
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.6 30.7 - - + -
54A ASP* 4.4 12.9 + - - +
56A ILE* 3.6 31.9 - - + +
61A MET* 4.4 16.2 - - + -
65A GLU 2.9 18.1 + - - +
66A ALA* 3.5 7.6 - - - +
68A ASN* 1.3 74.7 - - - +
70A ILE* 1.3 63.2 + - - +
72A GLY* 3.2 10.8 + - - -
73A CYS* 3.4 15.7 + - - -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.7 32.3 + - + -
16A PHE* 3.9 21.1 - - + -
18A LEU* 3.7 28.7 - - + -
50A VAL* 5.9 0.4 - - + -
53A ILE* 4.1 26.2 - - + -
66A ALA 2.9 17.7 + - - +
67A GLN* 3.6 9.0 - - - +
69A LYS* 1.3 77.3 - - - +
71A LYS* 1.3 62.2 + - + +
73A CYS* 3.3 24.1 + - - +
77A LEU* 3.9 13.9 - - + -
79A MET* 4.6 5.4 - - - -
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 5.5 1.1 - - - +
64A LEU* 5.8 1.8 - - - +
67A GLN* 2.8 49.1 + - - +
68A ASN* 3.3 14.4 + - - +
70A ILE* 1.3 74.7 - - + +
72A GLY* 1.3 62.0 + - - +
73A CYS 3.2 6.6 + - - +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN 2.9 14.2 + - - -
69A LYS* 3.2 6.2 + - - -
71A LYS* 1.3 75.8 - - - +
73A CYS* 1.3 62.4 + - - +
74A THR* 3.2 6.1 + - - -
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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