Contacts of the helix formed by residues 98 - 109 (chain B) in PDB entry 2AAO
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 GLU 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ASN* 4.3 7.6 - - - +
96A GLU* 5.4 1.6 - - - -
32B MSE 5.0 2.2 - - + -
56B VAL 4.3 1.9 - - - +
57B GLY* 3.8 19.7 - - - +
94B LYS 4.6 2.0 + - - +
95B ILE 5.0 1.0 + - - -
96B GLU 3.3 0.4 - - - -
97B ARG* 1.3 113.3 + - + +
99B ASP* 1.3 59.8 + - - +
100B HIS 3.3 2.9 - - - -
101B LEU* 3.1 16.0 + - + +
102B PHE* 2.8 29.2 + - - +
152B TYR* 3.1 30.8 + - + +
156B VAL* 3.9 22.1 - - - +
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Residues in contact with ASP 99 (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 HIS* 5.9 6.0 - - + +
25B GLU* 5.3 8.3 - - + +
28B GLY* 5.5 0.9 - - - -
29B LEU* 3.6 17.7 - - + +
32B MSE 3.3 12.8 - - - +
89B THR* 3.5 18.2 - - - +
95B ILE 2.7 22.2 - - - +
96B GLU* 3.2 33.9 + - + +
97B ARG 3.5 0.8 + - - -
98B GLU* 1.3 72.4 - - - +
100B HIS* 1.3 65.3 + - + +
102B PHE* 3.8 5.9 - - - +
103B ALA* 2.9 27.0 + - - +
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Residues in contact with HIS 100 (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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17A ILE* 3.8 28.3 - - + +
20A SER* 6.4 0.7 - - - -
21A LEU* 3.9 9.8 - - + +
25A GLU* 2.8 28.9 + - - -
90A LEU* 5.4 0.4 - - - +
96A GLU* 3.2 57.8 + - - +
97A ARG* 5.3 0.2 - - - -
99A ASP* 3.4 13.7 + - + -
100A HIS* 3.9 11.1 + + - -
25B GLU* 3.2 24.5 + - + -
98B GLU 3.3 0.8 - - - -
99B ASP* 1.3 75.1 - - + +
101B LEU* 1.3 68.1 + - - +
103B ALA* 3.0 15.5 + - - +
104B ALA 3.0 9.9 + - - -
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Residues in contact with LEU 101 (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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17A ILE* 4.2 12.3 - - + -
96A GLU* 5.0 3.3 + - - +
98B GLU* 3.1 22.0 + - + +
100B HIS* 1.3 79.8 - - - +
102B PHE* 1.3 62.8 + - - +
104B ALA* 3.2 5.2 + - + +
105B PHE* 3.1 17.5 + - - +
152B TYR* 3.8 7.9 - - - +
155B PHE* 3.5 35.5 - - + -
156B VAL* 3.9 29.2 - - + -
159B MSE 3.6 41.5 - - + -
160B GLN 6.1 0.7 - - - +
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Residues in contact with PHE 102 (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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28B GLY 3.3 18.8 - - - +
31B GLU* 3.6 17.5 - - + -
32B MSE 3.3 60.8 - - + -
35B MSE 3.7 19.3 - - - -
56B VAL* 3.9 16.2 - - + -
98B GLU 2.8 12.7 + - - +
99B ASP 3.8 3.8 - - - +
100B HIS 3.1 0.2 - - - -
101B LEU* 1.3 79.6 - - - +
103B ALA* 1.3 57.0 + - - +
105B PHE* 3.3 7.6 + + + +
106B THR* 3.0 31.5 + - - -
152B TYR* 3.5 47.7 + + - -
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Residues in contact with ALA 103 (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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16A VAL* 4.7 2.6 - - - +
20A SER* 5.4 5.8 + - - -
24B GLU* 3.5 28.3 - - + +
25B GLU* 3.9 17.9 - - + +
28B GLY* 4.0 12.7 - - - -
99B ASP 2.9 14.6 + - - +
100B HIS* 3.0 8.7 + - - +
102B PHE* 1.3 73.6 - - - +
104B ALA* 1.3 65.1 + - - +
106B THR* 3.5 2.3 + - - -
