Contacts of the helix formed by residues 116 - 126 (chain A) in PDB entry 3AP1
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ALA 3.3 11.6 + - - -
113A TRP 3.7 1.2 - - - +
114A SER 3.2 1.5 - - - -
115A LYS* 1.3 76.1 - - - +
117A GLY* 1.3 64.7 + - - +
118A ARG 3.6 2.3 + - - -
119A GLU* 3.1 29.7 + - - +
120A LYS* 2.9 23.4 + - - +
1001T GLU* 3.4 9.7 + - - -
1002T ASP* 3.0 37.0 + - - -
1003T PHE* 4.1 0.7 - - - -
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Residues in contact with GLY 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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114A SER 5.1 1.1 - - - -
115A LYS 3.4 6.6 + - - -
116A SER* 1.3 70.2 + - - +
118A ARG* 1.3 63.3 + - - +
120A LYS* 3.4 6.0 + - - +
121A LEU* 3.0 23.3 + - - +
1002T ASP* 4.9 0.4 + - - -
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Residues in contact with ARG 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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116A SER* 3.3 0.8 + - - -
117A GLY* 1.3 75.0 - - - +
119A GLU* 1.3 59.1 + - - +
121A LEU* 3.2 17.7 + - + +
122A ARG* 2.9 64.7 + - + +
282B ILE* 3.9 26.3 + - - +
284B ARG* 5.7 3.8 - - - +
1001T GLU* 3.2 42.6 - - - +
1005T ASP* 4.6 4.0 + - - -
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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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113A TRP* 3.6 15.3 - - - +
116A SER* 3.1 27.1 + - - +
118A ARG* 1.3 76.6 - - - +
120A LYS* 1.3 58.4 + - - +
122A ARG* 3.2 8.3 + - - +
123A LEU* 2.8 46.2 + - + +
101B ARG* 2.9 43.5 + - - -
105B ARG* 2.9 28.5 + - - +
1001T GLU* 4.2 2.6 + - - +
1003T PHE* 3.5 26.5 - - + +
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Residues in contact with LYS 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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113A TRP 3.6 7.5 + - - +
114A SER* 4.1 27.1 - - - +
116A SER 2.9 16.5 + - - +
117A GLY* 3.8 6.3 - - - +
119A GLU* 1.3 76.4 - - - +
121A LEU* 1.3 54.5 + - - +
123A LEU* 3.3 6.8 + - - +
124A ASP* 2.7 67.9 + - - +
130A ASP* 3.8 29.3 + - - -
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Residues in contact with LEU 121 (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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117A GLY 3.0 13.6 + - - +
118A ARG* 3.3 20.0 - - - +
120A LYS* 1.3 78.1 - - - +
122A ARG* 1.3 56.6 + - - +
124A ASP* 3.4 7.4 + - + +
125A GLU* 3.0 35.4 + - + +
281B LYS* 5.4 6.5 - - - +
282B ILE* 4.0 20.2 - - + -
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Residues in contact with ARG 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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118A ARG* 2.9 54.4 + - + +
119A GLU* 3.2 21.3 + - - +
121A LEU* 1.3 74.5 - - - +
123A LEU* 1.3 62.8 + - - +
125A GLU* 3.3 4.0 + - - +
126A ALA* 3.1 22.5 + - - +
99B GLU* 5.7 1.2 + - - -
101B ARG* 3.4 45.8 - - - +
280B SER* 4.9 1.6 + - - -
282B ILE* 3.9 44.2 + - + +
283B GLU* 5.1 5.9 - - - +
284B ARG* 4.9 3.6 - - - +
1001T GLU* 5.8 0.7 - - - -
1003T PHE 4.5 4.6 + - - -
1004T GLU 4.2 2.8 + - - -
1005T ASP* 2.9 38.1 + - - +
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Residues in contact with LEU 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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113A TRP* 3.9 32.8 - - + +
114A SER* 5.7 0.4 - - - +
119A GLU* 2.8 30.8 + - + +
120A LYS* 3.7 6.7 - - - +
122A ARG* 1.3 76.6 - - - +
124A ASP* 1.3 61.8 + - - +
126A ALA* 3.0 9.4 + - + +
128A VAL* 2.8 48.1 + - + +
133A LEU* 4.4 14.8 - - + -
100B THR 3.3 26.7 - - - +
101B ARG* 4.0 13.5 - - + -
102B ILE* 3.7 17.9 - - + -
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Residues in contact with ASP 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 LYS* 2.7 57.8 + - - +
121A LEU* 3.7 9.5 + - + +
123A LEU* 1.3 72.3 - - - +
125A GLU* 1.3 57.8 + - + +
127A GLY* 3.0 19.2 + - - -
128A VAL 4.0 4.1 - - - +
129A THR* 3.5 33.0 - - + +
130A ASP 4.3 1.7 + - - -
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Residues in contact with GLU 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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121A LEU* 3.0 27.5 + - + +
122A ARG 3.7 4.0 - - - +
123A LEU 3.2 0.2 - - - -
124A ASP* 1.3 75.8 - - - +
126A ALA* 1.3 58.3 + - - +
127A GLY 3.3 1.4 + - - -
98B GLU* 3.8 14.2 - - - +
279B LEU 4.6 2.4 - - - +
280B SER* 3.6 24.8 - - - +
281B LYS* 3.3 47.3 + - + +
282B ILE* 3.7 20.4 - - + -
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Residues in contact with ALA 126 (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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122A ARG 3.1 11.5 + - - +
123A LEU* 3.0 12.8 + - - +
125A GLU* 1.3 77.0 - - - +
127A GLY* 1.3 54.4 + - - +
128A VAL* 3.1 10.8 - - + -
98B GLU* 3.6 22.9 - - + +
99B GLU 3.2 27.1 - - - +
100B THR* 4.8 0.7 - - - -
101B ARG* 5.6 2.0 - - - -
148B HIS* 2.8 28.9 + - - +
280B SER* 4.8 1.8 - - - -
283B GLU* 5.3 0.9 - - - +
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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