Contacts of the helix formed by residues 60 - 70 (chain R) in PDB entry 2A1T
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 CYS 60 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R HIS* 4.9 4.5 - - - -
55R VAL* 3.5 26.5 - - + -
56R ALA 3.6 3.6 - - - -
57R GLY* 3.4 37.7 - - - -
59R LYS* 1.3 78.2 - - - +
61R ASP* 1.3 55.6 + - - +
62R LYS 2.7 1.7 + - - -
63R VAL* 2.7 35.5 + - - +
64R ALA 3.4 4.6 + - - -
78R VAL* 3.7 17.9 - - + -
79R ALA 3.4 18.4 - - - -
80R GLN* 3.5 10.9 + - - +
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Residues in contact with ASP 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R LYS 4.2 3.8 - - - +
60R CYS* 1.3 72.4 - - - +
62R LYS* 1.3 86.6 + - - +
63R VAL 3.1 0.4 - - - -
64R ALA* 3.4 15.9 - - + -
65R GLN* 2.7 26.5 + - - +
78R VAL* 5.2 5.2 - - + -
80R GLN* 3.9 13.5 + - - +
187R LYS* 6.3 0.7 - - - +
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Residues in contact with LYS 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R ASP* 2.8 39.5 - - + +
59R LYS 4.0 2.0 - - - +
60R CYS 2.7 5.9 + - - +
61R ASP* 1.3 84.8 + - - +
63R VAL* 1.3 59.6 + - + +
65R GLN* 3.6 7.6 + - - +
66R ASP* 3.6 18.3 - - - +
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Residues in contact with VAL 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 4.0 24.2 - - + +
31R ASP* 3.6 11.9 - - - -
32R SER* 3.2 35.9 - - - +
33R LEU* 3.4 35.4 - - + +
55R VAL* 4.3 10.1 - - + -
59R LYS 5.1 1.8 - - - +
60R CYS 2.7 15.4 + - - +
62R LYS* 1.3 72.7 - - + +
64R ALA* 1.3 63.3 + - - +
65R GLN 3.1 1.8 - - - -
66R ASP* 3.2 18.0 + - + +
67R LEU* 3.4 11.7 + - + +
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Residues in contact with ALA 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R VAL* 3.7 29.1 - - + +
60R CYS 3.4 3.4 + - - -
61R ASP* 3.0 22.9 + - + +
63R VAL* 1.3 78.0 - - - +
65R GLN* 1.3 60.8 + - - +
67R LEU* 3.6 5.7 + - - +
68R CYS* 3.3 27.6 + - - -
76R VAL* 3.8 6.1 - - + +
78R VAL* 3.7 17.0 - - + -
185R SER* 5.8 1.3 - - - -
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Residues in contact with GLN 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R ASP 2.7 19.7 + - - +
62R LYS* 3.6 8.1 - - - +
63R VAL 3.1 0.2 - - - -
64R ALA* 1.3 70.0 - - - +
66R ASP* 1.3 70.7 + - - +
68R CYS* 3.4 18.5 + - - +
69R LYS* 3.5 11.3 + - - +
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Residues in contact with ASP 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R ASP 5.6 1.4 - - - +
32R SER* 5.5 2.4 - - - -
33R LEU* 5.1 17.8 + - + +
62R LYS 3.6 16.1 - - - +
63R VAL* 3.2 12.1 + - - +
65R GLN* 1.3 76.5 - - - +
67R LEU* 1.3 58.9 + - - +
68R CYS 3.1 1.3 - - - -
69R LYS* 2.8 27.0 + - - +
70R VAL* 3.2 16.1 + - + +
178R THR 3.9 1.4 - - - +
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Residues in contact with LEU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R ALA* 4.3 1.6 - - + -
33R LEU* 3.6 44.6 - - + +
37R THR* 4.6 1.3 - - + -
41R ILE* 4.1 18.2 - - + -
53R CYS* 3.7 32.3 - - + -
55R VAL* 3.9 25.1 - - + -
63R VAL 3.4 9.1 + - - +
64R ALA 3.7 6.3 - - - +
65R GLN 3.5 0.2 - - - -
66R ASP* 1.3 75.7 - - - +
68R CYS* 1.3 62.1 + - - +
70R VAL* 3.1 22.9 + - + +
73R ILE* 3.8 15.8 - - + +
76R VAL* 3.9 18.6 - - + -
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Residues in contact with CYS 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R ALA 3.3 16.5 + - - +
65R GLN* 3.5 13.7 - - - +
66R ASP 3.0 0.6 + - - -
67R LEU* 1.3 80.7 - - - +
69R LYS* 1.3 57.0 + - + +
70R VAL 3.4 0.9 + - - +
76R VAL* 3.6 19.1 - - - -
181R GLY 3.0 14.0 - - - +
182R SER* 3.2 2.6 - - - -
183R ALA* 3.1 48.0 + - - +
185R SER* 3.9 14.8 - - - -
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Residues in contact with LYS 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R GLN 3.5 8.9 + - - +
66R ASP* 2.8 12.9 + - - +
68R CYS* 1.3 73.4 - - + +
70R VAL* 1.3 55.7 + - - +
178R THR 3.2 9.9 - - - +
179R SER* 3.2 12.4 - - - -
180R GLY 3.0 23.4 + - - +
181R GLY 2.6 23.5 - - - +
182R SER* 5.0 1.1 - - - +
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R LEU* 5.5 2.0 - - + -
38R LEU* 4.0 23.8 - - + -
41R ILE* 4.1 12.1 - - + -
66R ASP* 3.3 14.6 - - + +
67R LEU* 3.1 24.0 + - + +
68R CYS 3.9 3.1 - - - +
69R LYS* 1.3 78.4 - - - +
71R ALA* 1.3 70.4 + - - +
72R GLY 3.6 3.0 + - - -
73R ILE* 3.7 26.6 + - + +
176R ALA* 4.8 2.5 - - + -
177R ALA 3.4 7.2 - - - +
178R THR* 3.3 24.5 - - - +
181R GLY 3.2 15.1 - - - +
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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