Contacts of the helix formed by residues 99 - 111 (chain D) in PDB entry 2VWI
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 SER 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D GLY 4.8 0.7 - - - +
98D GLY* 1.3 74.1 - - - -
100D VAL* 1.3 63.4 + - - +
101D LEU* 3.3 10.7 + - - +
102D ASP* 3.0 45.1 + - - +
103D ILE* 3.6 8.7 + - - +
149D ALA 3.9 8.3 - - - -
150D GLY* 3.9 14.8 - - - -
152D ILE 3.2 12.3 - - - -
153D LEU* 3.9 5.5 - - - +
154D LEU* 4.5 4.5 - - - +
1300D ANP 3.9 14.6 + - - -
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Residues in contact with VAL 100 (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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99D SER* 1.3 72.5 - - - +
101D LEU* 1.3 56.3 + - - +
103D ILE* 3.2 12.7 + - + +
104D ILE* 3.0 25.3 + - + +
118D LEU* 4.2 18.6 - - + -
126D ILE* 3.9 19.1 - - + -
149D ALA* 3.5 10.3 + - + +
152D ILE* 2.9 40.3 + - + +
154D LEU* 4.0 16.4 - - + -
220D LEU* 3.6 32.8 - - + -
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Residues in contact with LEU 101 (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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99D SER* 3.1 9.8 - - - +
100D VAL* 1.3 76.7 - - - +
102D ASP* 1.3 59.7 + - - +
104D ILE* 3.6 15.0 - - + +
105D LYS* 2.9 51.2 + - + +
148D LYS* 6.1 3.6 - - - -
149D ALA* 3.4 8.4 + - + -
150D GLY* 3.7 26.5 - - - +
219D GLU* 3.8 21.1 - - - +
223D GLY 5.2 2.7 - - - +
1300D ANP 5.6 7.4 - - - +
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLY 5.6 0.9 - - - +
98D GLY* 3.5 10.8 - - - -
99D SER* 3.0 37.8 + - - +
101D LEU* 1.3 76.8 - - - +
103D ILE* 1.3 62.3 + - + +
105D LYS* 3.9 19.2 + - - +
106D HIS* 3.1 23.7 + - - +
1300D ANP 4.5 13.3 + - - -
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Residues in contact with ILE 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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97D GLY 5.8 1.6 - - - +
99D SER 3.9 6.5 - - - +
100D VAL* 3.2 19.2 + - + +
102D ASP* 1.3 75.5 - - + +
104D ILE* 1.3 64.0 + - - +
106D HIS* 3.2 9.7 + - + +
107D ILE* 3.1 30.5 + - + +
118D LEU* 3.8 27.8 - - + -
126D ILE* 5.4 6.7 - - + -
154D LEU* 3.5 30.3 - - + -
298D GLU* 5.9 2.0 - - - +
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Residues in contact with ILE 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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100D VAL* 3.0 16.5 + - + +
101D LEU* 3.3 14.6 + - + +
103D ILE* 1.3 74.6 - - - +
105D LYS* 1.3 58.8 + - + +
107D ILE* 3.1 4.0 + - - +
108D VAL* 2.9 38.8 + - + +
117D VAL* 4.0 20.8 - - + +
118D LEU* 4.8 3.8 - - + -
149D ALA* 3.8 17.5 - - + -
219D GLU* 3.6 25.1 - - + +
220D LEU* 3.8 27.8 - - + -
223D GLY* 3.4 32.5 - - - +
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Residues in contact with LYS 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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101D LEU* 2.9 48.2 + - + +
102D ASP* 3.9 16.8 + - - +
104D ILE* 1.3 75.0 - - + +
106D HIS* 1.3 57.9 + - - +
108D VAL* 3.8 7.3 - - - +
109D ALA* 2.9 32.2 + - - +
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Residues in contact with HIS 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 ASP 3.1 14.7 + - - +
103D ILE* 3.3 14.1 - - + +
104D ILE 3.2 0.2 - - - -
105D LYS* 1.3 78.1 - - - +
107D ILE* 1.3 68.3 + - + +
109D ALA* 3.7 4.8 + - - +
110D LYS* 3.3 58.7 + - + +
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Residues in contact with ILE 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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103D ILE* 3.1 31.6 + - + +
104D ILE 3.8 4.7 - - - +
106D HIS* 1.3 85.8 - - + +
108D VAL* 1.3 65.2 + - - +
109D ALA 3.3 0.4 - - - -
110D LYS* 3.3 13.9 + - - +
112D GLU* 3.2 55.0 + - + +
113D HIS* 4.0 2.6 + - - +
117D VAL* 3.7 41.7 - - + +
118D LEU* 4.0 5.4 - - + -
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Residues in contact with VAL 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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104D ILE* 2.9 35.0 + - + +
105D LYS* 3.9 7.4 - - - +
107D ILE* 1.3 77.7 - - - +
109D ALA* 1.3 58.9 - - - +
111D GLY* 3.5 7.8 + - - -
113D HIS* 3.5 44.1 + - + +
117D VAL* 4.5 6.7 - - + -
222D THR 5.1 0.2 - - - +
223D GLY* 4.5 7.4 - - - +
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Residues in contact with ALA 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 LYS 2.9 19.0 + - - +
106D HIS* 4.0 6.7 - - - +
108D VAL* 1.3 75.8 - - - +
110D LYS* 1.3 63.2 + - + +
111D GLY* 3.5 0.5 + - - -
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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 HIS* 3.3 49.4 + - + +
107D ILE* 3.3 12.2 + - - +
109D ALA* 1.3 77.7 - - + +
111D GLY* 1.3 61.1 + - - +
112D GLU* 3.3 36.4 + - + +
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Residues in contact with GLY 111 (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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107D ILE 3.3 2.8 + - - -
108D VAL 3.5 3.2 + - - -
109D ALA 3.2 5.6 + - - -
110D LYS* 1.3 78.3 - - - +
112D GLU* 1.3 58.4 + - - +
113D HIS* 3.3 23.4 + - - -
114D LYS* 3.7 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