Contacts of the helix formed by residues 19 - 32 (chain C) in PDB entry 4O46
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 ARG 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG* 4.5 10.1 - - - +
59A SER* 3.8 12.2 + - - +
85A TYR* 3.1 21.0 + - - +
88A LYS* 4.1 9.9 - - - +
89A ILE* 3.5 39.1 - - - +
92A GLU* 2.8 43.0 + - - -
14C ALA* 2.8 20.3 + - - +
17C ALA* 3.5 15.5 - - - +
18C GLU* 1.3 71.4 - - - +
20C TYR* 1.3 58.2 + - - +
21C ASP* 3.3 3.1 - - - -
22C ASP* 2.9 37.2 + - + +
23C MET 3.1 20.6 + - - -
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Residues in contact with TYR 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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15C GLU* 3.9 17.7 + - + +
18C GLU* 3.6 42.2 + - + +
19C ARG* 1.3 72.1 - - - +
21C ASP* 1.4 60.1 + - - +
23C MET* 3.4 29.4 - - - +
24C ALA* 2.9 31.4 + - - +
47C VAL* 4.4 6.5 - - + -
48C ALA* 3.9 9.3 - - - +
51C ASN* 3.4 54.0 + - + -
52C VAL* 3.5 10.8 - - + +
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Residues in contact with ASP 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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19C ARG 3.3 0.8 - - - -
20C TYR* 1.4 75.8 - - - +
22C ASP* 1.4 59.9 + - - +
24C ALA* 3.4 3.1 + - - +
25C ALA* 3.0 29.2 + - - +
52C VAL* 3.5 28.2 - - - +
56C ARG* 4.1 16.6 + - - -
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 2.7 39.5 + - + +
88A LYS* 3.4 21.1 + - - -
10C LYS* 5.1 5.4 - - + +
14C ALA* 4.1 4.9 - - + +
19C ARG* 2.9 35.8 + - - +
21C ASP* 1.4 75.6 - - - +
23C MET* 1.4 62.7 + - - +
25C ALA* 3.5 8.4 + - - +
26C ALA* 3.1 23.2 + - - +
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Residues in contact with MET 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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11C ALA* 3.4 21.8 - - + +
14C ALA* 3.7 9.4 - - + +
15C GLU* 3.6 43.7 - - + +
19C ARG 3.1 13.5 + - - +
20C TYR* 3.4 31.9 - - - +
21C ASP 3.3 0.2 - - - -
22C ASP* 1.4 72.5 - - - +
24C ALA* 1.4 59.4 + - - +
26C ALA* 3.2 4.9 + - - +
27C MET* 3.0 29.0 + - + +
44C LEU* 3.3 42.8 - - + +
47C VAL* 4.2 4.5 - - + -
48C ALA* 3.7 13.2 - - + -
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Residues in contact with ALA 24 (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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20C TYR 2.9 17.7 + - - +
21C ASP* 3.7 4.7 - - - +
23C MET* 1.4 73.9 - - - +
25C ALA* 1.4 53.9 + - - +
27C MET* 3.4 1.6 + - - +
28C LYS* 2.8 35.7 + - - +
48C ALA* 3.5 14.7 - - + +
49C TYR* 3.8 36.8 + - + +
52C VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 25 (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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21C ASP 3.0 17.3 + - - +
22C ASP* 3.6 9.4 - - - +
23C MET 3.3 0.2 - - - -
24C ALA* 1.4 76.7 - - - +
26C ALA* 1.4 59.7 + - - +
28C LYS* 3.5 8.2 + - - +
29C ASN* 3.2 21.8 + - - +
49C TYR* 5.4 0.4 - - - -
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Residues in contact with ALA 26 (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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7C LEU* 3.5 31.1 - - + +
10C LYS* 4.4 10.3 - - + -
11C ALA* 4.1 13.7 - - + +
22C ASP 3.1 13.9 + - - +
23C MET 3.5 7.4 - - - +
25C ALA* 1.4 71.8 - - - +
