Contacts of the helix formed by residues 106 - 121 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.2 31.6 - - + -
101B ALA* 4.4 15.0 - - + -
103B ALA* 4.1 25.1 - - + -
104B PRO 3.4 9.3 + - - +
105B LYS* 1.3 77.0 - - - +
107B ARG* 1.3 68.8 + - - +
108B PRO* 3.1 4.0 - - - -
109B HIS* 2.9 25.2 + - + +
110B ILE* 3.0 23.8 + - + +
113B MSE 5.3 5.1 - - - +
132B ALA* 4.7 14.8 - - + -
147B ILE* 5.5 8.3 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASP* 2.7 37.7 + - - -
59A GLY 5.2 3.8 + - - -
60A LYS* 4.7 21.4 - - - +
104B PRO 5.3 3.8 + - - -
105B LYS* 5.4 1.9 - - - +
106B MSE 1.3 82.1 - - - +
108B PRO* 1.3 65.2 - - + +
109B HIS 3.2 0.9 + - - -
110B ILE* 3.2 33.0 + - + +
111B ASP* 4.5 3.8 + - - -
130B VAL 5.2 0.6 + - - -
131B LYS* 4.5 2.6 - - - +
132B ALA* 3.9 27.3 + - - +
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS* 3.9 16.6 - - + +
106B MSE 3.1 13.7 - - - +
107B ARG* 1.3 95.2 - - + +
109B HIS* 1.3 72.6 + - + +
110B ILE 3.6 0.2 - - - -
111B ASP* 5.1 3.0 + - - +
112B ALA* 5.3 2.9 + - - +
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS 4.6 4.7 + - - -
106B MSE 2.9 22.9 + - + +
108B PRO* 1.3 90.1 - - + +
110B ILE* 1.3 64.8 + - - +
111B ASP 3.4 2.2 - - - -
112B ALA* 3.1 14.9 + - + +
113B MSE 3.0 31.8 + - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.9 4.9 - - + -
106B MSE 3.0 25.9 + - + +
107B ARG* 3.2 36.6 + - + +
109B HIS* 1.3 76.6 - - - +
111B ASP* 1.3 62.5 + - - +
113B MSE 3.0 18.4 + - - +
114B ARG* 2.9 35.2 + - - +
130B VAL* 3.6 48.7 - - + +
131B LYS* 4.9 3.8 - - - +
132B ALA* 5.0 1.6 - - + -
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG 4.5 3.8 + - - -
108B PRO 5.1 1.9 + - - +
109B HIS 3.4 0.4 - - - -
110B ILE* 1.3 77.0 - - - +
112B ALA* 1.3 65.6 + - - +
114B ARG* 3.2 35.0 + - - +
115B ALA* 2.9 25.1 + - - +
125B ILE* 4.2 6.9 - - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO 5.3 2.6 + - - +
109B HIS* 3.1 20.7 + - + +
111B ASP* 1.3 78.7 - - - +
113B MSE 1.3 63.3 + - + +
115B ALA* 3.4 6.9 + - - +
116B LYS* 3.2 33.2 + - - +
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Residues in contact with MSE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 4.2 17.9 - - + -
42B LEU* 6.3 0.4 - - + -
99B ILE* 3.7 23.6 - - + -
106B MSE 5.3 5.2 - - - +
109B HIS* 3.0 25.8 + - + +
110B ILE* 3.0 21.7 + - - +
112B ALA* 1.3 77.7 - - + +
114B ARG* 1.3 62.3 + - - +
116B LYS* 3.4 8.1 + - - +
117B ILE* 3.0 35.7 + - + +
130B VAL* 3.4 30.3 - - + -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.4 15.8 + - - +
110B ILE* 2.9 23.7 + - - +
111B ASP* 3.2 35.6 + - - +
113B MSE 1.3 76.3 - - - +
115B ALA* 1.3 57.6 + - - +
117B ILE* 3.4 2.6 + - - +
118B ALA* 2.8 31.7 + - - +
125B ILE* 2.8 51.5 + - + +
126B GLU* 4.0 7.7 - - - +
128B VAL* 2.7 33.7 + - + +
129B ASN* 4.4 3.9 + - - +
130B VAL* 3.8 24.2 - - + +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP 2.9 16.3 + - - +
112B ALA* 3.6 8.1 - - - +
113B MSE 3.3 0.2 - - - -
114B ARG* 1.3 77.0 - - - +
116B LYS* 1.3 58.5 + - + +
118B ALA* 3.3 4.9 + - - +
119B GLU* 2.9 28.1 + - - +
125B ILE* 4.0 16.3 - - + +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 3.6 40.7 + - - +
112B ALA* 3.2 22.1 + - - +
113B MSE 3.9 6.3 - - - +
114B ARG 3.3 0.2 - - - -
115B ALA* 1.3 73.9 - - + +
117B ILE* 1.3 62.3 + - + +
119B GLU* 3.2 6.6 + - - +
120B ASP* 2.9 33.4 + - - -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 5.8 2.2 - - + +
42B LEU* 3.7 30.7 - - + -
45B LEU* 3.5 27.8 - - + -
78B LEU* 4.7 2.7 - - + -
95B VAL* 4.7 1.3 - - + -
97B ILE* 5.1 6.5 - - + -
113B MSE 3.0 34.0 + - + +
114B ARG 3.8 3.4 - - - +
116B LYS* 1.3 76.8 - - + +
118B ALA* 1.3 58.1 + - - +
120B ASP* 3.2 5.9 + - - +
121B LEU* 2.9 42.2 + - + +
128B VAL* 3.9 19.1 - - + -
130B VAL* 4.2 20.6 - - + -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG 2.8 18.5 + - - +
115B ALA* 3.5 5.4 - - - +
117B ILE* 1.3 76.1 - - - +
119B GLU* 1.3 64.2 + - - +
121B LEU 3.3 0.2 + - - -
122B GLN* 2.9 19.8 + - - -
123B CYS* 3.1 37.3 + - - +
124B ASP 4.0 2.2 - - - +
125B ILE* 3.7 26.0 - - + +
128B VAL* 4.2 2.7 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 4.2 9.1 + - - +
79B ARG* 5.0 1.9 + - - -
115B ALA 2.9 13.5 + - - +
116B LYS* 3.2 13.4 + - - +
118B ALA* 1.3 79.1 - - - +
120B ASP* 1.3 73.1 + - - +
122B GLN* 3.4 14.4 + - - +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 5.4 0.3 - - - +
75B ARG* 2.9 44.9 + - - +
78B LEU* 4.0 24.5 - - + +
79B ARG* 2.8 48.8 + - + +
82B PHE* 4.0 14.4 - - - +
116B LYS 2.9 17.1 + - - +
117B ILE 3.8 3.1 - - - +
119B GLU* 1.3 83.6 - - - +
121B LEU* 1.3 60.3 + - - +
122B GLN* 3.2 5.0 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 4.2 4.5 - - + -
49B ILE* 3.7 32.8 - - + -
78B LEU* 3.8 18.4 - - + -
82B PHE* 3.5 44.4 - - + -
92B ILE* 3.8 21.3 + - + +
95B VAL* 4.3 10.5 - - + -
117B ILE* 2.9 38.5 + - + +
120B ASP* 1.3 78.1 - - - +
122B GLN* 1.3 71.1 + - - +
123B CYS* 3.2 18.1 + - - +
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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