Contacts of the helix formed by residues 10 - 22 (chain B) in PDB entry 2OB1
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 TYR 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ASP* 1.3 60.0 + - + +
12B ALA* 3.2 20.1 - - + +
13B LEU* 2.9 32.3 - - + +
14B SER* 2.7 33.0 + - - -
52B LEU* 5.6 0.8 - - - +
59B ALA* 5.8 3.2 - - - +
62B LYS* 5.9 5.1 - - - +
63B VAL* 3.4 22.6 - - - +
106B CYS 4.2 1.2 + - - -
107B GLY* 3.2 17.9 - - - -
108B SER* 2.5 42.4 + - - -
109B ASP 4.3 0.3 + - - -
129B TYR* 5.6 5.8 - - - -
132B SER* 5.6 1.6 - - - -
255B ARG* 4.3 17.0 - - - +
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Residues in contact with ASP 11 (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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10B TYR* 1.3 76.2 - - + +
12B ALA* 1.3 66.0 + - - +
14B SER* 3.2 6.1 + - - -
15B CYS* 3.0 40.2 + - - -
66B ALA* 5.2 9.7 - - - +
255B ARG* 3.3 25.6 + - - +
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Residues in contact with ALA 12 (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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10B TYR* 3.2 22.4 - - + +
11B ASP* 1.3 77.0 - - - +
13B LEU* 1.3 56.1 - - - +
15B CYS* 3.3 7.0 + - - +
16B LYS* 2.9 30.6 + - - +
81B ARG* 3.8 30.1 - - - +
108B SER* 5.1 0.2 - - - -
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Residues in contact with LEU 13 (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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10B TYR* 2.9 26.1 - - + +
12B ALA* 1.3 72.5 - - - +
14B SER* 1.3 57.9 + - - +
16B LYS* 3.2 8.2 + - + +
17B LEU* 2.8 63.7 + - + +
45B HIS* 5.1 6.5 - - + -
48B TYR* 4.0 32.8 - - + -
49B LEU* 5.2 0.7 - - + -
52B LEU* 3.8 29.2 - - + -
63B VAL* 4.3 8.5 - - + -
108B SER* 3.5 26.0 - - - +
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Residues in contact with SER 14 (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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10B TYR 2.7 25.2 + - - -
11B ASP* 3.6 5.2 - - - -
13B LEU* 1.3 75.4 - - - +
15B CYS* 1.3 59.4 + - - +
17B LEU* 3.4 1.8 + - - +
18B ALA* 2.8 31.1 + - - +
62B LYS 4.2 0.3 + - - -
63B VAL* 3.2 36.4 - - - +
66B ALA* 3.5 28.1 - - - +
67B MET* 4.0 7.6 - - - -
74B MET* 4.7 2.2 - - - -
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Residues in contact with CYS 15 (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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11B ASP* 3.0 34.6 + - - +
12B ALA* 3.6 9.9 - - - +
14B SER* 1.3 77.3 - - - +
16B LYS* 1.3 65.2 + - - +
18B ALA* 3.4 1.9 + - - +
19B ALA* 3.0 18.9 + - - +
74B MET* 3.5 31.6 - - - -
75B ASN* 4.6 1.2 - - - +
78B THR* 3.3 31.4 + - + +
81B ARG* 5.8 6.7 - - - +
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Residues in contact with LYS 16 (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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12B ALA 2.9 17.7 + - - +
13B LEU* 3.5 10.3 - - + +
15B CYS* 1.3 77.5 - - - +
17B LEU* 1.3 63.7 + - + +
19B ALA* 3.3 2.6 + - - +
20B ILE* 3.0 34.9 + - + +
25B LEU* 3.9 9.9 - - + -
41B TYR* 3.7 8.7 - - - +
45B HIS* 3.8 24.0 - - + +
78B THR* 3.8 7.3 - - - +
82B THR* 3.3 26.3 + - - +
111B ARG* 5.2 1.4 - - - +
201B GLU* 5.2 5.9 + - - -
2003B PO4 2.7 43.2 + - - +
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Residues in contact with LEU 17 (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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13B LEU* 2.8 49.2 + - + +
14B SER 4.0 0.9 - - - +
16B LYS* 1.3 71.9 - - - +
18B ALA* 1.3 57.1 + - - +
20B ILE* 3.3 5.9 + - + +
21B SER* 2.8 30.7 + - - -
45B HIS* 3.7 43.3 - - + +
46B ARG* 5.5 0.7 - - - -
49B LEU* 3.6 30.3 - - + -
63B VAL* 3.8 1.6 - - + -
67B MET* 3.5 37.7 - - + +
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Residues in contact with ALA 18 (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 SER 2.8 18.1 + - - +
15B CYS 3.7 3.6 - - - +
16B LYS 3.3 0.2 - - - -
17B LEU* 1.3 76.3 - - - +
19B ALA* 1.3 60.7 + - - +
21B SER* 3.3 6.0 + - - -
22B VAL* 3.1 25.6 + - - +
67B MET* 3.6 17.8 - - - +
70B SER* 3.5 24.9 + - - +
74B MET* 4.3 5.2 - - + -
75B ASN* 3.5 18.0 + - - +
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Residues in contact with ALA 19 (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 CYS 3.0 17.6 + - - +
16B LYS 3.8 2.7 - - - +
18B ALA* 1.3 76.7 - - - +
20B ILE* 1.3 59.3 - - - +
22B VAL* 3.5 7.2 - - - +
23B GLY 3.3 2.3 + - - -
24B TYR* 2.9 31.6 + - + -
25B LEU* 3.4 18.4 + - + -
75B ASN* 3.7 17.9 + - - +
78B THR* 3.7 24.7 - - + -
79B TYR 4.6 0.2 - - - +
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Residues in contact with ILE 20 (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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16B LYS* 3.0 28.0 + - + +
17B LEU* 3.7 7.0 - - + +
19B ALA* 1.3 74.6 - - - +
21B SER* 1.3 66.3 + - - +
23B GLY* 2.9 14.7 + - - -
25B LEU* 3.4 22.0 - - + +
26B PRO* 5.0 0.2 - - + -
41B TYR* 3.7 20.4 - - + -
42B THR* 3.9 37.1 - - + +
45B HIS* 3.4 45.8 - - + +
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Residues in contact with SER 21 (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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17B LEU 2.8 21.2 + - - -
18B ALA* 3.3 8.7 + - - -
20B ILE* 1.3 74.5 - - - +
22B VAL* 1.3 60.3 + - - +
23B GLY* 3.4 0.7 + - - -
67B MET* 5.4 8.1 - - - -
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Residues in contact with VAL 22 (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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18B ALA 3.1 14.7 + - - +
19B ALA* 3.5 15.3 - - - +
21B SER* 1.3 76.9 - - - +
23B GLY* 1.3 55.3 + - - +
24B TYR* 3.6 24.2 - - + -
75B ASN* 3.8 16.8 - - - +
305B LEU* 3.4 28.7 - - - +
306B GLN* 3.6 40.8 - - + +
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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