Contacts of the helix formed by residues 63 - 72 (chain B) in PDB entry 1YQZ
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B MET* 4.0 2.9 - - - -
60B LEU* 5.1 9.9 - - + -
62B TYR* 1.3 77.2 - - - +
64B PRO* 1.3 76.8 - - + +
65B GLU* 3.6 9.3 + - - +
66B LYS* 3.1 41.2 + - - +
67B PHE* 2.9 20.6 + - - +
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Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG 5.6 1.6 - - - +
37B ASP* 6.3 0.2 - - - -
38B MET* 3.9 22.0 - - + +
63B THR* 1.3 86.8 - - - +
65B GLU* 1.3 64.2 + - + +
67B PHE* 3.3 2.2 + - + +
68B TYR* 3.0 25.6 + - - +
73B ILE 4.7 1.7 - - - +
75B VAL* 3.3 29.7 + - + +
77B THR* 3.8 33.0 - - + +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B THR* 3.1 10.4 + - - +
64B PRO* 1.3 81.1 - - + +
66B LYS* 1.3 59.1 + - + +
68B TYR* 3.4 5.2 + - - +
69B ASP* 3.0 37.2 + - - +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 5.5 4.2 + - - +
61B ALA 3.9 8.8 + - - +
62B TYR* 3.9 27.1 - - + +
63B THR* 3.1 41.3 + - - +
65B GLU* 1.3 77.2 - - + +
67B PHE* 1.3 61.4 + - - +
69B ASP* 3.3 8.2 + - - +
70B ARG* 3.0 31.5 + - - +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA* 4.0 21.3 - - + -
18B SER* 4.5 0.7 - - - -
31B ILE* 4.2 5.8 - - + -
38B MET* 3.5 22.9 - - + -
62B TYR* 3.6 27.1 - + + -
63B THR 2.9 15.1 + - - +
64B PRO* 3.7 4.5 - - + +
66B LYS* 1.3 76.9 - - - +
68B TYR* 1.3 58.2 + - - +
70B ARG* 4.8 0.2 - - - -
71B LYS* 2.8 62.4 + - + +
72B GLN 3.6 0.3 + - - -
73B ILE* 3.6 42.7 + - + +
75B VAL* 3.5 21.3 - - + -
442B COA 3.7 24.2 - - + -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PRO 3.0 16.8 + - - +
65B GLU* 3.7 6.1 - - - +
67B PHE* 1.3 75.5 - - - +
69B ASP* 1.3 73.6 + - - +
72B GLN* 2.8 54.0 + - + +
73B ILE 3.5 26.4 + - - +
74B THR* 3.7 21.1 - - + -
75B VAL 5.9 0.2 - - - +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU* 3.0 25.7 + - - +
66B LYS* 3.3 8.6 + - - +
68B TYR* 1.3 86.9 - - - +
70B ARG* 1.3 56.2 + - - +
72B GLN* 3.2 15.3 - - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B TYR* 3.1 32.3 + - + -
66B LYS 3.0 17.4 + - - +
67B PHE 4.2 0.9 - - - +
69B ASP* 1.3 79.5 - - - +
71B LYS* 1.3 91.6 + - + +
72B GLN* 3.7 8.5 + - - -
442B COA 5.1 16.3 + - - -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.0 32.5 + - - +
21B ARG* 2.9 39.3 + - + +
22B ARG* 6.0 2.0 - - - +
62B TYR* 3.6 22.4 + - - -
67B PHE* 2.8 49.2 + - + +
70B ARG* 1.3 105.9 - - + +
72B GLN* 1.3 68.2 + - - +
73B ILE* 3.2 14.0 + - + +
442B COA 3.1 17.4 + - - -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.0 25.8 + - - +
29B ILE 4.8 2.1 + - - +
68B TYR* 2.8 48.4 + - + +
69B ASP* 3.2 21.8 - - - +
70B ARG 3.7 5.7 + - - -
71B LYS* 1.3 82.1 + - - +
73B ILE* 1.3 58.0 + - - +
74B THR* 4.2 0.7 + - - -
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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