Contacts of the strand formed by residues 51 - 57 (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 VAL 51 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22R THR* 3.5 7.0 - - - +
24R VAL* 3.6 30.5 - - + -
41R ILE 4.8 2.2 - - - +
44R ALA* 3.7 22.0 - - + -
45R THR* 3.8 25.1 - - + +
49R GLY 2.7 14.8 + - - +
50R GLU* 1.3 71.0 - - - +
52R SER* 1.3 60.6 + - - +
53R CYS* 5.2 0.2 - - + -
72R GLY 3.2 23.3 + - - +
73R ILE* 3.5 17.6 - - + -
74R ALA* 2.7 33.2 + - - +
75R LYS 3.9 0.2 - - - +
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Residues in contact with SER 52 (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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21R SER* 4.9 1.4 - - - -
22R THR 2.9 8.8 + - - -
23R LEU* 2.9 26.3 - - - -
24R VAL 3.0 4.2 + - - -
50R GLU* 3.3 15.4 + - - +
51R VAL* 1.3 76.1 - - - +
53R CYS* 1.3 61.0 + - - +
75R LYS* 3.2 22.3 + - - +
77R LEU* 3.9 11.9 - - - -
105R TYR* 3.5 29.6 + - - -
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Residues in contact with CYS 53 (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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23R LEU* 3.9 1.1 - - - -
24R VAL* 3.1 25.1 - - + +
26R ALA* 4.2 13.7 - - - -
37R THR* 5.1 2.5 - - - -
41R ILE* 5.2 1.6 - - + -
52R SER* 1.3 77.2 - - - +
54R LEU* 1.3 59.9 + - - +
55R VAL 3.7 0.7 + - - -
67R LEU* 3.7 39.9 - - - -
73R ILE* 4.3 17.3 - - + -
75R LYS 2.9 13.7 + - - +
76R VAL* 3.5 6.3 - - - +
77R LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 54 (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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23R LEU* 3.3 20.6 - - + +
24R VAL 2.8 9.9 + - - +
25R ILE* 3.7 16.2 - - + +
26R ALA* 2.8 30.0 + - - +
53R CYS* 1.3 69.5 - - - +
55R VAL* 1.3 60.8 + - - +
56R ALA* 3.9 11.3 + - + +
77R LEU* 3.5 17.0 - - + +
79R ALA* 4.1 16.6 - - + -
92R LEU* 6.1 2.0 - - + -
95R LEU* 3.6 36.3 - - + -
96R ILE* 3.7 26.0 - - + -
99R THR* 4.7 6.5 - - + +
188R ALA* 4.2 9.2 - - + -
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Residues in contact with VAL 55 (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* 4.0 4.7 - - + -
28R HIS* 3.5 28.5 - - + +
53R CYS 3.7 0.6 + - - -
54R LEU* 1.3 72.5 - - - +
56R ALA* 1.3 57.4 + - - +
60R CYS* 3.5 18.0 - - + -
63R VAL* 4.3 16.4 - - + -
64R ALA* 3.7 28.9 - - + +
67R LEU* 3.9 12.6 - - + -
76R VAL* 4.1 8.5 - - + -
77R LEU 2.9 18.8 + - - +
78R VAL* 3.7 10.3 - - + -
79R ALA 3.0 21.2 + - - -
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Residues in contact with ALA 56 (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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25R ILE* 6.2 1.6 - - + -
26R ALA 5.9 0.4 + - - -
28R HIS* 2.6 30.5 + - - -
54R LEU* 3.9 17.4 + - + +
55R VAL* 1.3 73.4 - - - +
57R GLY* 1.3 58.1 + - - +
60R CYS* 3.6 3.4 - - - -
79R ALA* 3.4 19.3 - - + +
84R TYR* 4.6 2.0 - - + -
87R LEU* 3.3 9.7 - - + +
92R LEU* 3.7 33.0 - - + -
95R LEU* 4.8 2.0 - - + -
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Residues in contact with GLY 57 (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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28R HIS* 4.2 6.5 - - - -
56R ALA* 1.3 76.6 - - - +
58R THR* 1.3 59.2 + - - -
60R CYS* 3.4 8.0 - - - -
79R ALA 3.1 5.5 + - - -
80R GLN* 3.2 8.3 - - - -
81R HIS 2.8 32.7 + - - -
84R TYR* 3.6 18.0 - - - -
87R LEU* 4.5 3.8 - - - -
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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