Contacts of the helix formed by residues 81 - 90 (chain C) in PDB entry 1VLP
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 PRO 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 4.2 9.9 - - + -
25C THR* 3.7 25.1 - - + +
79C TYR 3.2 7.2 - - - +
80C LEU* 1.3 87.0 - - + +
82C SER* 1.3 66.7 + - - +
83C ALA* 4.3 5.4 - - + +
84C TYR* 3.1 23.0 + - + +
85C ILE* 3.1 11.8 + - - +
259C THR* 3.9 21.1 - - + +
260C PHE* 4.0 15.0 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 3.5 3.2 + - - -
81C PRO* 1.3 71.8 - - - +
83C ALA* 1.3 58.4 + - - +
85C ILE* 3.2 10.4 + - - +
86C LYS* 3.0 28.7 + - - +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 3.6 16.3 - - + -
25C THR* 6.2 0.2 - - - +
81C PRO* 3.2 6.3 - - + +
82C SER* 1.3 78.6 - - - +
84C TYR* 1.3 57.0 + - - +
86C LYS* 3.5 9.4 + - - +
87C TYR* 3.0 28.4 + - - +
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.8 22.1 - - + +
20C HIS* 2.8 41.7 + + - +
21C ALA* 3.5 42.8 - - + -
24C PHE* 3.8 20.3 - - + -
25C THR* 5.0 0.4 - - - +
65C PHE* 4.9 0.5 - - - -
80C LEU* 4.2 20.0 - - + -
81C PRO* 3.1 20.2 + - + +
83C ALA* 1.3 75.6 - - - +
85C ILE* 1.3 74.3 + - + +
87C TYR* 3.2 13.6 + + - +
88C ILE* 3.0 56.0 + - + +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.6 24.7 - - + +
70C ILE* 3.8 19.5 - - + -
73C LEU* 4.8 4.9 - - + -
74C LYS* 4.1 27.8 - - + -
80C LEU* 4.0 33.9 - - + +
81C PRO 3.1 14.7 + - - +
82C SER* 3.2 10.1 + - - +
84C TYR* 1.3 80.5 - - + +
86C LYS* 1.3 59.2 + - - +
88C ILE* 3.5 14.8 + - + +
89C SER* 2.7 33.9 + - - +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 5.8 1.6 - - - -
82C SER 3.0 16.5 + - - +
83C ALA* 3.7 9.2 - - - +
85C ILE* 1.3 76.9 - - - +
87C TYR* 1.3 62.7 + - - +
89C SER* 3.3 5.7 + - - -
90C SER* 3.1 24.0 + - - -
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C HIS* 3.0 37.9 + + - -
24C PHE* 3.4 46.0 - + + -
83C ALA 3.0 18.4 + - - +
84C TYR* 3.2 12.8 + + - +
86C LYS* 1.3 78.3 - - - +
88C ILE* 1.3 75.4 + - + +
89C SER 3.4 0.3 + - - -
90C SER* 3.5 13.0 + - - -
93C TYR* 3.3 37.9 - + + +
126C LYS* 3.4 31.4 + - + +
127C ASP* 4.4 3.6 + - - -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ARG* 4.5 2.4 - - - -
20C HIS* 3.8 9.0 - - + -
65C PHE* 3.7 43.4 + - + +
70C ILE* 3.6 23.6 - - + -
73C LEU* 4.0 15.7 - - + -
84C TYR* 3.0 66.0 + - + +
85C ILE* 3.6 12.8 - - + +
87C TYR* 1.3 84.3 - - + +
89C SER* 1.3 60.4 + - - +
90C SER 3.4 1.1 - - - +
93C TYR* 3.8 17.8 - - + +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.3 39.4 - - - +
417B ARG* 3.0 29.9 + - - +
70C ILE* 3.7 14.5 - - - +
85C ILE 2.7 23.3 + - - -
86C LYS* 3.7 6.3 - - - -
87C TYR 3.2 0.2 - - - -
88C ILE* 1.3 76.6 - - - +
90C SER* 1.3 66.1 + - - +
91C SER 3.6 0.9 + - - -
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Residues in contact with SER 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ARG* 3.8 5.2 + - - -
86C LYS* 3.1 12.3 + - - -
87C TYR* 3.5 15.9 - - - -
88C ILE 3.4 1.5 - - - +
89C SER* 1.3 80.5 - - - +
91C SER* 1.3 64.4 + - - +
92C ASN* 3.1 28.6 + - - +
93C TYR* 3.0 21.1 + - - +
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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