Contacts of the helix formed by residues 62 - 73 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D GLY* 4.7 0.7 - - - -
22D LYS* 4.0 8.5 - - + +
23D ASP* 3.4 31.0 - - + +
60D GLY 3.7 0.6 + - - +
61D MET* 1.3 79.7 - - - +
63D HIS* 1.3 66.0 + - - +
64D LEU* 3.6 7.5 + - - +
65D GLU* 2.8 47.4 + - - +
66D ALA* 3.1 19.3 + - - +
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Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ARG* 6.1 1.2 - - - +
46B ILE* 3.6 46.1 + - + +
85B SER* 6.0 0.8 - - - -
18D LEU* 3.1 44.9 + - + +
19D GLN* 3.7 5.8 - - - -
20D GLY 2.9 30.3 + - - +
21D GLY* 4.3 0.4 - - - -
23D ASP* 3.0 11.4 + - - +
24D PHE* 4.2 3.5 - - + -
28D LEU* 4.2 9.8 - - + +
61D MET 4.0 0.2 + - - -
62D THR* 1.3 73.7 - - - +
64D LEU* 1.3 60.0 + - - +
66D ALA* 3.2 3.8 + - - +
67D GLN* 2.9 47.2 + - + +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 3.6 32.1 - - - +
30B ILE 5.0 4.0 - - - +
31B SER* 3.7 24.5 - - - +
46B ILE* 3.9 26.1 - - + +
47B GLY* 5.1 2.5 - - - +
23D ASP* 4.9 1.3 + - - +
62D THR* 3.3 7.9 + - - +
63D HIS* 1.3 80.0 - - - +
65D GLU* 1.3 58.8 + - + +
67D GLN* 3.3 13.2 + - - +
68D ASN* 2.9 53.3 + - - +
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLY 4.3 2.1 - - - +
61D MET* 3.4 17.9 - - + +
62D THR* 2.8 55.3 + - - +
64D LEU* 1.3 76.7 - - + +
66D ALA* 1.3 63.6 + - - +
68D ASN* 3.3 7.8 + - - +
69D LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 4.2 10.5 - - + -
28D LEU* 3.6 31.2 - - + -
53D ILE* 3.9 14.1 - - + -
61D MET* 3.8 13.6 - - - -
62D THR 3.1 8.7 + - - +
63D HIS 3.6 7.0 - - - +
65D GLU* 1.3 73.5 - - - +
67D GLN* 1.3 68.4 + - - +
69D LYS* 3.3 3.3 + - - +
70D ILE* 3.0 29.0 + - - +
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Residues in contact with GLN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.0 25.0 + - - -
47B GLY* 3.2 24.1 + - - -
84B GLU 4.5 1.1 - - - -
85B SER* 4.0 13.7 + - - +
87B LEU* 3.6 30.1 - - + +
18D LEU* 5.0 2.4 - - + +
63D HIS* 2.9 34.9 + - + +
64D LEU* 3.5 14.3 - - - +
65D GLU 3.3 0.2 - - - -
66D ALA* 1.3 78.0 - - - +
68D ASN* 1.3 59.4 + - - +
70D ILE* 3.3 6.5 + - - +
71D LYS* 2.8 48.3 + - + +
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Residues in contact with ASN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 5.4 5.0 + - - +
64D LEU* 2.9 45.5 + - - +
65D GLU* 3.7 6.3 - - - +
67D GLN* 1.3 76.3 - - - +
69D LYS* 1.3 64.6 + - - +
71D LYS* 3.5 13.2 + - - +
72D GLY* 3.0 20.3 + - - -
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ILE* 3.6 28.9 - - + +
54D ASP* 4.6 9.6 - - + +
56D ILE* 3.7 29.8 - - + -
61D MET* 3.8 20.4 - - + -
65D GLU 3.0 14.2 + - - +
66D ALA* 3.3 10.1 + - - +
68D ASN* 1.3 76.2 - - - +
70D ILE* 1.3 60.0 + - - +
72D GLY* 3.3 10.3 + - - -
73D CYS* 3.4 15.9 + - - -
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.8 22.2 - - + -
14D TRP* 3.6 33.0 + - + +
16D PHE* 3.7 21.5 - - + -
18D LEU* 3.8 24.2 - - + -
50D VAL* 6.2 0.2 - - + -
53D ILE* 3.8 30.1 - - + -
66D ALA 3.0 20.4 + - - +
67D GLN 3.7 3.4 - - - +
69D LYS* 1.3 74.4 - - - +
71D LYS* 1.3 64.0 + - - +
73D CYS* 3.2 18.2 + - - +
77D LEU* 4.0 18.2 - - + -
79D MET* 4.7 2.5 - - - -
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLY* 4.6 3.8 + - - -
84B GLU* 2.5 43.7 + - - +
86B ASP 5.2 1.8 - - - -
87B LEU* 3.8 23.6 - - + -
14D TRP* 5.5 1.1 - - - +
67D GLN* 2.8 35.2 + - + +
68D ASN* 3.8 13.2 - - - +
70D ILE* 1.3 75.4 - - - +
72D GLY* 1.3 60.4 + - - +
73D CYS 3.5 7.1 + - - +
74D THR* 5.4 1.2 - - - +
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASN 3.0 15.1 + - - -
69D LYS* 3.3 5.8 + - - -
70D ILE 3.2 0.4 - - - -
71D LYS* 1.3 74.6 - - - +
73D CYS* 1.3 62.0 + - - +
74D THR* 3.7 12.2 + - - +
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Residues in contact with CYS 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 5.5 2.3 + - - +
14D TRP* 4.0 15.0 + - + -
54D ASP* 4.4 26.7 - - - -
69D LYS* 3.5 15.7 - - - -
70D ILE 3.2 12.2 + - - +
71D LYS 3.6 8.3 - - - +
72D GLY* 1.3 78.3 - - - +
74D THR* 1.3 62.2 + - - +
76D SER 3.3 18.8 - - - +
77D LEU* 3.8 23.6 - - + -
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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