27C MET* 1.3 61.5 + - - +
29C ASN* 3.3 9.1 + - - +
30C VAL* 3.1 32.1 + - - +
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Residues in contact with MET 27 (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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8C VAL* 4.7 4.3 - - - -
11C ALA* 3.5 25.8 - - + -
23C MET* 3.0 18.8 + - + +
24C ALA* 4.0 3.4 - - - +
26C ALA* 1.3 73.6 - - - +
28C LYS* 1.4 55.5 + - - +
30C VAL* 3.4 27.3 + - + +
31C THR* 2.8 36.7 + - - -
37C LEU* 4.7 3.8 - - + -
41C GLU* 3.2 43.1 - - + +
44C LEU* 3.8 16.4 - - - +
45C LEU* 3.7 37.7 - - + +
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Residues in contact with LYS 28 (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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24C ALA 2.8 18.7 + - - +
25C ALA* 3.7 9.6 - - - +
27C MET* 1.4 75.3 - - - +
29C ASN* 1.4 55.4 + - - +
31C THR* 3.2 4.2 + - - -
32C GLU* 2.9 56.7 + - - +
45C LEU* 4.4 0.6 - - - +
49C TYR* 3.6 13.5 - - - +
99C ASP* 3.1 30.6 + - - +
103C LEU* 3.7 30.1 - - + -
28D LYS* 4.0 11.9 - - - +
32D GLU* 3.4 23.3 + - - -
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Residues in contact with ASN 29 (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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2C VAL* 4.7 10.4 - - - +
7C LEU* 3.6 33.2 - - + +
25C ALA 3.2 12.2 + - - +
26C ALA 3.3 9.8 + - - +
28C LYS* 1.4 79.4 - - - +
30C VAL* 1.4 60.3 + - - +
32C GLU* 3.4 23.9 + - - +
33C LEU* 3.4 20.4 + - - +
98D GLN* 5.3 5.3 - - - +
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Residues in contact with VAL 30 (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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4C ARG* 3.5 42.6 + - + +
7C LEU* 3.6 24.2 - - + -
8C VAL* 3.9 22.7 - - + +
26C ALA 3.1 18.5 + - - +
27C MET* 3.6 18.8 - - + +
28C LYS 3.3 0.2 - - - -
29C ASN* 1.4 73.9 - - - +
31C THR* 1.4 61.8 + - - +
33C LEU* 3.1 27.6 + - - +
34C ASN 4.5 0.2 + - - -
35C GLU 4.7 1.0 - - - +
37C LEU* 3.7 11.9 - - + +
41C GLU* 4.7 0.2 - - - -
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Residues in contact with THR 31 (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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27C MET 2.8 17.5 + - - -
28C LYS* 3.4 9.0 - - - -
30C VAL* 1.4 75.0 - - - +
32C GLU* 1.3 56.5 + - - +
33C LEU 3.0 6.1 + - - -
34C ASN* 3.1 13.2 + - - -
35C GLU 4.6 3.7 + - - +
37C LEU* 3.8 24.7 - - - +
45C LEU* 3.9 9.2 - - - +
103C LEU* 3.8 21.3 - - + -
107C TYR* 3.4 26.9 - - + +
108C LEU* 3.7 29.1 - - + +
111C ASN* 5.6 0.2 + - - -
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Residues in contact with GLU 32 (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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28C LYS* 2.9 35.4 + - - +
29C ASN* 3.6 21.3 + - - +
30C VAL 3.3 0.6 - - - -
31C THR* 1.3 73.6 - - - +
33C LEU* 1.3 57.6 + - - +
34C ASN 3.2 3.4 + - - -
103C LEU* 4.3 6.3 - - + +
107C TYR* 3.7 33.4 + - + +
28D LYS* 3.4 23.7 + - - -
32D GLU* 2.9 26.2 - - - +
99D ASP* 4.5 3.6 - - - +
102D SER* 3.1 31.2 + - - +
103D LEU* 5.6 1.1 - - - +
106D ASN* 4.1 1.2 + - - -
107D TYR* 5.8 0.3 - - - -
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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