Contacts of the helix formed by residues 117 - 126 (chain B) in PDB entry 3AP3
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 GLY 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B LYS 4.1 0.2 + - - -
116B SER* 1.3 77.9 + - - +
118B ARG* 1.3 59.4 + - - +
119B GLU 3.7 0.2 - - - -
120B LYS* 4.4 3.3 - - - +
121B LEU* 3.9 18.0 + - - +
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Residues in contact with ARG 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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282A ILE* 5.6 2.7 - - - +
116B SER* 3.1 1.7 + - - +
117B GLY* 1.3 77.0 - - - +
119B GLU* 1.3 59.8 + - - +
120B LYS 3.4 0.4 - - - -
121B LEU* 3.6 9.3 - - + +
122B ARG* 3.2 75.7 + - - +
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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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101A ARG* 3.4 41.3 + - - +
102A ILE* 5.3 0.5 - - - +
105A ARG* 3.1 32.6 + - - -
113B TRP* 4.5 14.8 - - + +
116B SER* 2.8 20.7 + - - +
118B ARG* 1.3 76.1 - - - +
120B LYS* 1.3 54.7 + - - +
122B ARG* 3.1 15.2 + - - +
123B LEU* 2.5 55.2 + - + +
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Residues in contact with LYS 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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113B TRP 4.1 9.2 + - - +
114B SER* 4.4 23.1 - - - +
116B SER* 3.9 17.5 + - - +
117B GLY 4.2 4.0 + - - +
118B ARG 3.4 0.4 - - - -
119B GLU* 1.3 74.7 - - - +
121B LEU* 1.3 67.6 + - - +
123B LEU* 2.8 19.5 + - + +
124B ASP* 2.8 47.5 + - - +
130B ASP* 3.7 31.5 + - - -
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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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282A ILE* 4.1 22.4 - - + -
117B GLY 3.9 12.0 + - - +
118B ARG* 3.6 13.2 + - + +
120B LYS* 1.3 78.5 - - - +
122B ARG* 1.3 68.3 + - - +
124B ASP* 3.6 5.5 + - - +
125B GLU* 3.4 25.9 + - + +
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Residues in contact with ARG 122 (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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101A ARG* 3.0 55.0 - - - +
282A ILE* 3.7 26.3 - - + +
118B ARG* 3.2 64.4 + - - +
119B GLU* 3.1 20.4 + - - +
121B LEU* 1.3 83.8 - - - +
123B LEU* 1.3 65.1 + - - +
125B GLU* 3.0 16.1 + - - +
126B ALA* 3.3 6.6 + - - +
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Residues in contact with LEU 123 (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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100A THR 3.2 27.1 - - - +
101A ARG* 4.3 7.4 - - + +
102A ILE* 4.2 14.8 - - + -
113B TRP* 4.1 23.1 - - + +
119B GLU* 2.5 47.4 + - + +
120B LYS* 2.8 9.2 + - + +
122B ARG* 1.3 71.3 - - - +
124B ASP* 1.3 61.6 + - - +
126B ALA* 3.2 9.2 + - - +
128B VAL* 2.9 51.1 + - + +
133B LEU* 5.2 12.8 - - + -
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Residues in contact with ASP 124 (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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120B LYS* 2.8 57.1 + - - +
121B LEU* 4.1 4.9 + - - +
123B LEU* 1.3 69.5 - - - +
125B GLU* 1.3 55.2 + - + +
127B GLY* 2.6 29.8 + - - -
128B VAL 3.6 4.2 - - - +
129B THR* 3.3 36.8 - - + +
130B ASP* 4.2 2.9 + - - +
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Residues in contact with GLU 125 (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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98A GLU* 3.3 16.5 - - - +
279A LEU 4.8 1.7 - - - +
280A SER* 4.2 13.4 - - - +
281A LYS* 3.6 34.7 + - - +
282A ILE* 4.8 9.6 - - + -
121B LEU* 3.4 24.9 + - + +
122B ARG* 3.0 14.1 + - - +
124B ASP* 1.3 78.3 - - + +
126B ALA* 1.3 56.6 + - - +
127B GLY* 3.0 3.7 + - - -
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Residues in contact with ALA 126 (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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98A GLU* 3.5 24.6 - - + +
99A GLU 3.2 27.8 - - - +
100A THR* 4.6 2.0 - - - +
101A ARG* 5.8 1.6 - - + -
148A HIS* 2.9 26.0 + - - +
280A SER* 5.3 1.5 - - - -
283A GLU* 5.3 0.7 - - - +
122B ARG 3.3 5.7 + - - +
123B LEU* 3.2 15.6 + - - +
124B ASP 3.0 1.0 + - - -
125B GLU* 1.3 77.6 - - - +
127B GLY* 1.3 54.4 - - - +
128B VAL* 3.2 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