Contacts of the helix formed by residues 115 - 124 (chain A) in PDB entry 3VOE
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 VAL 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.7 30.7 - - + -
32A TYR* 3.8 39.3 - - + +
33A LEU* 3.8 21.3 - - + -
43A PHE* 6.0 3.6 - - + -
111A CYS 3.0 17.2 + - - +
112A HIS* 5.4 0.4 - - - -
114A LEU* 1.3 79.8 - - + +
116A GLY* 1.3 62.7 + - - +
117A GLN 3.5 0.7 - - - -
119A LEU* 2.9 53.1 + - + +
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Residues in contact with GLY 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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112A HIS* 3.0 26.1 + - - +
113A GLN* 2.8 6.9 + - - -
115A VAL* 1.3 79.3 - - - +
117A GLN* 1.3 61.7 + - - +
119A LEU* 4.6 1.5 - - - +
120A HIS* 3.7 15.9 + - - +
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Residues in contact with GLN 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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113A GLN 3.3 10.6 + - - +
116A GLY* 1.3 74.9 - - - +
118A ASP* 1.3 81.1 + - - +
120A HIS* 3.3 8.0 + - - +
121A GLN* 2.9 46.3 + - + +
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Residues in contact with ASP 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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32A TYR* 3.1 37.6 + - + +
114A LEU* 3.4 17.0 + - - +
115A VAL 3.9 1.4 + - - -
116A GLY 3.5 0.6 - - - -
117A GLN* 1.3 98.0 - - - +
119A LEU* 1.3 61.0 + - - +
121A GLN* 3.5 8.8 - - - +
122A GLU* 2.8 33.3 + - - +
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Residues in contact with LEU 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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25A LYS* 3.6 42.4 - - + +
28A LEU* 3.7 22.7 - - + -
29A LEU* 3.9 24.5 - - + +
32A TYR* 4.5 6.1 - - + -
115A VAL* 2.9 29.7 + - + +
116A GLY* 4.6 1.3 - - - +
118A ASP* 1.3 76.8 - - - +
120A HIS* 1.3 56.1 + - - +
122A GLU* 3.3 5.1 + - - +
123A LEU* 2.9 41.6 + - + +
15B GLY* 4.6 14.8 - - - -
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Residues in contact with HIS 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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116A GLY 3.7 11.9 + - - +
117A GLN* 3.3 11.3 + - - +
118A ASP 3.2 0.2 - - - -
119A LEU* 1.3 77.6 - - - +
121A GLN* 1.3 56.1 + - - +
123A LEU* 3.3 5.9 + - + +
124A THR* 2.7 59.0 + - + +
132A VAL* 4.2 11.4 - - + +
136A GLU* 3.4 21.2 + - - -
13B PRO* 4.7 9.5 - - + +
14B LEU* 3.8 29.5 + - + +
15B GLY 4.9 2.7 - - - -
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Residues in contact with GLN 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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117A GLN* 2.9 37.8 + - + +
118A ASP* 3.1 14.5 + - - +
120A HIS* 1.3 77.6 + - + +
122A GLU* 1.3 61.4 + - - +
124A THR* 3.8 6.4 + - - -
125A LYS* 3.5 21.0 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.0 9.1 + - - +
28A LEU* 3.6 33.7 - - + +
32A TYR* 3.7 17.5 + - + +
118A ASP 2.8 17.3 + - - +
119A LEU 3.8 2.7 - - - +
121A GLN* 1.3 76.2 - - - +
123A LEU* 1.3 63.9 + - - +
125A LYS* 2.8 56.6 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.8 4.7 - - + +
24A LYS* 4.1 17.0 - - + +
25A LYS* 4.6 17.5 - - + -
28A LEU* 4.1 19.3 - - + -
119A LEU* 2.9 35.6 + - + +
120A HIS* 3.8 6.5 - - - +
122A GLU* 1.3 78.3 - - - +
124A THR* 1.3 57.6 + - - +
125A LYS* 3.3 3.5 + - - +
126A ASN* 4.7 1.9 + - - -
127A LEU* 4.6 1.0 - - - +
14B LEU* 4.4 19.3 - - + -
15B GLY* 4.4 23.8 - - - +
18B ILE* 4.9 4.0 - - + -
142B VAL* 3.6 49.2 - - + +
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Residues in contact with THR 124 (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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120A HIS* 2.7 39.4 + - + +
121A GLN* 3.8 7.1 + - - -
123A LEU* 1.3 74.1 - - + +
125A LYS* 1.3 62.3 + - - +
126A ASN 3.3 2.9 - - - -
127A LEU* 3.2 27.6 + - + +
132A VAL* 3.7 35.7 - - + -
14B LEU* 3.7 27.1 - - + -
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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