Contacts of the strand formed by residues 70 - 78 (chain F) 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 VAL 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E VAL* 4.2 6.7 - - + -
69E ALA 3.2 2.8 + - - +
70E VAL* 3.2 29.6 - - + +
71E VAL 3.2 21.1 + - - -
64F THR* 5.4 7.0 - - + -
66F VAL* 3.8 23.3 - - + -
69F ALA* 1.3 76.5 - - - +
71F VAL* 1.3 66.3 + - - +
72F THR* 4.0 20.6 - - + -
70G VAL* 3.2 34.1 - - + +
71G VAL* 5.6 0.4 - - - -
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E VAL* 5.6 0.2 - - - -
71E VAL* 3.3 17.5 - - + +
92E THR* 3.0 35.0 - - - +
70F VAL* 1.3 79.4 - - - +
72F THR* 1.3 69.3 + - - +
75F THR* 4.2 17.7 - - - +
92F THR* 3.6 19.1 - - - +
93F GLY* 3.4 20.9 - - - +
70G VAL 3.2 6.9 + - - -
71G VAL* 3.3 13.1 - - + +
72G THR 3.1 22.5 + - - +
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E VAL 3.1 6.0 + - - +
72E THR* 3.1 27.6 - - + +
73E GLY 3.2 21.1 + - - +
61F GLU* 4.9 7.6 + - - +
70F VAL* 4.0 19.5 + - + -
71F VAL* 1.3 81.5 - - - +
73F GLY* 1.3 60.8 + - - +
74F VAL 4.3 0.4 + - - -
61G GLU* 5.2 7.6 - - - +
72G THR* 3.1 28.3 - - + +
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Residues in contact with GLY 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLY* 3.3 9.4 - - - -
71F VAL* 6.4 0.2 - - - -
72F THR* 1.3 75.6 - - - +
74F VAL* 1.3 62.4 + - - +
75F THR* 5.5 0.2 - - - -
72G THR 3.2 8.5 + - - +
73G GLY* 3.3 7.9 - - - -
74G VAL* 3.1 24.4 + - - +
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Residues in contact with VAL 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLY 3.1 5.8 + - - +
74E VAL* 3.3 29.2 - - + +
75E THR 3.1 24.0 + - - +
51F GLY* 4.7 17.9 - - - -
52F VAL 5.2 3.4 - - - +
53F ALA* 3.8 26.7 - - + +
72F THR 4.3 0.4 - - - -
73F GLY* 1.3 75.3 - - - -
75F THR* 1.3 71.6 + - - +
76F ALA* 5.0 4.5 - - + +
51G GLY* 4.8 8.3 - - - +
53G ALA* 5.3 1.1 - - + -
74G VAL* 3.3 30.3 - - + +
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Residues in contact with THR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E THR* 3.3 16.4 - - + +
92E THR* 4.1 24.7 - - + +
71F VAL* 4.2 19.8 - - - +
73F GLY 5.5 0.2 - - - -
74F VAL* 1.3 77.9 + - - +
76F ALA* 1.3 64.1 + - - +
77F VAL* 4.5 13.5 - - + -
92F THR* 4.7 10.3 - - + +
74G VAL* 3.1 7.8 + - - +
75G THR* 3.3 19.2 + - + +
76G ALA 3.1 23.0 + - - +
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E THR 3.1 8.2 + - - +
76E ALA* 3.3 6.4 - - + -
77E VAL 3.2 19.6 + - - -
49F VAL* 3.3 24.9 - - + +
50F HIS 5.2 6.5 - - - +
51F GLY* 5.4 2.7 - - - -
74F VAL* 5.0 7.4 - - + +
75F THR* 1.3 74.9 - - - +
77F VAL* 1.3 68.1 + - - +
49G VAL* 3.9 16.2 - - + -
51G GLY* 5.4 4.7 - - - +
76G ALA* 3.3 7.9 - - + +
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Residues in contact with VAL 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E THR* 6.2 0.7 - - + -
77E VAL* 3.4 28.5 - - + -
90E ALA* 3.8 16.4 - - + -
75F THR* 4.5 12.1 - - + -
76F ALA* 1.3 85.0 - - - +
78F ALA* 1.3 57.8 + - - +
79F GLN* 4.3 17.7 - - + +
90F ALA* 4.0 15.0 - - + -
49G VAL* 3.2 10.9 - - - +
76G ALA 3.2 4.4 + - - -
77G VAL* 3.4 29.0 - - + -
78G ALA 3.0 18.9 + - - +
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E VAL 3.0 12.3 + - - +
78E ALA* 4.4 1.6 - - - -
79E GLN* 2.3 38.6 + - - +
47F GLY 3.9 4.0 - - - -
48F VAL 3.5 44.2 - - - +
49F VAL* 4.3 0.2 - - + -
77F VAL* 1.3 73.3 - - - +
79F GLN* 1.3 59.3 + - - +
47G GLY 3.7 9.9 - - - +
49G VAL* 4.1 4.5 - - + -
78G ALA* 4.1 4.0 - - - -
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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