107B TYR* 3.1 21.1 + - - +
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Residues in contact with ALA 104 (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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13A ALA* 4.1 13.0 - - + +
16A VAL* 4.0 15.7 - - + -
17A ILE* 3.9 27.8 - - + +
100B HIS 3.0 6.3 + - - -
101B LEU 3.2 8.7 + - - +
103B ALA* 1.3 74.2 - - - +
105B PHE* 1.3 67.6 + - - +
107B TYR* 3.1 10.6 + - - +
108B PHE* 3.1 21.9 + - + -
155B PHE* 4.1 13.9 - - + -
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Residues in contact with PHE 105 (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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31B GLU* 3.6 22.7 - - - -
35B MSE 5.3 1.8 - - - -
101B LEU 3.1 11.9 + - - +
102B PHE* 3.3 17.2 + + - +
104B ALA* 1.3 75.7 - - - +
106B THR* 1.3 59.4 + - - +
108B PHE* 3.1 8.6 + - - +
109B ASP* 3.0 27.9 + - + +
114B GLY* 3.3 31.0 - - - -
115B TYR* 4.1 2.7 - - - -
116B ILE* 3.6 22.8 - - + +
150B ILE 3.5 21.3 - - - -
151B ASP 3.6 4.0 - - - -
152B TYR* 3.5 43.3 - + + -
155B PHE* 3.6 27.2 - + + -
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Residues in contact with THR 106 (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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24B GLU 5.6 0.2 - - - -
27B ALA* 3.8 31.2 - - + +
28B GLY* 3.5 9.6 - - - -
31B GLU* 3.3 36.9 - - + +
102B PHE* 3.0 19.4 + - - -
103B ALA* 3.7 6.1 - - - -
104B ALA 3.1 0.4 - - - -
105B PHE* 1.3 75.3 - - - +
107B TYR* 1.3 65.9 + - - +
109B ASP* 3.3 24.4 - - - +
110B LYS* 4.8 0.3 - - - -
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Residues in contact with TYR 107 (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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12A MSE 5.9 1.8 - - + -
16A VAL* 3.6 41.3 - - + -
24B GLU* 6.2 3.8 - - + -
103B ALA 3.1 13.2 + - - +
104B ALA 3.1 9.3 + - - +
106B THR* 1.3 78.3 - - - +
108B PHE* 1.3 82.7 + + - +
110B LYS* 3.5 41.9 + - - +
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Residues in contact with PHE 108 (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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9A PHE* 3.8 30.3 - + - -
12A MSE 4.0 24.9 - - + -
13A ALA* 3.9 31.2 - - + -
16A VAL* 3.8 20.4 - - + -
104B ALA 3.1 25.1 + - - -
105B PHE 3.1 2.7 + - - +
107B TYR* 1.3 94.3 - + - +
109B ASP* 1.3 57.4 + - - +
110B LYS* 2.9 16.1 + - - +
116B ILE* 3.6 25.9 - - + +
120B GLU* 3.6 29.1 - - - +
121B LEU* 5.3 4.0 - - + -
155B PHE* 4.2 8.7 - + - -
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Residues in contact with ASP 109 (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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31B GLU* 2.4 34.7 - - - +
105B PHE* 3.0 19.0 + - + +
106B THR* 3.3 15.4 + - - +
108B PHE* 1.3 73.1 - - - +
110B LYS* 1.3 63.4 + - - +
111B ASP 3.0 1.5 + - - -
112B GLY* 3.0 18.3 + - - -
113B SER* 3.1 3.2 + - - -
114B GLY 2.9 17.4 + - - -
115B TYR 3.9 6.1 - - - -
116B ILE* 4.1 8.5 - - + +
120B GLU* 3.8 6.3 - - - -
299B CA 2.3 31.2 - - - -
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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