Contacts of the helix formed by residues 10 - 23 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP* 1.3 59.4 + - - +
12C ALA* 3.5 4.3 - - - +
13C LEU* 3.9 14.2 - - + +
14C SER* 2.7 39.1 + - - +
52C LEU* 4.5 7.4 - - + -
56C SER* 5.0 1.4 + - - -
58C ARG* 6.3 0.7 - - + -
59C ALA* 3.4 35.0 - - + +
62C LYS* 4.4 27.4 - - + -
63C VAL* 3.7 25.9 - - + +
135C LEU* 3.5 29.3 - - + +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TYR* 1.3 73.9 - - - +
12C ALA* 1.3 70.6 + - - +
14C SER* 3.2 6.7 + - - -
15C CYS* 3.0 37.6 + - - -
66C ALA* 6.0 1.8 - - - -
81C ARG* 5.6 3.5 + - - -
206C TYR* 4.8 8.7 + - - -
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.5 2.7 - - - +
11C ASP* 1.3 81.9 + - - +
13C LEU* 1.3 56.8 - - - +
15C CYS* 3.2 8.5 + - - +
16C LYS* 2.9 28.9 + - - +
78C THR* 5.5 0.2 - - - +
81C ARG* 3.7 28.9 - - - +
108C SER* 5.0 4.7 - - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.5 18.8 + - + +
11C ASP 3.3 0.4 - - - -
12C ALA* 1.3 77.4 - - - +
14C SER* 1.3 58.0 + - - +
16C LYS* 3.2 8.4 + - + +
17C LEU* 2.8 62.9 + - + +
45C HIS* 5.4 6.5 - - + -
48C TYR* 4.1 28.3 - - + -
49C LEU* 5.4 2.0 - - + -
52C LEU* 3.8 28.5 - - + -
63C VAL* 4.3 8.7 - - + -
108C SER* 3.4 33.5 + - - +
110C LEU* 6.4 0.2 - - + -
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR 2.7 23.8 + - - -
11C ASP* 3.2 5.6 + - - -
13C LEU* 1.3 73.2 - - - +
15C CYS* 1.3 67.0 + - - +
18C ALA* 2.9 25.8 + - - +
62C LYS 4.1 0.5 + - - -
63C VAL* 3.1 38.3 + - - +
66C ALA* 3.5 28.1 - - - +
67C MET* 3.6 8.9 - - - +
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Residues in contact with CYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 3.0 31.6 + - - -
12C ALA* 3.5 9.9 - - - +
14C SER* 1.3 80.3 - - - +
16C LYS* 1.3 63.2 + - - +
18C ALA* 3.3 5.4 + - - +
19C ALA* 3.0 23.9 + - - +
74C MET* 5.0 20.9 - - - -
75C ASN* 4.6 1.8 - - - +
78C THR* 3.2 26.8 + - + +
81C ARG* 5.9 7.0 - - - +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA 2.9 16.3 + - - +
13C LEU* 3.2 9.8 + - + +
15C CYS* 1.3 77.2 - - - +
17C LEU* 1.3 57.8 + - + +
19C ALA* 3.3 2.6 + - - +
20C ILE* 3.0 35.9 + - + +
25C LEU* 3.7 14.1 - - + -
41C TYR* 3.6 10.8 - - - +
45C HIS* 3.8 24.9 - - + -
78C THR* 3.9 9.2 - - + -
82C THR* 3.1 29.2 + - - +
111C ARG* 4.6 2.0 - - - +
201C GLU* 5.0 6.2 + - - -
2004C PO4 2.6 43.1 + - - +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 2.8 45.5 + - + +
14C SER 3.9 0.9 - - - +
16C LYS* 1.3 77.7 - - - +
18C ALA* 1.3 51.9 + - - +
20C ILE* 3.3 6.2 + - + +
21C SER* 2.7 35.7 + - - -
45C HIS* 3.5 43.3 - - + +
46C ARG* 4.6 3.1 - - + +
49C LEU* 3.8 27.8 - - + -
63C VAL* 3.7 19.5 - - + -
67C MET* 3.7 19.9 - - + +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C SER 2.9 18.3 + - - +
15C CYS* 3.6 5.4 - - - +
17C LEU* 1.3 76.5 - - - +
19C ALA* 1.4 58.0 + - - +
21C SER* 3.2 6.1 + - - -
22C VAL* 2.9 36.1 + - + +
67C MET* 4.1 15.1 - - - +
70C SER* 3.4 36.3 - - - +
75C ASN* 3.7 6.5 - - - +
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C CYS 3.0 12.5 + - - +
16C LYS 3.6 7.9 - - - +
18C ALA* 1.4 72.9 - - - +
20C ILE* 1.3 61.3 - - - +
23C GLY 2.9 7.8 + - - -
24C TYR* 2.9 46.3 + - + -
25C LEU* 3.4 16.1 + - + -
75C ASN* 4.0 11.8 + - - +
78C THR* 3.9 22.4 - - + -
79C TYR 4.9 0.2 - - - +
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Residues in contact with ILE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 4.0 3.8 + - - -
16C LYS* 3.0 26.2 + - + +
17C LEU* 3.6 10.1 - - + +
19C ALA* 1.3 74.5 - - - +
21C SER* 1.3 67.6 + - - +
23C GLY* 3.1 13.5 + - - -
25C LEU* 3.4 18.1 - - + +
41C TYR* 3.6 20.9 - - + -
42C THR* 3.7 41.2 - - + +
45C HIS* 3.3 47.1 - - + +
46C ARG* 5.2 5.6 - - + -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.3 23.4 + - - -
46A ARG* 2.8 32.2 + - - +
17C LEU 2.7 21.9 + - - -
18C ALA* 3.2 8.9 + - - -
20C ILE* 1.3 73.4 - - - +
22C VAL* 1.3 62.0 + - - +
46C ARG* 5.7 5.6 + - - +
67C MET* 4.4 13.1 - - - +
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.4 7.4 + - - -
50A ILE* 5.2 4.8 - - + +
68A ARG* 6.0 0.2 - - - +
18C ALA* 2.9 20.8 + - + +
21C SER* 1.3 81.5 - - - +
23C GLY* 1.3 56.5 + - - +
24C TYR* 3.6 27.4 - - + -
70C SER* 5.3 3.1 - - - +
75C ASN* 4.1 8.3 - - - +
305C LEU* 3.9 23.6 - - + +
306C GLN* 3.7 34.5 - - + +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.6 12.8 - - - -
19C ALA 2.9 4.6 + - - -
20C ILE 3.1 9.3 + - - -
22C VAL* 1.3 78.6 - - - +
24C TYR* 1.3 58.3 + - - +
25C LEU* 3.2 8.2 + - - +
26C PRO 4.4 1.2 - - - +
301C ARG* 2.7 29.3 + - - -
305C LEU* 3.6 9.9 - - - +
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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
------------------------------------------------------------
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