Contacts of the helix formed by residues 63 - 72 (chain E) in PDB entry 2VUU
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 ASN 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58E GLY* 4.8 1.0 - - - -
59E PRO* 2.9 42.3 + - + +
60E LEU 3.3 6.7 + - - +
61E LEU 4.0 3.1 - - - +
62E ASN* 1.3 80.0 - - - +
64E VAL* 1.3 66.6 + - - +
65E PRO* 3.1 20.1 - - - +
66E LEU* 3.0 39.8 + - - +
67E MET* 3.4 10.3 + - - +
94E ASP* 5.3 0.6 + - - -
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Residues in contact with VAL 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E ASN* 5.7 1.1 - - - -
63E ASN* 1.3 73.6 - - - +
65E PRO* 1.3 77.5 - - + +
67E MET* 3.5 21.7 - - + +
68E ASP* 2.8 30.4 + - - +
94E ASP* 4.3 21.5 - - + +
101E ARG* 4.7 16.4 - - - +
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Residues in contact with PRO 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ASN* 3.1 18.6 - - - +
64E VAL* 1.3 100.2 - - + +
66E LEU* 1.3 61.9 + - - +
68E ASP* 3.4 9.2 + - + +
69E THR* 3.0 27.6 + - - -
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 3.9 28.5 - - + -
56E PHE* 4.5 16.1 - - + +
57E GLN 4.8 1.1 - - - -
58E GLY* 3.5 28.0 - - - +
59E PRO 3.4 13.7 - - - +
60E LEU* 4.3 7.4 - - + -
63E ASN* 3.0 35.0 + - - +
65E PRO* 1.3 79.5 - - - +
67E MET* 1.3 61.0 + - + +
69E THR* 3.2 8.3 + - - -
70E LEU* 2.8 35.8 + - + -
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Residues in contact with MET 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LEU* 3.6 30.7 - - + +
63E ASN 3.5 14.6 - - - +
64E VAL* 3.1 15.9 + - + +
66E LEU* 1.3 82.1 - - + +
68E ASP* 1.3 63.1 + - - +
70E LEU* 3.2 5.7 + - - +
71E PHE* 2.9 32.6 + - - -
91E ILE* 3.7 16.2 - - + +
94E ASP* 3.4 38.8 - - + +
95E LEU* 3.3 37.5 - - + -
98E ALA* 3.7 13.7 - - + -
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E VAL* 2.8 27.3 + - - +
65E PRO* 3.6 8.1 - - + +
67E MET* 1.3 73.7 - - - +
69E THR* 1.3 65.9 + - - +
71E PHE* 3.4 4.5 + - - +
72E GLU* 3.2 26.4 + - - +
98E ALA* 4.4 7.0 - - - +
101E ARG* 2.9 35.1 + - - +
102E ALA* 5.9 0.2 - - - +
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Residues in contact with THR 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 2.6 37.9 + - - +
56E PHE* 3.9 25.1 - - + -
65E PRO 3.0 14.1 + - - -
66E LEU* 3.6 8.8 - - - -
68E ASP* 1.3 77.8 - - - +
70E LEU* 1.3 59.7 + - - +
72E GLU* 2.9 26.8 + - - +
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 3.9 25.0 - - + +
10E VAL 3.6 19.5 - - - +
11E VAL* 3.7 24.5 - - + -
33E ARG* 2.6 45.7 + - - +
34E ALA 3.9 3.8 - - - -
35E GLN* 3.8 21.5 - - + +
56E PHE* 4.3 12.7 - - + -
60E LEU* 6.2 0.2 - - + -
66E LEU* 2.8 17.8 + - + +
67E MET* 3.3 10.1 - - - +
69E THR* 1.3 76.0 - - - +
71E PHE* 1.3 74.9 + - + +
79E ILE* 4.9 0.7 - - + -
95E LEU* 4.9 2.7 - - + -
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Residues in contact with PHE 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 3.9 22.0 - - + -
67E MET 2.9 24.6 + - - +
68E ASP* 3.4 4.0 + - - +
69E THR 3.2 0.2 - - - -
70E LEU* 1.3 83.5 - - + +
72E GLU* 1.3 65.5 + - - +
73E GLY 3.1 1.2 + - - -
74E ALA* 3.0 19.3 + - + +
77E ALA* 4.3 13.5 - - + -
79E ILE* 4.7 4.9 - - + -
95E LEU* 3.4 39.7 - - + -
98E ALA* 3.1 32.8 - - + +
99E ALA* 3.5 22.4 - - + -
102E ALA* 3.7 28.8 - - + +
104E THR* 3.9 1.4 + - - -
105E ILE* 4.3 10.5 - - + +
108E TYR* 4.4 4.9 - + - -
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Residues in contact with GLU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 2.9 35.5 + - - +
68E ASP* 3.2 15.2 + - + +
69E THR* 2.9 42.9 + - - +
71E PHE* 1.3 75.2 - - - +
73E GLY* 1.3 60.2 + - - +
74E ALA 3.2 0.4 + - - -
102E ALA* 5.5 1.6 - - - -
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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