Contacts of the helix formed by residues 65 - 71 (chain B) in PDB entry 2UUY
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 ARG 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B TYR* 3.7 3.6 - - - -
63B TYR* 3.6 8.3 - - - +
64B SER* 1.3 101.1 + - - +
66B MET* 1.3 66.6 + - - +
68B GLU* 3.2 40.0 + - + +
69B CYS* 3.2 9.9 + - - +
1076B CL 4.3 13.9 - - + -
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Residues in contact with MET 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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45B TYR* 3.4 51.4 - - + -
52B CYS* 3.6 39.3 - - - +
53B LYS 4.9 0.2 - - - +
54B VAL* 5.0 4.0 - - + +
65B ARG* 1.3 71.4 - - - +
67B GLY* 1.3 58.2 + - - +
69B CYS* 3.1 4.9 + - - +
70B ALA* 2.8 32.1 + - + +
1076B CL 3.9 10.0 - - + +
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Residues in contact with GLY 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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65B ARG 3.2 0.2 - - - -
66B MET* 1.3 81.0 - - - +
68B GLU* 1.3 64.7 + - - +
70B ALA* 3.9 7.3 - - - +
71B ARG* 3.2 26.9 + - - +
1076B CL 3.2 18.4 - - - +
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Residues in contact with GLU 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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63B TYR* 3.7 23.8 - - + -
65B ARG* 3.2 42.5 + - + +
67B GLY* 1.3 77.1 - - - +
69B CYS* 1.3 63.2 + - - +
71B ARG* 2.9 46.9 + - - +
72B ASN* 2.8 28.6 + - - -
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Residues in contact with CYS 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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45B TYR* 3.5 25.6 - - + -
46B TYR 3.5 4.3 - - - -
47B CYS* 3.4 23.6 - - - -
52B CYS* 2.0 50.2 - - + -
63B TYR* 3.6 22.0 - - + -
65B ARG 3.2 6.1 + - - +
66B MET 3.1 8.4 + - - +
68B GLU* 1.3 76.0 - - - +
70B ALA* 1.3 58.0 + - - +
72B ASN* 2.9 28.6 + - - +
73B CYS* 3.3 1.4 + - - +
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Residues in contact with ALA 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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52B CYS* 3.7 12.1 - - + +
66B MET* 2.8 26.6 + - + +
67B GLY* 3.9 7.9 - - - +
68B GLU 3.3 0.4 - - - -
69B CYS* 1.3 73.6 - - - +
71B ARG* 1.3 62.8 + - - +
72B ASN 3.1 1.2 + - - -
73B CYS* 3.2 21.6 + - - +
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Residues in contact with ARG 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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67B GLY 3.2 11.1 + - - +
68B GLU* 2.9 51.9 + - - +
70B ALA* 1.3 76.0 - - - +
72B ASN* 1.3 72.2 + - - +
73B CYS 3.5 1.5 + - - -
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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