Contacts of the strand formed by residues 61 - 66 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C THR* 3.2 4.0 + - - +
60C LYS 2.3 31.6 + - - +
61C GLU* 3.0 32.8 - - + +
62C GLN 3.1 9.2 + - - -
64C THR* 5.4 3.9 + - - +
72C THR* 5.3 6.7 - - - +
59D THR* 3.6 20.8 + - - +
60D LYS* 1.3 71.3 - - - +
62D GLN* 1.3 68.1 + - - +
63D VAL 4.0 0.2 - - - -
64D THR* 4.7 13.0 - - - +
72D THR* 4.9 10.0 + - - +
61E GLU* 3.0 31.6 - - + +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 4.6 14.6 - - + +
62C GLN* 3.1 30.7 + - - +
63C VAL 2.9 31.5 + - - +
60D LYS* 4.0 22.9 - - + +
61D GLU* 1.3 74.2 - - - +
63D VAL* 1.3 69.2 + - + +
61E GLU 3.1 8.0 + - - +
62E GLN* 3.1 41.0 - - - +
63E VAL* 5.1 2.7 - - + +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 5.1 2.2 - - - +
63C VAL* 3.3 23.1 - - + +
65C ASN* 5.4 0.9 - - - +
62D GLN* 1.3 87.3 - - + +
64D THR* 1.3 64.7 + - - +
65D ASN* 3.6 26.0 - - - +
62E GLN 2.9 19.0 + - - +
63E VAL* 3.3 17.6 - - + -
64E THR* 3.1 16.6 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL 3.1 10.2 + - - +
64C THR* 3.8 17.8 + - + -
65C ASN 2.8 30.0 + - - +
66C VAL* 5.3 2.9 - - + -
61D GLU* 4.7 18.5 - - - +
63D VAL* 1.3 75.4 + - - +
65D ASN* 1.3 68.3 + - - +
66D VAL* 4.2 18.8 - - + +
70D VAL* 5.4 6.7 - - + -
61E GLU* 5.3 4.0 + - - +
62E GLN 5.3 0.3 + - - -
64E THR* 3.8 17.8 + - + +
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Residues in contact with ASN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ASN* 3.3 30.1 + - + +
63D VAL* 3.6 22.9 - - - +
64D THR* 1.3 82.3 - - - +
66D VAL* 1.3 62.8 + - - +
63E VAL* 5.3 1.6 - - - +
64E THR 2.8 12.3 + - - +
65E ASN* 3.2 23.5 + - + +
66E VAL 3.1 24.0 + - - +
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASN 3.1 7.6 + - - +
66C VAL* 3.4 9.6 - - + +
67C GLY 3.0 24.3 + - - -
64D THR* 4.2 15.0 - - + -
65D ASN* 1.3 79.9 - - - +
67D GLY* 1.3 63.0 + - - +
68D GLY 3.9 11.4 - - - +
69D ALA* 3.9 29.6 - - - +
70D VAL* 3.9 27.1 - - + -
64E THR* 5.3 3.4 - - + +
66E VAL* 3.4 13.0 - - + +
68E GLY 4.1 3.8 - - - +
70E VAL* 4.2 14.6 - - + -
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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