Contacts of the helix formed by residues 71 - 79 (chain B) in PDB entry 3VF0
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 THR 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASP 3.9 8.7 - - - +
70B VAL* 1.3 84.9 - - - +
72B ASN* 1.3 65.4 + - - +
73B GLN* 3.5 7.0 + - - +
74B GLU* 3.1 41.2 + - - +
75B VAL* 3.4 5.4 + - - +
89B VAL* 4.8 2.7 - - - -
91B LYS* 4.0 3.8 - - - +
3006B GOL 3.5 29.6 - - - +
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 1.3 68.2 - - - +
73B GLN* 1.3 57.3 + - - +
75B VAL* 3.0 6.2 + - - +
76B HIS* 2.9 45.9 + - + +
87B CYS 4.2 11.7 + - - -
88B PHE* 5.0 0.4 - - - +
89B VAL* 3.7 36.6 + - - +
91B LYS* 3.6 12.9 - - - +
3006B GOL 2.9 33.8 + - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.2 6.0 - - - +
72B ASN* 1.3 72.5 - - - +
74B GLU* 1.3 50.6 + - - +
76B HIS* 3.2 18.9 + - - +
77B ASP* 2.7 68.9 + - - +
3006B GOL 2.7 23.3 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 4.1 2.1 - - - +
70B VAL* 3.3 27.7 - - + -
71B THR* 3.1 25.1 + - + +
73B GLN* 1.3 74.6 - - - +
75B VAL* 1.4 57.9 + - - +
77B ASP* 3.5 9.3 + - - +
78B LEU* 2.9 27.4 + - - +
118B LEU* 4.1 22.9 - - + +
119B ARG* 2.8 48.1 + - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.4 5.8 - - + -
66B LEU* 3.9 28.7 - - + -
70B VAL* 4.1 9.0 - - + -
71B THR 3.4 8.5 + - - +
72B ASN 3.0 7.6 + - - +
74B GLU* 1.4 72.5 - - - +
76B HIS* 1.3 65.3 + - - +
78B LEU* 3.3 9.7 + - + +
79B LEU* 3.0 40.0 + - + +
87B CYS* 3.7 23.3 - - - -
89B VAL* 3.8 20.2 - - + -
96B ALA* 4.3 12.1 - - + -
98B VAL* 4.4 0.2 - - + -
118B LEU* 5.9 0.7 - - + -
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 2.9 42.4 + - + +
73B GLN* 3.5 24.0 + - - +
75B VAL* 1.3 76.0 - - - +
77B ASP* 1.4 56.5 + - - +
79B LEU 3.4 2.8 - - - -
80B SER* 3.1 28.2 + - - -
84B LEU* 3.9 30.3 - - + +
87B CYS* 4.0 30.4 - - + +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLN* 2.7 49.2 + - - +
74B GLU* 3.6 9.0 - - - +
76B HIS* 1.4 70.5 - - - +
78B LEU* 1.3 65.0 + - - +
80B SER* 3.1 24.7 + - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.6 20.0 - - + -
66B LEU* 5.1 3.8 - - + -
74B GLU 2.9 18.4 + - - +
75B VAL* 3.3 9.4 + - - +
77B ASP* 1.3 76.8 - - - +
79B LEU* 1.4 60.5 + - + +
80B SER* 3.6 2.8 + - - -
81B ASP* 5.1 0.9 + - - -
82B TYR* 5.2 0.2 - - - -
113B PHE* 3.3 59.8 - - + -
116B SER* 5.5 0.7 - - - +
117B ARG 6.1 0.7 - - - +
118B LEU* 4.5 27.6 - - + -
123B LEU* 3.8 27.4 - - + -
125B VAL* 6.0 0.2 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.5 8.3 - - + -
63B ILE* 3.9 12.8 - - + -
75B VAL* 3.0 35.9 + - + +
76B HIS 3.4 4.7 - - - -
78B LEU* 1.4 78.4 - - + +
80B SER* 1.4 56.9 + - - +
81B ASP 3.2 3.4 - - - -
82B TYR* 3.0 44.4 + - + +
84B LEU* 3.6 17.6 - - + +
98B VAL* 3.9 31.0 - - + -
100B LEU* 5.2 2.7 - - + -
109B ALA* 4.3 12.1 - - + -
113B PHE* 4.1 25.4 - - + -
125B VAL* 6.0 0.7 - - + -
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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