Contacts of the helix formed by residues 106 - 121 (chain A) 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 MSE 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ILE* 4.4 28.9 - - + -
101A ALA* 4.2 16.6 - - + +
103A ALA* 3.5 34.1 - - + -
104A PRO 3.3 8.8 + - - +
105A LYS* 1.3 76.6 - - - +
107A ARG* 1.3 67.0 + - - +
108A PRO* 3.1 4.3 - - - -
109A HIS* 2.7 34.1 + - + +
110A ILE* 2.8 23.4 + - + +
113A MSE 4.5 14.8 - - + -
132A ALA* 4.5 11.2 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO 4.6 9.2 + - - -
105A LYS* 6.0 0.4 - - - -
106A MSE 1.3 86.7 - - - +
108A PRO* 1.3 66.8 - - + +
109A HIS 3.2 0.7 + - - -
110A ILE* 3.2 26.8 + - + +
111A ASP* 4.1 7.3 + - - +
130A VAL 4.8 0.6 + - - -
131A LYS* 3.5 7.1 - - - +
132A ALA* 2.8 60.8 + - - +
57C ASP* 2.6 32.0 + - - -
60C LYS* 5.7 13.1 - - + +
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LYS* 4.3 11.0 - - + -
106A MSE 3.2 12.6 - - - +
107A ARG* 1.3 97.8 - - + +
109A HIS* 1.3 71.6 + - + +
110A ILE 3.9 0.2 + - - -
111A ASP* 4.7 5.4 + - - +
112A ALA* 4.8 5.9 + - - +
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Residues in contact with HIS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LYS 4.4 17.0 - - - -
106A MSE 2.7 13.6 + - + +
108A PRO* 1.3 91.0 + - + +
110A ILE* 1.3 62.7 + - - +
111A ASP 3.5 0.7 - - - -
112A ALA* 3.3 12.5 + - + +
113A MSE 3.1 39.8 + - + +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 4.6 6.3 - - + -
106A MSE 2.8 32.3 + - + +
107A ARG* 3.2 37.5 + - + +
109A HIS* 1.3 72.9 - - - +
111A ASP* 1.3 61.7 + - - +
113A MSE 2.8 38.7 + - + +
114A ARG* 2.9 22.8 + - - +
130A VAL* 3.7 49.6 - - + +
131A LYS* 4.9 1.6 - - - +
132A ALA* 5.1 0.2 - - + -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG 4.1 6.1 + - - +
108A PRO 5.1 4.7 - - - +
109A HIS 3.5 0.2 - - - -
110A ILE* 1.3 81.7 - - - +
112A ALA* 1.3 62.7 + - - +
114A ARG* 3.2 33.9 + - - +
115A ALA* 3.0 24.6 + - - +
125A ILE* 4.2 7.2 - - + +
60C LYS* 5.8 1.9 + - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PRO 4.8 3.7 + - - +
109A HIS* 3.3 19.3 + - + +
110A ILE 3.1 0.8 - - - -
111A ASP* 1.3 77.3 - - - +
113A MSE 1.3 63.3 + - - +
115A ALA* 3.5 6.7 + - - +
116A LYS* 3.2 37.0 + - - +
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Residues in contact with MSE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 5.4 7.9 - - - -
99A ILE* 4.2 15.0 - - + -
106A MSE 4.5 19.3 - - + -
109A HIS* 3.1 37.9 + - + +
110A ILE* 2.8 30.3 + - + +
112A ALA* 1.3 77.0 - - + +
114A ARG* 1.3 63.1 + - - +
116A LYS* 3.2 12.0 + - + +
117A ILE* 2.9 37.9 + - + +
130A VAL* 4.4 8.1 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 2.9 25.1 + - + +
111A ASP* 3.4 33.6 + - - +
113A MSE 1.3 75.9 - - - +
115A ALA* 1.3 52.5 + - - +
117A ILE* 3.1 4.5 + - - +
118A ALA* 2.6 37.4 + - - +
125A ILE* 2.7 52.6 + - + +
126A GLU* 4.2 2.6 - - - +
128A VAL* 2.6 34.8 + - + +
129A ASN* 4.4 3.5 - - - +
130A VAL* 4.0 20.4 - - + +
54C ALA* 4.0 23.1 + - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP 3.0 15.4 + - - +
112A ALA* 3.7 8.1 - - - +
114A ARG* 1.3 76.1 - - - +
116A LYS* 1.3 58.4 + - + +
118A ALA* 3.2 8.4 + - - +
119A GLU* 2.8 31.6 + - - +
125A ILE* 4.0 10.7 - - + +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 6.5 0.4 - - + -
75A ARG* 3.7 43.7 - - - +
112A ALA* 3.2 23.5 + - - +
113A MSE 3.2 11.3 + - + +
115A ALA* 1.3 77.0 - - + +
117A ILE* 1.3 64.1 + - + +
119A GLU* 3.2 7.8 + - - +
120A ASP* 3.0 30.2 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 5.9 2.2 - - + -
42A LEU* 3.9 27.1 - - + -
45A LEU* 3.5 12.3 - - + -
78A LEU* 4.7 3.1 - - + -
95A VAL* 4.8 0.2 - - + -
97A ILE* 3.8 25.4 - - + -
113A MSE 2.9 29.0 + - + +
114A ARG 3.5 4.5 - - - +
116A LYS* 1.3 73.2 - - + +
118A ALA* 1.3 67.8 + - - +
120A ASP* 3.1 6.4 + - - +
121A LEU* 2.9 48.9 + - + +
128A VAL* 3.7 17.9 - - + -
130A VAL* 4.0 14.6 - - + -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG 2.6 20.2 + - - +
115A ALA* 3.4 8.7 - - - +
117A ILE* 1.3 72.5 - - - +
119A GLU* 1.3 57.1 + - - +
121A LEU 3.5 0.2 + - - -
122A GLN* 3.0 23.4 + - - -
123A CYS* 3.0 39.3 + - - +
124A ASP 4.0 1.3 - - - +
125A ILE* 3.8 26.0 - - + +
128A VAL* 4.2 2.9 - - + +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ARG* 3.6 19.6 + - - +
115A ALA 2.8 14.1 + - - +
116A LYS* 3.3 10.8 - - - +
118A ALA* 1.3 77.9 - - - +
120A ASP* 1.3 64.7 + - - +
122A GLN* 3.2 18.3 + - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.8 0.3 - - - +
75A ARG* 2.8 44.6 + - - +
78A LEU* 4.0 22.8 - - + +
79A ARG* 3.1 46.9 + - + +
82A PHE* 3.8 18.9 - - - +
116A LYS 3.0 16.0 + - - +
117A ILE 3.9 3.1 - - - +
119A GLU* 1.3 78.8 - - - +
121A LEU* 1.3 60.8 + - - +
122A GLN* 3.4 3.9 - - - +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.3 5.4 - - + -
49A ILE* 3.7 33.0 - - + -
78A LEU* 4.0 19.1 - - + -
82A PHE* 3.1 41.0 - - + -
92A ILE* 4.1 17.8 + - + +
95A VAL* 4.5 11.0 - - + -
117A ILE* 2.9 40.9 + - + +
120A ASP* 1.3 81.6 - - - +
122A GLN* 1.3 70.5 + - - +
123A CYS* 3.3 19.3 + - - +
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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