Contacts of the helix formed by residues 109 - 121 (chain D) in PDB entry 1VHA
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 HIS 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D LYS 3.6 23.3 + - - -
106D MSE 2.7 19.5 + - + +
108D PRO* 1.3 79.6 - - + +
110D ILE* 1.3 62.9 + - - +
111D ASP 3.3 2.9 - - - -
112D ALA* 3.2 23.7 + - + +
113D MSE 3.3 20.3 + - + +
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Residues in contact with ILE 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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99D ILE* 5.0 2.2 - - + -
106D MSE 3.2 21.6 + - + +
107D ARG* 3.2 39.5 - - - +
108D PRO 3.3 1.6 - - - -
109D HIS* 1.3 76.3 - - - +
111D ASP* 1.3 63.1 + - - +
113D MSE 3.1 18.5 + - - +
114D ARG* 3.0 35.2 + - - +
130D VAL* 3.2 49.8 - - + +
132D ALA* 4.7 6.5 - - + -
60F LYS* 4.8 12.1 - - - +
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Residues in contact with ASP 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 ARG 5.0 0.6 + - - -
108D PRO 4.4 6.8 + - - +
109D HIS 3.3 0.8 - - - -
110D ILE* 1.3 78.3 - - - +
112D ALA* 1.3 66.8 + - - +
114D ARG* 3.3 30.9 + - - +
115D ALA* 3.0 25.1 + - - +
125D ILE* 4.3 7.6 - - + +
60F LYS* 4.8 9.1 + - - -
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Residues in contact with ALA 112 (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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108D PRO 5.2 0.4 + - - -
109D HIS* 3.2 20.2 + - + +
111D ASP* 1.3 78.6 - - - +
113D MSE 1.3 62.1 + - + +
115D ALA* 3.6 5.3 + - - +
116D LYS* 3.2 36.7 + - + +
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Residues in contact with MSE 113 (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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41D ALA* 3.7 21.8 - - + -
42D LEU* 6.0 1.1 - - + -
97D ILE* 5.9 0.4 - - + -
99D ILE* 3.5 33.0 - - + -
106D MSE 4.7 12.3 - - + -
109D HIS* 3.3 17.9 + - + +
110D ILE* 3.1 17.4 + - - +
112D ALA* 1.3 75.9 - - + +
114D ARG* 1.3 60.0 + - - +
116D LYS* 3.2 8.3 + - - +
117D ILE* 2.8 44.6 + - + +
130D VAL* 3.8 20.2 - - + -
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Residues in contact with ARG 114 (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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110D ILE* 3.0 21.2 + - + +
111D ASP* 3.6 31.9 + - - +
113D MSE 1.3 78.4 - - - +
115D ALA* 1.3 52.9 + - - +
117D ILE* 3.2 8.1 + - - +
118D ALA* 2.7 36.7 + - - +
125D ILE* 2.7 47.5 + - + +
126D GLU* 4.0 6.9 - - - +
128D VAL* 2.7 30.1 + - + +
129D ASN* 4.6 3.5 - - - +
130D VAL* 3.8 22.4 - - + +
54F ALA* 4.2 19.1 + - - +
60F LYS* 6.1 1.0 - - - +
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Residues in contact with ALA 115 (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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111D ASP 3.0 16.8 + - - +
112D ALA* 3.7 6.7 - - - +
114D ARG* 1.3 77.2 - - - +
116D LYS* 1.3 65.2 + - + +
118D ALA* 3.2 5.2 + - - +
119D GLU* 3.0 22.7 + - - +
125D ILE* 3.9 15.2 - - + +
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Residues in contact with LYS 116 (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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75D ARG* 3.2 56.5 + - - +
112D ALA* 3.2 23.4 + - + +
113D MSE 3.2 7.5 + - - +
115D ALA* 1.3 79.5 - - + +
117D ILE* 1.3 61.7 + - + +
119D GLU* 3.4 5.5 + - - +
120D ASP* 3.2 16.1 + - - -
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Residues in contact with ILE 117 (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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41D ALA* 5.8 0.9 - - + -
42D LEU* 3.6 31.0 - - + -
45D LEU* 3.5 23.3 - - + -
78D LEU* 4.6 2.7 - - + -
97D ILE* 4.1 20.6 - - + -
113D MSE 2.8 34.5 + - + +
114D ARG 3.6 3.4 - - - +
116D LYS* 1.3 75.4 - - + +
118D ALA* 1.3 66.0 + - - +
119D GLU 3.1 0.2 - - - -
120D ASP* 3.3 6.9 + - - +
121D LEU* 3.0 32.8 + - + +
128D VAL* 3.8 17.9 - - + -
130D VAL* 4.2 14.4 - - + -
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Residues in contact with ALA 118 (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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114D ARG 2.7 21.8 + - - +
115D ALA* 3.5 5.4 - - - +
117D ILE* 1.3 73.3 - - - +
119D GLU* 1.3 57.5 + - - +
121D LEU 3.3 0.5 + - - -
122D GLN* 2.8 24.1 + - - -
123D CYS* 3.1 36.5 + - - +
124D ASP 4.0 2.0 - - - +
125D ILE* 3.7 27.8 - - + +
128D VAL* 4.3 3.4 - - + -
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Residues in contact with GLU 119 (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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75D ARG* 3.2 20.3 + - - -
79D ARG* 6.0 0.2 - - - +
115D ALA 3.0 12.4 + - - +
116D LYS* 3.5 11.2 - - - +
117D ILE 3.1 0.2 - - - -
118D ALA* 1.3 73.2 - - - +
120D ASP* 1.3 69.8 + - - +
121D LEU 3.0 1.6 - - - -
122D GLN* 3.0 20.3 + - - +
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Residues in contact with ASP 120 (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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42D LEU* 5.2 0.9 - - - +
75D ARG* 2.6 52.7 + - - +
78D LEU* 3.8 27.4 - - + +
79D ARG* 3.2 42.1 + - + +
82D PHE* 3.6 23.0 - - - +
116D LYS 3.2 14.0 + - - +
117D ILE* 3.9 1.1 - - - +
119D GLU* 1.3 77.7 - - - +
121D LEU* 1.3 58.7 + - - +
122D GLN* 4.4 2.6 - - - +
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Residues in contact with LEU 121 (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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45D LEU* 4.1 7.9 - - + -
49D ILE* 3.3 35.7 - - + -
78D LEU* 4.3 10.3 - - + -
82D PHE* 3.3 45.4 - - + -
92D ILE* 4.0 17.2 + - + +
95D VAL* 4.3 12.1 - - + -
117D ILE* 3.0 35.8 + - + +
120D ASP* 1.3 78.7 - - - +
122D GLN* 1.3 72.1 + - - +
123D CYS* 2.9 21.9 + - - +
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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