Contacts of the helix formed by residues 69 - 74 (chain A) in PDB entry 5AQX
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A THR* 3.5 35.4 + - - +
14A THR* 4.7 7.1 - - - +
40A SER 4.4 1.6 + - - -
68A PHE* 1.3 93.6 - - - +
70A ALA* 1.3 63.7 + - - +
71A LYS 3.2 3.8 - - - +
72A ARG* 3.2 40.8 + - - +
73A LEU* 3.9 3.0 + - - +
90A TRP* 3.2 37.1 + - + +
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Residues in contact with ALA 70 (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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13A THR 5.3 0.6 + - - -
40A SER 5.6 1.3 + - - +
67A VAL* 5.0 3.8 - - + -
68A PHE 3.3 4.4 - - - +
69A ASP* 1.3 77.7 - - - +
71A LYS* 1.4 50.8 + - - +
72A ARG 3.2 0.2 - - - -
73A LEU* 3.0 14.1 + - + +
74A ILE* 2.8 35.0 + - - +
116A PRO* 3.7 21.5 - - + +
119A ILE* 3.8 30.5 - - + -
120A SER* 4.1 7.9 - - - +
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Residues in contact with LYS 71 (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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11A LEU* 2.9 29.2 + - + +
12A GLY* 3.5 14.6 - - - +
13A THR* 3.4 41.5 + - + +
69A ASP 4.9 0.2 - - - -
70A ALA* 1.4 75.3 - - - +
72A ARG* 1.3 63.3 + - - +
73A LEU 3.5 0.2 + - - -
74A ILE* 3.6 21.8 - - + +
120A SER* 4.8 4.1 + - - +
146A VAL* 5.1 1.8 - - - +
147A PRO* 3.6 28.7 - - - +
150A PHE* 4.0 16.2 - - + -
154A GLN* 5.1 0.9 + - - -
175A GLU* 2.8 28.6 + - - -
1391A DMS 3.8 13.5 + - + +
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Residues in contact with ARG 72 (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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13A THR* 4.1 9.7 - - + +
69A ASP* 3.2 41.2 + - - +
70A ALA 3.2 0.6 - - - -
71A LYS* 1.3 77.2 - - - +
73A LEU* 1.3 58.9 + - - +
76A ARG* 2.7 32.7 + - - -
82A VAL* 4.6 3.7 - - - +
86A ASP* 3.5 26.2 + - - +
90A TRP* 4.0 10.1 - - + -
203A GLY* 3.0 21.4 + - - -
204A THR* 3.4 14.1 - - - +
226A THR* 2.9 34.9 + - - -
227A HIS* 3.3 30.3 + - - -
1391A DMS 3.3 23.2 + - + +
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Residues in contact with LEU 73 (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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69A ASP 4.3 4.5 - - - +
70A ALA* 3.0 10.9 + - - +
72A ARG* 1.3 79.1 - - - +
74A ILE* 1.3 63.8 + - - +
75A GLY 3.5 0.5 + - - -
76A ARG* 3.2 18.6 + - - +
83A VAL* 3.6 36.8 - - + -
86A ASP* 5.4 0.4 - - + +
90A TRP* 3.4 42.6 - - + -
92A PHE* 5.1 1.6 - - + -
94A VAL* 4.3 11.9 - - + -
101A PRO* 4.1 13.5 - - + +
103A VAL* 4.1 25.6 - - + -
116A PRO* 3.6 22.7 - - + +
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Residues in contact with ILE 74 (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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11A LEU* 5.5 2.0 - - + -
70A ALA 2.8 15.8 + - - +
71A LYS* 3.6 23.3 - - + +
72A ARG 3.7 0.4 - - - -
73A LEU* 1.3 72.7 - - - +
75A GLY* 1.3 61.9 + - - +
76A ARG* 3.0 10.2 + - - +
116A PRO* 3.7 5.8 - - + -
117A GLU* 4.0 20.9 - - - +
120A SER* 3.8 24.2 - - - +
150A PHE* 3.9 23.8 - - + -
154A GLN* 3.5 16.3 + - - +
157A ALA* 3.4 35.7 - - + +
158A THR* 3.9 14.1 - - + +
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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