Contacts of the strand formed by residues 61 - 66 (chain G) in PDB entry 2N0A
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 GLU 61 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F THR* 3.2 3.7 + - - +
60F LYS 2.3 31.3 + - - +
61F GLU* 3.1 33.8 - - + +
62F GLN 3.1 8.7 + - - -
63F VAL 5.0 0.3 - - - +
64F THR* 5.3 3.6 + - - +
72F THR* 5.2 7.2 - - - +
59G THR* 3.6 19.9 + - - +
60G LYS* 1.3 71.5 - - - +
62G GLN* 1.3 67.2 + - - +
64G THR* 4.7 12.8 - - - +
72G THR* 4.9 9.5 + - - +
61H GLU* 3.0 30.0 - - + +
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Residues in contact with GLN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LYS* 4.6 16.1 - - + +
62F GLN* 3.1 31.2 + - - +
63F VAL 2.9 31.2 + - - +
60G LYS* 4.0 22.5 - - + +
61G GLU* 1.3 73.7 - - - +
63G VAL* 1.3 68.0 + - + +
61H GLU 3.1 8.5 + - - +
62H GLN* 3.1 41.7 - - - +
63H VAL* 5.1 2.3 - - - +
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Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLN* 5.1 2.9 - - + +
63F VAL* 3.3 23.3 - - + +
65F ASN* 5.3 1.1 - - - +
62G GLN* 1.3 86.6 - - + +
64G THR* 1.3 65.4 + - - +
65G ASN* 3.6 26.5 - - - +
62H GLN 2.9 19.7 + - - +
63H VAL* 3.3 17.6 - - + -
64H THR* 3.1 16.5 + - - -
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Residues in contact with THR 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL 3.1 10.9 + - - +
64F THR* 3.8 17.6 + - + -
65F ASN 2.8 30.4 + - - +
66F VAL* 5.3 3.4 - - + -
61G GLU* 4.7 18.7 - - - +
63G VAL* 1.3 75.7 + - - +
65G ASN* 1.3 68.7 + - - +
66G VAL* 4.2 19.1 - - + +
70G VAL* 5.4 6.5 - - + -
61H GLU* 5.3 4.2 + - - +
64H THR* 3.8 17.5 + - + +
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Residues in contact with ASN 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASN* 3.2 30.2 + - + +
63G VAL* 3.6 22.5 - - - +
64G THR* 1.3 83.4 - - - +
66G VAL* 1.3 63.4 + - - +
63H VAL* 5.3 1.4 - - - +
64H THR 2.8 13.7 + - - +
65H ASN* 3.2 23.6 + - + +
66H VAL 3.1 23.4 + - - +
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Residues in contact with VAL 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASN 3.1 7.3 + - - +
66F VAL* 3.4 8.8 - - + +
67F GLY 3.0 24.6 + - - -
64G THR* 4.2 14.4 - - + -
65G ASN* 1.3 80.0 - - - +
67G GLY* 1.3 61.6 + - - +
68G GLY 3.9 11.9 - - - +
69G ALA* 3.9 29.2 - - - +
70G VAL* 3.8 26.7 - - + -
64H THR* 5.3 3.8 - - + +
66H VAL* 3.4 16.4 - - + +
68H GLY 4.1 4.0 - - - +
70H VAL* 4.2 11.7 - - + -
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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