Contacts of the helix formed by residues 101 - 110 (chain D) in PDB entry 1VBF
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 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.1 6.2 - - - +
51D ILE* 3.6 29.4 - - + +
99D GLU* 2.5 21.5 + - - +
100D ILE* 1.3 78.6 - - + +
102D GLU* 1.3 58.8 + - - +
103D LYS* 2.9 27.9 + - - +
104D MSE 3.1 15.4 + - + -
105D TYR* 2.9 25.5 + - - +
122D LEU* 4.1 1.6 - - - -
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ILE 3.6 5.2 + - - +
101D ASN* 1.3 69.9 + - - +
103D LYS* 1.3 69.2 + - + +
105D TYR* 2.9 9.6 + - + +
106D ASN* 2.7 43.9 + - - +
122D LEU* 3.9 27.4 - - + +
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.2 25.1 - - + -
49D PRO* 6.4 0.2 - - + -
101D ASN* 2.9 12.8 + - - +
102D GLU* 1.3 77.0 - - + +
104D MSE 1.3 57.8 + - - +
106D ASN* 3.3 10.0 + - - +
107D TYR* 3.0 28.9 + - - +
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Residues in contact with MSE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 3.9 36.1 - - + -
48D LEU* 3.3 22.2 - - + +
51D ILE* 3.4 36.6 - - + -
52D ASN 4.9 4.5 - - - +
53D THR* 5.6 0.9 - - - +
80D GLY* 3.4 41.3 - - - +
81D ILE* 3.9 4.5 - - + +
99D GLU* 3.8 20.2 - - + +
101D ASN* 3.1 15.7 + - + +
103D LYS* 1.3 76.0 - - - +
105D TYR* 1.3 64.6 + - - +
107D TYR* 3.2 11.3 + - - +
108D ALA* 3.0 26.3 + - - +
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Residues in contact with TYR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D THR* 6.0 2.5 - - + -
99D GLU* 4.4 14.1 - - + +
101D ASN 2.9 12.8 + - - +
102D GLU* 3.1 14.6 - - + +
104D MSE 1.3 77.1 - - - +
106D ASN* 1.3 68.8 + - - +
108D ALA* 3.6 2.8 + - - +
109D SER* 3.0 34.2 + - - -
120D LEU* 3.2 48.7 + - + +
121D ILE 4.0 14.6 - - - -
122D LEU* 3.7 35.0 + - + -
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLU* 2.7 42.6 + - - +
103D LYS* 3.6 8.6 - - - +
105D TYR* 1.3 85.4 - - - +
107D TYR* 1.3 63.2 + - - +
109D SER* 2.9 21.7 - - - -
110D LYS* 4.0 9.2 + - - +
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 2.9 28.3 + - - -
29D LEU 3.6 1.6 - - - -
30D PRO* 3.1 37.1 - - + +
47D ILE* 5.0 7.4 - - + -
81D ILE* 4.1 26.0 - - + -
103D LYS 3.0 14.0 + - - +
104D MSE 3.2 19.0 + - - +
106D ASN* 1.3 78.7 - - - +
108D ALA* 1.3 67.3 + - - +
110D LYS* 3.9 15.8 + - - +
111D LEU* 4.7 2.1 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D THR* 4.5 6.7 - - + -
80D GLY 3.3 25.4 - - - +
81D ILE 3.8 16.6 - - - +
82D GLY 4.2 2.2 - - - +
104D MSE 3.0 10.0 + - - +
105D TYR* 4.3 2.7 - - - +
107D TYR* 1.3 81.4 - - - +
109D SER* 1.3 66.7 + - - +
110D LYS 3.0 1.4 + - - -
111D LEU* 3.1 15.8 + - - +
112D LEU* 3.3 26.2 + - + +
120D LEU* 5.6 1.1 - - + -
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Residues in contact with SER 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D TYR* 3.0 22.4 + - - -
106D ASN* 2.9 22.2 - - - -
107D TYR 3.2 0.2 - - - -
108D ALA* 1.3 76.9 - - - +
110D LYS* 1.3 62.3 + - - +
112D LEU* 3.6 8.7 + - - +
113D SER* 3.8 10.2 + - - -
120D LEU* 4.9 14.4 - - - +
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASN 4.0 12.8 - - - +
107D TYR* 4.1 10.1 - - - +
108D ALA 3.0 0.8 + - - -
109D SER* 1.3 75.8 - - - +
111D LEU* 1.3 58.3 + - + +
113D SER* 2.4 32.4 + - - -
114D TYR* 4.8 2.1 - - - -
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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