Contacts of the helix formed by residues 86 - 94 (chain B) in PDB entry 1A7A
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 ASN 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 5.3 1.0 - - - +
10B ALA* 3.4 30.4 + - + +
11B ASP 5.3 1.0 + - - +
14B LEU* 3.7 20.7 - - + +
85B GLN* 1.3 70.3 - - - +
87B HIS* 1.3 54.8 + - - +
89B ALA* 2.9 7.8 + - - +
90B ALA* 2.6 36.4 + - - +
102B TRP* 3.4 6.2 - - - -
103B LYS* 3.0 44.4 + - - +
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Residues in contact with HIS 87 (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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14B LEU* 3.5 27.8 - - + +
17B TRP* 3.5 70.9 - + + -
18B GLY* 3.3 13.2 - - - +
21B ALA* 3.8 21.2 - - + +
58B VAL* 3.8 10.7 - - + +
85B GLN* 4.1 23.2 - - + -
86B ASN* 1.3 76.2 + - - +
88B ALA* 1.3 63.7 + - - +
90B ALA* 3.7 0.9 - - - +
91B ALA 2.9 24.3 + - - -
351B MSE 5.1 11.4 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY* 4.7 1.1 - - - -
22B LEU* 4.4 8.1 - - + -
56B MSE 4.1 2.5 - - + +
57B THR* 3.7 7.6 - - - +
58B VAL* 3.5 45.5 - - + +
61B ALA* 4.5 1.4 - - + +
85B GLN* 3.1 11.5 + - + +
87B HIS* 1.3 80.7 - - - +
89B ALA* 1.3 69.8 + - - +
91B ALA* 3.4 6.9 + - - +
92B ILE* 3.3 26.2 + - - +
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Residues in contact with ALA 89 (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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9B VAL* 4.1 14.3 - - + +
56B MSE 3.6 25.3 - - + +
84B THR* 4.0 9.6 - - + -
85B GLN 2.8 13.4 + - - +
86B ASN* 3.1 14.4 - - - +
88B ALA* 1.3 78.9 - - - +
90B ALA* 1.3 62.5 + - - +
92B ILE* 3.2 4.9 + - - +
93B ALA* 3.1 18.5 + - - +
99B VAL* 4.1 4.1 - - + +
101B ALA 4.1 13.0 - - - +
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Residues in contact with ALA 90 (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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9B VAL* 4.3 6.4 - - + +
11B ASP 3.5 25.4 - - - +
12B ILE* 3.8 10.6 - - - +
14B LEU* 4.1 2.0 - - + -
15B ALA* 3.7 20.6 - - - +
86B ASN 2.6 18.5 + - - +
87B HIS 3.7 2.2 - - - +
89B ALA* 1.3 70.0 - - - +
91B ALA* 1.3 67.3 + - - +
93B ALA* 2.8 9.5 + - - +
94B LYS* 2.8 24.8 + - - +
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Residues in contact with ALA 91 (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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15B ALA* 4.0 13.8 - - - +
18B GLY* 3.8 22.9 - - - -
19B ARG* 4.0 16.0 + - - +
22B LEU* 4.1 17.0 - - + -
87B HIS 2.9 21.4 + - - +
88B ALA* 3.7 6.3 - - - +
89B ALA 3.4 0.2 - - - -
90B ALA* 1.3 73.6 - - - +
92B ILE* 1.3 63.5 + - - +
94B LYS* 3.4 5.0 + - - +
95B ALA* 3.1 19.6 + - - +
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Residues in contact with ILE 92 (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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22B LEU* 4.7 0.7 - - + -
56B MSE 3.2 31.6 - - + -
61B ALA* 3.7 34.5 - - + +
64B ILE* 4.2 11.7 - - + -
65B GLU* 3.8 23.6 - - + +
88B ALA 3.3 4.9 + - - +
89B ALA 3.2 1.9 + - - +
90B ALA 3.1 0.8 - - - -
91B ALA* 1.3 75.6 - - + +
93B ALA* 1.3 66.8 + - - +
95B ALA* 2.9 19.1 + - + +
97B ILE* 3.4 30.4 + - + -
99B VAL* 3.1 22.2 - - + -
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Residues in contact with ALA 93 (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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7B TYR* 3.8 38.6 - - + -
9B VAL* 3.9 11.7 - - + -
12B ILE* 3.7 15.3 - - + -
89B ALA 3.1 10.8 + - - +
90B ALA 2.8 11.1 + - - +
92B ILE* 1.3 71.7 - - - +
94B LYS* 1.3 55.3 + - - +
96B GLY* 2.7 28.8 + - - -
97B ILE 3.7 11.9 + - - +
99B VAL* 3.9 1.7 - - + +
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Residues in contact with LYS 94 (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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7B TYR* 5.9 0.7 - - - -
12B ILE* 3.6 18.0 - - + +
15B ALA* 3.6 26.3 - - + +
16B ALA* 5.7 2.8 - - - +
19B ARG* 6.2 3.6 - - + +
90B ALA 2.8 14.7 + - - +
91B ALA* 3.6 8.5 - - - +
93B ALA* 1.3 73.2 - - - +
95B ALA* 1.3 55.4 + - - +
96B GLY* 3.0 4.9 + - - -
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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