Contacts of the helix formed by residues 117 - 125 (chain A) in PDB entry 3AEV
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 ASP 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ALA* 4.9 0.2 - - - -
115A GLY 4.1 1.2 + - - -
116A LYS* 1.3 78.2 - - - +
118A PHE* 1.3 65.9 + - - +
119A GLU* 3.3 11.6 + - - +
120A ALA* 3.2 32.4 + - - +
121A ALA* 3.2 10.4 + - - +
123A ARG* 5.6 0.3 + - - -
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Residues in contact with PHE 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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104A GLU* 4.2 11.7 - - + -
107A LEU* 4.6 13.2 - - + -
108A ARG* 3.5 64.4 - - + +
111A ALA* 5.2 3.8 - - + +
116A LYS 4.0 0.2 + - - -
117A ASP* 1.3 75.7 - - - +
119A GLU* 1.3 66.7 + - - +
121A ALA* 3.1 16.5 + - + +
122A TRP* 3.0 56.8 + + + +
126A TRP* 5.9 0.2 - + - -
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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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117A ASP* 3.3 10.1 + - - +
118A PHE* 1.3 77.8 - - - +
120A ALA* 1.3 62.4 + - - +
122A TRP* 3.4 8.5 + - + +
123A ARG* 3.0 43.1 + - + +
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Residues in contact with ALA 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 LYS* 4.5 16.2 - - + +
117A ASP* 3.2 21.5 + - - +
119A GLU* 1.3 76.7 - - - +
121A ALA* 1.3 59.5 + - - +
123A ARG* 3.1 22.9 + - - +
124A GLU* 2.8 52.3 + - - +
159A TRP* 4.7 0.2 - - - -
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Residues in contact with ALA 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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107A LEU* 3.7 23.1 - - + +
111A ALA* 4.1 10.5 - - + -
117A ASP 3.2 10.2 + - - +
118A PHE* 3.1 15.9 + - + +
120A ALA* 1.3 75.6 - - - +
122A TRP* 1.3 57.5 + - - +
125A VAL* 2.8 29.3 + - - +
126A TRP 3.1 6.8 + - - -
159A TRP* 3.7 31.6 - - + -
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Residues in contact with TRP 122 (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 GLU* 4.4 12.8 - - - -
107A LEU* 4.6 0.6 - - + +
118A PHE* 3.0 43.2 + + + +
119A GLU* 3.4 12.6 - - + +
121A ALA* 1.3 78.5 - - - +
123A ARG* 1.3 59.3 + - - +
126A TRP* 3.2 61.8 + + + -
127A VAL* 2.9 53.6 + - + +
130A GLU* 5.5 2.0 - - - -
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Residues in contact with ARG 123 (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 ASP* 5.6 0.2 + - - -
119A GLU* 3.0 52.3 + - - +
120A ALA* 3.1 26.4 + - - +
122A TRP* 1.3 78.7 - - + +
124A GLU* 1.3 72.2 + - + +
127A VAL* 4.5 8.8 - - - +
128A PRO* 3.7 12.8 - - - +
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Residues in contact with GLU 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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116A LYS* 3.7 19.8 + - - +
120A ALA* 2.8 29.1 + - - +
123A ARG* 1.3 94.0 + - + +
125A VAL* 1.3 61.6 + - + +
128A PRO* 3.5 14.0 - - - +
154A HIS 4.2 0.3 - - - +
155A VAL* 3.5 13.2 - - - +
156A PRO* 3.5 27.5 - - + +
158A GLU* 4.7 1.4 - - - +
159A TRP* 2.9 31.4 + - - +
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Residues in contact with VAL 125 (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 LEU* 3.8 22.0 - - + -
121A ALA 2.8 13.4 + - - +
124A GLU* 1.3 85.3 - - - +
126A TRP* 1.3 68.1 + - - +
127A VAL 3.5 0.7 - - - -
128A PRO* 3.3 2.5 - - - +
129A LEU* 3.1 44.9 + - + +
136A VAL* 5.8 0.7 - - + -
140A PHE* 4.8 6.5 - - + -
155A VAL* 4.0 7.6 - - + -
159A TRP* 3.4 48.7 - - + -
163A LEU* 4.1 13.9 - - + -
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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