Contacts of the helix formed by residues 63 - 71 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F GLY* 4.9 0.4 - - - -
59F PRO* 3.0 41.0 + - + +
60F LEU* 3.0 6.7 + - - +
61F LEU 3.0 4.2 + - - +
62F ASN* 1.3 79.0 - - - +
64F VAL* 1.3 62.5 + - - +
65F PRO* 3.6 15.5 - - - +
66F LEU* 2.8 42.0 + - - +
67F MET* 3.3 17.0 + - - +
94F ASP* 5.0 1.6 + - - -
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Residues in contact with VAL 64 (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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62F ASN 3.6 4.0 + - - +
63F ASN* 1.3 70.1 - - - +
65F PRO* 1.3 74.9 - - + +
67F MET* 3.1 10.5 + - + +
68F ASP* 2.8 39.2 + - - +
94F ASP* 4.0 28.0 - - + +
101F ARG* 3.6 20.4 - - - +
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Residues in contact with PRO 65 (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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62F ASN 4.9 2.0 - - - +
63F ASN* 3.3 16.2 - - - +
64F VAL* 1.3 96.7 - - + +
66F LEU* 1.3 63.0 + - - +
68F ASP* 3.2 8.6 + - + +
69F THR* 3.1 24.5 + - - -
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Residues in contact with LEU 66 (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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35F GLN* 3.7 32.1 - - + -
56F PHE* 4.5 16.8 - - + +
57F GLN 4.7 1.6 - - - +
58F GLY* 3.8 31.6 - - - +
59F PRO 3.8 3.8 - - - +
60F LEU* 4.5 9.4 - - + -
63F ASN* 2.8 33.2 + - - +
65F PRO* 1.3 79.1 - - - +
67F MET* 1.3 59.1 + - - +
69F THR* 2.9 10.3 + - - -
70F LEU* 2.8 41.9 + - + -
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Residues in contact with MET 67 (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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60F LEU* 3.5 36.8 - - + +
63F ASN 3.4 12.3 - - - +
64F VAL* 3.1 14.3 + - + +
66F LEU* 1.3 79.3 - - + +
68F ASP* 1.3 63.7 + - - +
70F LEU* 3.2 6.1 + - - +
71F PHE* 3.1 32.1 + - - -
91F ILE* 3.8 8.7 - - + +
94F ASP* 3.4 33.2 - - + +
95F LEU* 3.4 51.1 - - + -
98F ALA* 3.7 12.8 - - + -
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Residues in contact with ASP 68 (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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64F VAL* 2.8 30.6 + - - +
65F PRO* 3.6 10.7 - - + +
67F MET* 1.3 70.1 - - - +
69F THR* 1.3 66.2 + - - +
71F PHE* 3.7 4.2 + - - +
72F GLU* 3.1 24.1 + - - +
98F ALA* 4.2 9.5 - - - +
101F ARG* 3.3 34.6 + - - +
102F ALA* 5.9 0.3 - - - +
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Residues in contact with THR 69 (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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33F ARG* 2.6 28.5 + - - +
56F PHE* 3.3 39.5 - - + -
65F PRO 3.1 14.7 + - - -
66F LEU* 2.9 11.2 + - - -
68F ASP* 1.3 75.0 - - - +
70F LEU* 1.3 62.4 + - - +
72F GLU* 2.9 28.6 + - - +
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Residues in contact with LEU 70 (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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9F ALA* 3.9 17.3 - - + +
10F VAL 3.8 5.8 - - - +
11F VAL* 3.4 31.6 - - + -
33F ARG* 2.7 55.6 + - - +
34F ALA 3.8 21.5 - - - +
35F GLN* 3.9 9.9 - - + +
56F PHE* 4.2 11.2 - - + -
66F LEU* 2.8 17.5 + - + +
67F MET* 3.3 10.3 - - - +
69F THR* 1.3 77.0 - - - +
71F PHE* 1.3 62.4 + - + +
79F ILE* 5.5 0.4 - - + -
95F LEU* 4.7 11.2 - - + -
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Residues in contact with PHE 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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9F ALA* 3.8 22.9 - - + -
67F MET* 3.1 23.6 + - - +
68F ASP* 3.7 4.0 + - - +
69F THR 3.2 0.2 - - - -
70F LEU* 1.3 79.0 - - + +
72F GLU* 1.3 65.0 + - - +
73F GLY 3.0 1.2 + - - -
74F ALA* 3.0 19.5 + - + +
77F ALA* 4.1 14.1 - - + -
79F ILE* 4.6 7.4 - - + -
95F LEU* 3.3 40.2 - - + -
98F ALA* 3.2 32.1 - - + +
99F ALA* 3.4 21.8 - - + -
102F ALA* 3.7 29.1 - - + +
104F THR* 4.0 1.6 + - - -
105F ILE* 4.2 10.5 - - + -
108F TYR* 4.2 6.3 - + - -
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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